From grothausmann.roman at mh-hannover.de Wed Oct 1 11:27:57 2014 From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann) Date: Wed, 01 Oct 2014 17:27:57 +0200 Subject: [ITK-users] patch to add a global hierarchical watershed segmentation mode to itksnap In-Reply-To: <53E85181.8040607@mh-hannover.de> References: <53E85181.8040607@mh-hannover.de> Message-ID: <542C1D7D.6000904@mh-hannover.de> Dear mailing list members, Finally, I got my idea about an interactive hierarchical Watershed SegmentationEditor realized. The idea originates from the SegmentationEditor of the InsightApplication demonstrated here: http://www.insight-journal.org/browse/publication/70 I decided to add such functionality to itksnap as it is the successor of the SegmentationEditor. The additions consist of a Click'n'Join mode, which either allows to join or split labels of the current segmentation by clicking, or instead uses a Global Watershed label image as a label source. The great feature of the itkWatershedFilter allows the level of the watershed hierarchy to be changed on-the-fly. The patch is against itksnap-3.0.0 and in beta-testing stage. Loading from files and "back" buttons are not yet implemented. Please feel free to test it too! Regards, Roman On 11/08/14 07:15, Dr. Roman Grothausmann wrote: > Dear mailing list members, > > > For a long time now I've been searching for a replacement of the old > SegmentationEditor (part of the InsightApplications) which I could not get to > work even with older ITK-3.x. Somewhere I was told that it was integrated and > maintained within itksnap. However the only tool in itksnap based on watershed > segmentation seems to be the adaptive brush. It is very handy, but > time-consuming in 3D and only for local segmentations. In contrast the > SegmentationEditor used a global hierarchical watershed segmentation to pick > labels from, see e.g. the video linked here: > http://www.insight-journal.org/browse/publication/70 > Quite often now I've stumbled over data, that would likely have profited a lot > of such a tool for segmentation. > > If such a tool working with ITK-4.x does not exist any more, I thought of > implementing it as a global WS segmentation mode in itksnap. That way making the > tool easier to find, to use and to ensure maintenance (should it be integrated > into the itksnap code base in the end) and also avoiding recoding a GUI with > mouse interaction and such. > > My current idea is to start, similar to the snake-tool, with pre-filtering like > smoothing and optional edge-detection. > Then the main edit mode to consist of the usual 4 subwindows showing an overlay > of the grey-image and the watershed segmentation of the hierarchical WS-filter > (hWS), side-by-side to another label-dataset (loaded like a tiled overlay) which > consist of the actually chosen labels from the hWS as the final data (FD). > The interaction I'm considering would be to LMB click on a label in the hWS > which is then added to the FD as the current fg label, or removed with a RMB. > The hierachrchy level of the hWS could be controlled by a slider or the mouse > wheel + Shift in nearly real time if some region demands higher or lower > detailed segmentation. When the fg label is changed, the segmentation added or > removed with further mouse interactions would modify the new fg label. > When all is done and the global WS mode is left, the FD label-dataset is added > to the main segmentation of itksnap. > > Would that be possible to implement in itksnap 3.x? > What source files of the itksnap code base should I look at for: > - the pre-filtering mode of the snake (for the smoothing and edge detection) > - the mouse interactions (for e.g. adding the whell + Shift interaction) > - possible examples for the dual layout > > Thanks for any comments, help or hints. > Roman > -- Dr. Roman Grothausmann Tomographie und Digitale Bildverarbeitung Tomography and Digital Image Analysis Institut f?r Funktionelle und Angewandte Anatomie, OE 4120 Medizinische Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover Tel. +49 511 532-9574 -------------- next part -------------- A non-text attachment was scrubbed... Name: itksnap-3.0.0_gWS_53.diff Type: text/x-patch Size: 151111 bytes Desc: not available URL: From matt.mccormick at kitware.com Wed Oct 1 15:40:44 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 1 Oct 2014 15:40:44 -0400 Subject: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released! Message-ID: On behalf of the Insight Toolkit Community, we are happy to announce the release of ITK 4.6.1! This is a patch release that addresses critical issues. The 4.6.1 release fixes DICOM, MetaIO, TIFF, and PNG IO issues, 32-bit WrapITK build errors, Python wrapping warnings, CMake configuration with COMPONENTS, performance and memory consumption of the ITKv4 implementation of the mutual information matching metric, and a many other issues. Congratulations and thanks to everyone who contributed to this release. We are particularly grateful for the collaborations with the 3D Slicer, Debian, GDCM, and MINC communities to address these issues. Questions and comments are welcome on the ITK mailing lists. The release files can be downloaded from: http://itk.org/ITK/resources/software.html The next feature release of 4.6.0 is scheduled for June. Enjoy ITK! Changes from v4.6.0 to v4.6.1: Arnaud Gelas (5): BUG: fix gdcm version in GDCMImageIO. COMP: missing cast when calling gdcm::DataElement::SetByteValue BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false BUG: split include directories into appropriate cmake variables HDF5 BUG: missing gdcm libraries when using system GDCM Brad King (2): COMP: Fix vxl_config_macros usage of CMake check macros BUG: Fix itk_module_config for repeated calls Bradley Lowekamp (8): ENH: Adding License file from upstream MetaIO ENH: Adding script to update MetaIO from upstream ENH: Remove ITK MetaIO to prepare for upstream import COMP: Fix variable type for Set/Get macros BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit BUG: Fix overflows computing size of read tiff image BUG: Use array delete operator for array new allocations Christopher Mullins (2): COMP: Allows latex to compile for ITKSoftwareGuide COMP: Wrap MeshBase templates David T. Chen (1): DOC: Fixed HistogramThresholdImageFitler Gert Wollny (1): COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) Girish Mallya (1): BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. Hans Johnson (12): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components PERF: Remove large foot print of PDF derivatives. PERF: Revert Remove large foot print of PDF derivatives. STYLE: Test against almost equal for floating point values STYLE: Non-exact floating point testing PERF: Distribute initialization per thread buffers ENH: Remove unnecessary mutable qualifier. STYLE: Remove comment with no meaning. ENH: Moved accumlator logic to main MI class ENH: Allow staggering of accumulations per thread. PERF: Zero reset thread buffers during finalize Matthew McCormick (31): BUG: ArchiveTestingData.py future imports must occur at the beginning. DOC: Remove Image2.cxx reference from Book 2. DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. DOC: Remove references to Book 1 sections from Book 2. DOC: Make BinaryThresholdImageFilter not floating. DOC: Fix Software Guide figure caption for FlipImageFilter. DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. DOC: ImageRandomConstIteratorWithIndex table reference. BUG: Bump GCCXML to 2014-08-06. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. BUG: Fix alpha assignment for RGBA TIFF. BUG: Fix Nifti IO read with large images. BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. DOC: itk::statistics -> itk::Statistics. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Fix missing prefix in ITKv3ImageRegistration20Test. BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform STYLE: Improve style in BinaryImageToLabelMapFilter. BUG: Fix BinaryImageToLabelMapFilter on 1D image. ENH: Improve precision of the joint PDF sum BUG: Fix BinShrinkImageFilter for different input/output image types. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. COMP: Add missing wrapping for TransformIOBaseTemplate. BUG: gdcm::StringFilter recognizes backslash delimiter. ENH: Bump ITK version to 4.6.1. MetaIO Maintainers (1): MetaIO (reduced) Michka Popoff (4): BUG: Improve SWIG version check BUG: Add VTK_VERSION for older VTK versions BUG: Update VTK minimum version (for release) BUG: Fix memory leak in MetaImageIO after exception Vladimir S. FONOV (1): BUG: Fixing incorrect MINC style inverse transform From matt.mccormick at kitware.com Wed Oct 1 15:50:33 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 1 Oct 2014 15:50:33 -0400 Subject: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released! In-Reply-To: References: Message-ID: Minor correction: > > The next feature release of 4.6.0 is scheduled for June. > The next feature release of 4.7.0 is scheduled for December. From joel.schaerer at laposte.net Thu Oct 2 05:33:06 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 02 Oct 2014 11:33:06 +0200 Subject: [ITK-users] Proper chaining of filters Message-ID: <542D1BD2.40801@laposte.net> Hi all, I've noticed a couple times that when building a pipeline with ITK, you need to keep a reference to all filters before the pipeline is updated. This seems a little counter-intuitive to me, so I would like to better understand the issue and see if there is a way around it. As an example, the following code doesn't work: DilateType::Pointer dilate = DilateType::New(); dilate->SetInput(thresh->GetOutput()); dilate->SetKernel(kernel); dilate_filters.push_back(dilate); for (int i=0; i<14; ++i) { DilateType::Pointer temp = DilateType::New(); temp->SetInput(dilate->GetOutput()); temp->SetKernel(kernel); dilate = temp; } dilate->Update(); Regions don't get propagated properly and I get the following exception when writing the output: C++ exception with description "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff9bb72cc0) Dimension: 3 Index: 0 0 0 Size: 0 0 0 Largest possible region: ImageRegion (0x7fff9bb72bc0) Dimension: 3 Index: [0, 0, 0] Size: [0, 0, 0] " thrown in the test body. My guess is that the filters get destroyed before they get a chance to be executed. If I explicitely keep references to each filter, it works: DilateType::Pointer dilate = DilateType::New(); dilate->SetInput(thresh->GetOutput()); dilate->SetKernel(kernel); // We need to keep a reference to each filter in the pipeline before it is updated std::vector dilate_filters; dilate_filters.push_back(dilate); for (int i=0; i<14; ++i) { DilateType::Pointer temp = DilateType::New(); temp->SetInput(dilate_filters.back()->GetOutput()); temp->SetKernel(kernel); dilate = temp; dilate_filters.push_back(temp); } dilate_filters.back()->Update(); My question is, why doesn't a filter keep a reference to the previous filter in the pipeline? Is there a way around this? Thanks! Jo?l From matt.mccormick at kitware.com Thu Oct 2 10:16:08 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 2 Oct 2014 10:16:08 -0400 Subject: [ITK-users] [ITK] Proper chaining of filters In-Reply-To: <542D1BD2.40801@laposte.net> References: <542D1BD2.40801@laposte.net> Message-ID: Hi Jo?l, Calling temp->SetInput(dilate->GetOutput()); Connects the DataObject generated by dilate to the temp filter. temp does not increment dilate's reference count, and it would be difficult to do since the SetInput input is the DataObject, not the ProcessObject. As a consequence, at least one SmartPointer needs to be kept in scope as with your second example. HTH, Matt On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer wrote: > Hi all, > > I've noticed a couple times that when building a pipeline with ITK, you need > to keep a reference to all filters before the pipeline is updated. This > seems a little counter-intuitive to me, so I would like to better understand > the issue and see if there is a way around it. > > As an example, the following code doesn't work: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > } > dilate->Update(); > > Regions don't get propagated properly and I get the following exception when > writing the output: > > C++ exception with description > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > fully contain requested paste IO regionPaste IO region: ImageIORegion > (0x7fff9bb72cc0) > Dimension: 3 > Index: 0 0 0 > Size: 0 0 0 > Largest possible region: ImageRegion (0x7fff9bb72bc0) > Dimension: 3 > Index: [0, 0, 0] > Size: [0, 0, 0] > " thrown in the test body. > > My guess is that the filters get destroyed before they get a chance to be > executed. If I explicitely keep references to each filter, it works: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > // We need to keep a reference to each filter in the pipeline before it is > updated > std::vector dilate_filters; > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate_filters.back()->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > dilate_filters.push_back(temp); > } > dilate_filters.back()->Update(); > > My question is, why doesn't a filter keep a reference to the previous filter > in the pipeline? Is there a way around this? > > Thanks! > > Jo?l > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From joel.schaerer at laposte.net Thu Oct 2 10:22:24 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 02 Oct 2014 16:22:24 +0200 Subject: [ITK-users] [ITK] Proper chaining of filters In-Reply-To: References: <542D1BD2.40801@laposte.net> Message-ID: <542D5FA0.8070903@laposte.net> Hi Matt, Thanks for the confirmation. I was thinking there might be another mechanism I wasn't aware of. Jo?l On 10/02/2014 04:16 PM, Matt McCormick wrote: > Hi Jo?l, > > Calling > > temp->SetInput(dilate->GetOutput()); > > Connects the DataObject generated by dilate to the temp filter. temp > does not increment dilate's reference count, and it would be difficult > to do since the SetInput input is the DataObject, not the > ProcessObject. > > As a consequence, at least one SmartPointer needs to be kept in scope > as with your second example. > > HTH, > Matt > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer wrote: >> Hi all, >> >> I've noticed a couple times that when building a pipeline with ITK, you need >> to keep a reference to all filters before the pipeline is updated. This >> seems a little counter-intuitive to me, so I would like to better understand >> the issue and see if there is a way around it. >> >> As an example, the following code doesn't work: >> >> DilateType::Pointer dilate = DilateType::New(); >> dilate->SetInput(thresh->GetOutput()); >> dilate->SetKernel(kernel); >> >> dilate_filters.push_back(dilate); >> for (int i=0; i<14; ++i) { >> DilateType::Pointer temp = DilateType::New(); >> temp->SetInput(dilate->GetOutput()); >> temp->SetKernel(kernel); >> dilate = temp; >> } >> dilate->Update(); >> >> Regions don't get propagated properly and I get the following exception when >> writing the output: >> >> C++ exception with description >> "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: >> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not >> fully contain requested paste IO regionPaste IO region: ImageIORegion >> (0x7fff9bb72cc0) >> Dimension: 3 >> Index: 0 0 0 >> Size: 0 0 0 >> Largest possible region: ImageRegion (0x7fff9bb72bc0) >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [0, 0, 0] >> " thrown in the test body. >> >> My guess is that the filters get destroyed before they get a chance to be >> executed. If I explicitely keep references to each filter, it works: >> >> DilateType::Pointer dilate = DilateType::New(); >> dilate->SetInput(thresh->GetOutput()); >> dilate->SetKernel(kernel); >> // We need to keep a reference to each filter in the pipeline before it is >> updated >> std::vector dilate_filters; >> dilate_filters.push_back(dilate); >> for (int i=0; i<14; ++i) { >> DilateType::Pointer temp = DilateType::New(); >> temp->SetInput(dilate_filters.back()->GetOutput()); >> temp->SetKernel(kernel); >> dilate = temp; >> dilate_filters.push_back(temp); >> } >> dilate_filters.back()->Update(); >> >> My question is, why doesn't a filter keep a reference to the previous filter >> in the pipeline? Is there a way around this? >> >> Thanks! >> >> Jo?l >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community From pedromorais-17 at hotmail.com Thu Oct 2 12:24:31 2014 From: pedromorais-17 at hotmail.com (Pedro Morais) Date: Thu, 2 Oct 2014 09:24:31 -0700 (PDT) Subject: [ITK-users] 3D generalized hough transform Message-ID: <1412267071841-7586297.post@n2.nabble.com> Hi all, I'm wonder if ITK has an implementation of a 3D generalized hough transform. Do you have any idea? Regards, Pedro -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From llliu at umich.edu Thu Oct 2 20:40:16 2014 From: llliu at umich.edu (Lianli Liu) Date: Thu, 2 Oct 2014 20:40:16 -0400 Subject: [ITK-users] vector image registration Message-ID: Hi all, I wonder if ITK is supporting vector image registration now? If not, any suggestions to achieve this goal? Thanks! Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: From ggigi78 at gmail.com Fri Oct 3 05:05:29 2014 From: ggigi78 at gmail.com (Gianluigi Caddeo) Date: Fri, 3 Oct 2014 10:05:29 +0100 Subject: [ITK-users] help installing ITK Message-ID: Hi all, during my installation on an ubuntu machine I had this problem: *[100%] Built target ITKv3ThinPlateSplineWarp/bin/sh: 1: DOXYGEN_EXECUTABLE-NOTFOUND: not foundmake[2]: *** [Utilities/Doxygen/CMakeFiles/Documentation] Errore 127make[1]: *** [Utilities/Doxygen/CMakeFiles/Documentation.dir/all] Errore 2make: *** [all] Errore* But doxygen exist and stay in my */usr/bin* directory How can I to force ITK to search doxygen in that directory? thanks a lot Gg -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Mon Oct 6 03:58:09 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Mon, 6 Oct 2014 09:58:09 +0200 Subject: [ITK-users] How to remove a tag from MetaDataDictionary? Message-ID: Hi all, I am trying to write a DICOM file in which, the orientation (among others) has changed in my pipeline... 1- After having a look https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 It appears to me that if the orientation is in the MetaDataDictionary, it is saved anyway into the DICOM image, there is no way to force the ImageIO to recompute it from the image and save it ??? If there is, can anyone give me a pointer? 2- Since I can't find a way to update the image orientation in itk::GDCMImageIO, I have been looking at removing the corresponding tag from the MetaDataDictionary. I could not find any method or any way to do it??? If there is, can anyone give me a pointer? I wish I would not have to copy the dictionary and add if statement to avoid copying the direction... Thanks in advance, Arnaud -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmasaunders123 at gmail.com Mon Oct 6 07:31:03 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Mon, 6 Oct 2014 12:31:03 +0100 Subject: [ITK-users] Overlap_image registration metrics Message-ID: Hello all, When computing metrics for image registration, does ITK calculated the metric for only the regions in the image that overlap? If so is this performed on just the initial regions that overlap or will this region of overlap increase during registration and thus require the region in which the metric is calculated to alter? Thanks for any help Emma -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.ulge at gmail.com Mon Oct 6 09:20:27 2014 From: marco.ulge at gmail.com (Marco Ulge) Date: Mon, 6 Oct 2014 06:20:27 -0700 (MST) Subject: [ITK-users] Texture Features extraction Message-ID: <1412601627242-34642.post@n7.nabble.com> Hello, i'm currently working on texture feature extraction and I'm following this examle: http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures It works fine and basically it's all i need. The only problem is that i need to able to specify an arbitrary window size (which is 3 in this example) but as soon as i try to assign it a different value this won't work anymore and i can't figure out why. Can anyone help me with this please? Thanks. Marco -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html Sent from the ITK - Users mailing list archive at Nabble.com. From dominique at toepfer-web.de Mon Oct 6 09:47:12 2014 From: dominique at toepfer-web.de (=?ISO-8859-1?Q?Dominique_T=F6pfer?=) Date: Mon, 06 Oct 2014 15:47:12 +0200 Subject: [ITK-users] Texture Features extraction In-Reply-To: <1412601627242-34642.post@n7.nabble.com> References: <1412601627242-34642.post@n7.nabble.com> Message-ID: <54329D60.9030004@toepfer-web.de> Hi Marco, you probably forgot to adjust the range of the for-loops. They are running from 1 to size-2 so that the window will not "leave" the image at its boundaries. HTH Dominique On 06.10.2014 15:20, Marco Ulge wrote: > Hello, > > i'm currently working on texture feature extraction and I'm following this > examle: > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > It works fine and basically it's all i need. The only problem is that i need > to able to specify an arbitrary window size (which is 3 in this example) but > as soon as i try to assign it a different value this won't work anymore and > i can't figure out why. > > Can anyone help me with this please? > > Thanks. > > Marco > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From marco.ulge at gmail.com Mon Oct 6 10:18:26 2014 From: marco.ulge at gmail.com (Marco Ulge) Date: Mon, 6 Oct 2014 07:18:26 -0700 (MST) Subject: [ITK-users] Texture Features extraction In-Reply-To: <54329D60.9030004@toepfer-web.de> References: <1412601627242-34642.post@n7.nabble.com> <54329D60.9030004@toepfer-web.de> Message-ID: <1412605106652-34644.post@n7.nabble.com> Thanks for your reply, so if i wanted to specify a window size of 5 (for example) i should iterate from 1 to size - 4? Thanks. Marco -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.html Sent from the ITK - Users mailing list archive at Nabble.com. From wjhzwy at gmail.com Mon Oct 6 10:27:10 2014 From: wjhzwy at gmail.com (Jiahui Wang) Date: Mon, 6 Oct 2014 10:27:10 -0400 Subject: [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer Message-ID: Dear All, I modified ImageRegistration8.cxx to run my own rigid registration. However, I found that the processing time of ITKv4 based RegularStepGradientDescentOptimizer is almost 10 times more than that of ITKv3 based one. The program was run on the same machine. The only difference is the ITK libraries. Could anyone give me some suggestions to solve this issue? Thanks, JW -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Oct 6 11:08:10 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 6 Oct 2014 11:08:10 -0400 Subject: [ITK-users] How to remove a tag from MetaDataDictionary? In-Reply-To: References: Message-ID: Hi Arnaud, > I am trying to write a DICOM file in which, the orientation (among others) > has changed in my pipeline... > > 1- After having a look > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > It appears to me that if the orientation is in the MetaDataDictionary, it is > saved anyway into the DICOM image, there is no way to force the ImageIO to > recompute it from the image and save it ??? > If there is, can anyone give me a pointer? If there is a Direction on the input image, it should use it [1]. But the DICOM tag 0020|0037 cannot be present. > 2- Since I can't find a way to update the image orientation in > itk::GDCMImageIO, I have been looking at removing the corresponding tag from > the MetaDataDictionary. I could not find any method or any way to do it??? > If there is, can anyone give me a pointer? > > I wish I would not have to copy the dictionary and add if statement to avoid > copying the direction... This is the method I usually apply... Sorry for the lack of new tricks! Matt [1] https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828 From matt.mccormick at kitware.com Mon Oct 6 11:12:52 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 6 Oct 2014 11:12:52 -0400 Subject: [ITK-users] Overlap_image registration metrics In-Reply-To: References: Message-ID: Hi Emma, > When computing metrics for image registration, does ITK calculated the > metric for only the regions in the image that overlap? Yes. See, for example, [1]. > If so is this performed on just the initial regions that overlap or will > this region of overlap increase during registration and thus require the > region in which the metric is calculated to alter? Yes. Ideally, as the registration progresses, the overlap increases, and the registration becomes progressively better. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312 From lasso at queensu.ca Mon Oct 6 11:44:08 2014 From: lasso at queensu.ca (Andras Lasso) Date: Mon, 6 Oct 2014 15:44:08 +0000 Subject: [ITK-users] [ITK] Speed of ITKv4 based Gradient Descent Optimizer In-Reply-To: References: Message-ID: See this long thread about this issue: http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html Short summary: There were some performance regressions in mutual information metric computation, threading, etc. that have been recently fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more accurate optimizer, but if you adjust the number of samples and stopping condition then usually the registration time only increases by about 30-50% (and you might get better quality results). You can see all the changes that have been done in 3D Slicer and BRAINS repositories to go from a 10x-100x slowdown to an approximately equivalent registration speed with ITKv4 compared to ITKv3. Andras From: Community [mailto:community-bounces at itk.org] On Behalf Of Jiahui Wang Sent: Monday, October 06, 2014 10:27 AM To: insight-users at itk.org Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer Dear All, I modified ImageRegistration8.cxx to run my own rigid registration. However, I found that the processing time of ITKv4 based RegularStepGradientDescentOptimizer is almost 10 times more than that of ITKv3 based one. The program was run on the same machine. The only difference is the ITK libraries. Could anyone give me some suggestions to solve this issue? Thanks, JW -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabian.trobles at gmail.com Tue Oct 7 03:13:06 2014 From: fabian.trobles at gmail.com (Fabian Torres) Date: Tue, 7 Oct 2014 15:13:06 +0800 Subject: [ITK-users] Polygon inside point Message-ID: Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dae.wong at gmail.com Tue Oct 7 03:38:49 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Tue, 7 Oct 2014 15:38:49 +0800 Subject: [ITK-users] region inside points Message-ID: Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Oct 7 03:40:40 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 07:40:40 +0000 Subject: [ITK-users] region inside points In-Reply-To: References: Message-ID: Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Oct 7 03:46:17 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 07:46:17 +0000 Subject: [ITK-users] region inside points In-Reply-To: References: , Message-ID: Sorry, I misread your post Fabian - I read it as you wanting the region _surrounding_ the white pixels. But dilate might be usable to fill the gaps, followed by skeletonization. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Tuesday, 7 October 2014 8:40 p.m. To: Fabian Torres; insight-users Subject: Re: [ITK-users] region inside points Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dae.wong at gmail.com Tue Oct 7 04:05:24 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Tue, 7 Oct 2014 16:05:24 +0800 Subject: [ITK-users] region inside points In-Reply-To: References: Message-ID: Hi Gib. Thanks for the quick response. The problem of using dilation and skeletonization is that some times the gap between pixels is big, and I will have to work with different and big structural elements to be sure that all the gaps were eliminated. I was hoping to find a class that works similar to a convex hull (it does not have to be convex) algorithm and then find the region surrounded by the hull. Thanks On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > Sorry, I misread your post Fabian - I read it as you wanting the region > _surrounding_ the white pixels. But dilate might be usable to fill the > gaps, followed by skeletonization. > ------------------------------ > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib > Bogle [g.bogle at auckland.ac.nz] > *Sent:* Tuesday, 7 October 2014 8:40 p.m. > *To:* Fabian Torres; insight-users > *Subject:* Re: [ITK-users] region inside points > > Maybe you could do something with BinaryImageDilateFilter. > ------------------------------ > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > *Sent:* Tuesday, 7 October 2014 8:38 p.m. > *To:* insight-users > *Subject:* [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an > object. Pixels in the surface have value of 1 while any other pixel has > value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Oct 7 04:08:23 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 08:08:23 +0000 Subject: [ITK-users] region inside points In-Reply-To: References: , Message-ID: Maybe there is a way to use a rolling ball. Richard Beare has some morphological filters that might be applicable, but I think it will always be a bit complicated. ________________________________ From: Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 9:05 p.m. To: Gib Bogle Cc: insight-users Subject: Re: [ITK-users] region inside points Hi Gib. Thanks for the quick response. The problem of using dilation and skeletonization is that some times the gap between pixels is big, and I will have to work with different and big structural elements to be sure that all the gaps were eliminated. I was hoping to find a class that works similar to a convex hull (it does not have to be convex) algorithm and then find the region surrounded by the hull. Thanks On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle > wrote: Sorry, I misread your post Fabian - I read it as you wanting the region _surrounding_ the white pixels. But dilate might be usable to fill the gaps, followed by skeletonization. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Tuesday, 7 October 2014 8:40 p.m. To: Fabian Torres; insight-users Subject: Re: [ITK-users] region inside points Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From rousseau at unistra.fr Tue Oct 7 04:11:03 2014 From: rousseau at unistra.fr (francois rousseau) Date: Tue, 7 Oct 2014 10:11:03 +0200 Subject: [ITK-users] Segmentation fault when using BSplineScatteredDataPointSetToImageFilter for 3D image Message-ID: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> Hi everyone, I?m trying to use the BSplineScatteredDataPointSetToImageFilter. No problem when applying it on 2D images (using itkBSplineScatteredDataPointSetToImageFilterTest.cxx). However, after setting const unsigned int ParametricDimension = 3; it crashes when I try to apply it on 3D image (segmentation fault). Can this code be used for 3D images? Thank you Fran?ois -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2828 bytes Desc: not available URL: From ggigi78 at gmail.com Tue Oct 7 09:12:21 2014 From: ggigi78 at gmail.com (Gianluigi Caddeo) Date: Tue, 7 Oct 2014 14:12:21 +0100 Subject: [ITK-users] 8. help installing ITK (Gianluigi Caddeo) solved Message-ID: Hi all, I solved my problem, I gave the correct path to the DOXYGEN_EXECUTABLE variable. Gg On Tue, Oct 7, 2014 at 9:05 AM, wrote: > Send Insight-users mailing list submissions to > insight-users at itk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/insight-users > or, via email, send a message with subject or body 'help' to > insight-users-request at itk.org > > You can reach the person managing the list at > insight-users-owner at itk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Insight-users digest..." > > > Today's Topics: > > 1. [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick) > 2. Re: [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick) > 3. Proper chaining of filters (Jo?l Schaerer) > 4. Re: [ITK] Proper chaining of filters (Matt McCormick) > 5. Re: [ITK] Proper chaining of filters (Jo?l Schaerer) > 6. 3D generalized hough transform (Pedro Morais) > 7. vector image registration (Lianli Liu) > 8. help installing ITK (Gianluigi Caddeo) > 9. How to remove a tag from MetaDataDictionary? (Arnaud Gelas) > 10. Overlap_image registration metrics (Emma Saunders) > 11. Texture Features extraction (Marco Ulge) > 12. Re: Texture Features extraction (Dominique T?pfer) > 13. Re: Texture Features extraction (Marco Ulge) > 14. Speed of ITKv4 based Gradient Descent Optimizer (Jiahui Wang) > 15. Re: How to remove a tag from MetaDataDictionary? (Matt McCormick) > 16. Re: Overlap_image registration metrics (Matt McCormick) > 17. Re: [ITK] Speed of ITKv4 based Gradient Descent Optimizer > (Andras Lasso) > 18. Polygon inside point (Fabian Torres) > 19. region inside points (Fabian Torres) > 20. Re: region inside points (Gib Bogle) > 21. Re: region inside points (Gib Bogle) > 22. Re: region inside points (Fabian Torres) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Oct 2014 15:40:44 -0400 > From: Matt McCormick > To: "community at itk.org" , "insight-users at itk.org" > , ITK > Subject: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released! > Message-ID: > < > CALzTN-TXyhZ2aDaA-UQoFgbg3fPPCPzYKKFpAmKvuquf1EXgrw at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On behalf of the Insight Toolkit Community, we are happy to announce > the release of ITK 4.6.1! > > This is a patch release that addresses critical issues. The 4.6.1 > release fixes DICOM, MetaIO, TIFF, and PNG IO issues, 32-bit WrapITK > build errors, Python wrapping warnings, CMake configuration with > COMPONENTS, performance and memory consumption of the ITKv4 > implementation of the mutual information matching metric, and a many > other issues. > > Congratulations and thanks to everyone who contributed to this > release. We are particularly grateful for the collaborations with the > 3D Slicer, Debian, GDCM, and MINC communities to address these issues. > Questions and comments are welcome on the ITK mailing lists. > > The release files can be downloaded from: > > http://itk.org/ITK/resources/software.html > > > The next feature release of 4.6.0 is scheduled for June. > > > Enjoy ITK! > > > > Changes from v4.6.0 to v4.6.1: > > Arnaud Gelas (5): > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is > false > BUG: split include directories into appropriate cmake variables HDF5 > BUG: missing gdcm libraries when using system GDCM > > Brad King (2): > COMP: Fix vxl_config_macros usage of CMake check macros > BUG: Fix itk_module_config for repeated calls > > Bradley Lowekamp (8): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > COMP: Fix variable type for Set/Get macros > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Fix overflows computing size of read tiff image > BUG: Use array delete operator for array new allocations > > Christopher Mullins (2): > COMP: Allows latex to compile for ITKSoftwareGuide > COMP: Wrap MeshBase templates > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row > images. > > Hans Johnson (12): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > > Matthew McCormick (31): > BUG: ArchiveTestingData.py future imports must occur at the > beginning. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > BUG: Bump GCCXML to 2014-08-06. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Call clear instead of empty on PatchBasedDenoising > EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > BUG: Fix alpha assignment for RGBA TIFF. > BUG: Fix Nifti IO read with large images. > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > COMP: Add missing wrapping for TransformIOBaseTemplate. > BUG: gdcm::StringFilter recognizes backslash delimiter. > ENH: Bump ITK version to 4.6.1. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (4): > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > > Vladimir S. FONOV (1): > BUG: Fixing incorrect MINC style inverse transform > > > ------------------------------ > > Message: 2 > Date: Wed, 1 Oct 2014 15:50:33 -0400 > From: Matt McCormick > To: "community at itk.org" , "insight-users at itk.org" > , ITK > Subject: Re: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released! > Message-ID: > < > CALzTN-S9DU8K8ACbgVP6L0ozXQGvcbnfXC7nz8iu_xqLTVtHsw at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Minor correction: > > > > > The next feature release of 4.6.0 is scheduled for June. > > > > The next feature release of 4.7.0 is scheduled for December. > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Oct 2014 11:33:06 +0200 > From: Jo?l Schaerer > To: itk > Subject: [ITK-users] Proper chaining of filters > Message-ID: <542D1BD2.40801 at laposte.net> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi all, > > I've noticed a couple times that when building a pipeline with ITK, you > need to keep a reference to all filters before the pipeline is updated. > This seems a little counter-intuitive to me, so I would like to better > understand the issue and see if there is a way around it. > > As an example, the following code doesn't work: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > } > dilate->Update(); > > Regions don't get propagated properly and I get the following exception > when writing the output: > > C++ exception with description > > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > fully contain requested paste IO regionPaste IO region: ImageIORegion > (0x7fff9bb72cc0) > Dimension: 3 > Index: 0 0 0 > Size: 0 0 0 > Largest possible region: ImageRegion (0x7fff9bb72bc0) > Dimension: 3 > Index: [0, 0, 0] > Size: [0, 0, 0] > " thrown in the test body. > > My guess is that the filters get destroyed before they get a chance to > be executed. If I explicitely keep references to each filter, it works: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > // We need to keep a reference to each filter in the pipeline before > it is updated > std::vector dilate_filters; > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate_filters.back()->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > dilate_filters.push_back(temp); > } > dilate_filters.back()->Update(); > > My question is, why doesn't a filter keep a reference to the previous > filter in the pipeline? Is there a way around this? > > Thanks! > > Jo?l > > > ------------------------------ > > Message: 4 > Date: Thu, 2 Oct 2014 10:16:08 -0400 > From: Matt McCormick > To: Jo?l Schaerer > Cc: itk > Subject: Re: [ITK-users] [ITK] Proper chaining of filters > Message-ID: > v6XSg at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Jo?l, > > Calling > > temp->SetInput(dilate->GetOutput()); > > Connects the DataObject generated by dilate to the temp filter. temp > does not increment dilate's reference count, and it would be difficult > to do since the SetInput input is the DataObject, not the > ProcessObject. > > As a consequence, at least one SmartPointer needs to be kept in scope > as with your second example. > > HTH, > Matt > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer > wrote: > > Hi all, > > > > I've noticed a couple times that when building a pipeline with ITK, you > need > > to keep a reference to all filters before the pipeline is updated. This > > seems a little counter-intuitive to me, so I would like to better > understand > > the issue and see if there is a way around it. > > > > As an example, the following code doesn't work: > > > > DilateType::Pointer dilate = DilateType::New(); > > dilate->SetInput(thresh->GetOutput()); > > dilate->SetKernel(kernel); > > > > dilate_filters.push_back(dilate); > > for (int i=0; i<14; ++i) { > > DilateType::Pointer temp = DilateType::New(); > > temp->SetInput(dilate->GetOutput()); > > temp->SetKernel(kernel); > > dilate = temp; > > } > > dilate->Update(); > > > > Regions don't get propagated properly and I get the following exception > when > > writing the output: > > > > C++ exception with description > > > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > > fully contain requested paste IO regionPaste IO region: ImageIORegion > > (0x7fff9bb72cc0) > > Dimension: 3 > > Index: 0 0 0 > > Size: 0 0 0 > > Largest possible region: ImageRegion (0x7fff9bb72bc0) > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [0, 0, 0] > > " thrown in the test body. > > > > My guess is that the filters get destroyed before they get a chance to be > > executed. If I explicitely keep references to each filter, it works: > > > > DilateType::Pointer dilate = DilateType::New(); > > dilate->SetInput(thresh->GetOutput()); > > dilate->SetKernel(kernel); > > // We need to keep a reference to each filter in the pipeline before > it is > > updated > > std::vector dilate_filters; > > dilate_filters.push_back(dilate); > > for (int i=0; i<14; ++i) { > > DilateType::Pointer temp = DilateType::New(); > > temp->SetInput(dilate_filters.back()->GetOutput()); > > temp->SetKernel(kernel); > > dilate = temp; > > dilate_filters.push_back(temp); > > } > > dilate_filters.back()->Update(); > > > > My question is, why doesn't a filter keep a reference to the previous > filter > > in the pipeline? Is there a way around this? > > > > Thanks! > > > > Jo?l > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > > ------------------------------ > > Message: 5 > Date: Thu, 02 Oct 2014 16:22:24 +0200 > From: Jo?l Schaerer > To: Matt McCormick > Cc: itk > Subject: Re: [ITK-users] [ITK] Proper chaining of filters > Message-ID: <542D5FA0.8070903 at laposte.net> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi Matt, > > Thanks for the confirmation. I was thinking there might be another > mechanism I wasn't aware of. > > Jo?l > > On 10/02/2014 04:16 PM, Matt McCormick wrote: > > Hi Jo?l, > > > > Calling > > > > temp->SetInput(dilate->GetOutput()); > > > > Connects the DataObject generated by dilate to the temp filter. temp > > does not increment dilate's reference count, and it would be difficult > > to do since the SetInput input is the DataObject, not the > > ProcessObject. > > > > As a consequence, at least one SmartPointer needs to be kept in scope > > as with your second example. > > > > HTH, > > Matt > > > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer > wrote: > >> Hi all, > >> > >> I've noticed a couple times that when building a pipeline with ITK, you > need > >> to keep a reference to all filters before the pipeline is updated. This > >> seems a little counter-intuitive to me, so I would like to better > understand > >> the issue and see if there is a way around it. > >> > >> As an example, the following code doesn't work: > >> > >> DilateType::Pointer dilate = DilateType::New(); > >> dilate->SetInput(thresh->GetOutput()); > >> dilate->SetKernel(kernel); > >> > >> dilate_filters.push_back(dilate); > >> for (int i=0; i<14; ++i) { > >> DilateType::Pointer temp = DilateType::New(); > >> temp->SetInput(dilate->GetOutput()); > >> temp->SetKernel(kernel); > >> dilate = temp; > >> } > >> dilate->Update(); > >> > >> Regions don't get propagated properly and I get the following exception > when > >> writing the output: > >> > >> C++ exception with description > >> > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > >> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > >> fully contain requested paste IO regionPaste IO region: ImageIORegion > >> (0x7fff9bb72cc0) > >> Dimension: 3 > >> Index: 0 0 0 > >> Size: 0 0 0 > >> Largest possible region: ImageRegion (0x7fff9bb72bc0) > >> Dimension: 3 > >> Index: [0, 0, 0] > >> Size: [0, 0, 0] > >> " thrown in the test body. > >> > >> My guess is that the filters get destroyed before they get a chance to > be > >> executed. If I explicitely keep references to each filter, it works: > >> > >> DilateType::Pointer dilate = DilateType::New(); > >> dilate->SetInput(thresh->GetOutput()); > >> dilate->SetKernel(kernel); > >> // We need to keep a reference to each filter in the pipeline before > it is > >> updated > >> std::vector dilate_filters; > >> dilate_filters.push_back(dilate); > >> for (int i=0; i<14; ++i) { > >> DilateType::Pointer temp = DilateType::New(); > >> temp->SetInput(dilate_filters.back()->GetOutput()); > >> temp->SetKernel(kernel); > >> dilate = temp; > >> dilate_filters.push_back(temp); > >> } > >> dilate_filters.back()->Update(); > >> > >> My question is, why doesn't a filter keep a reference to the previous > filter > >> in the pipeline? Is there a way around this? > >> > >> Thanks! > >> > >> Jo?l > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-users > >> _______________________________________________ > >> Community mailing list > >> Community at itk.org > >> http://public.kitware.com/mailman/listinfo/community > > > > ------------------------------ > > Message: 6 > Date: Thu, 2 Oct 2014 09:24:31 -0700 (PDT) > From: Pedro Morais > To: insight-users at itk.org > Subject: [ITK-users] 3D generalized hough transform > Message-ID: <1412267071841-7586297.post at n2.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Hi all, > > I'm wonder if ITK has an implementation of a 3D generalized hough > transform. > Do you have any idea? > > Regards, > Pedro > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 7 > Date: Thu, 2 Oct 2014 20:40:16 -0400 > From: Lianli Liu > To: "insight-users at itk.org" > Subject: [ITK-users] vector image registration > Message-ID: > < > CAGKqDmfV89qpnVG5tq4bvZrc6FDHhNRHrkvWg7qEXjh_pObKsQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I wonder if ITK is supporting vector image registration now? If not, any > suggestions to achieve this goal? > > Thanks! > Lianli > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141002/87f15593/attachment-0001.html > > > > ------------------------------ > > Message: 8 > Date: Fri, 3 Oct 2014 10:05:29 +0100 > From: Gianluigi Caddeo > To: insight-users at itk.org > Subject: [ITK-users] help installing ITK > Message-ID: > < > CADeTECOS-PqOswWC4H2Wo_f8eKjd24eN+eSDfRG+YK8LKF7+CA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > during my installation on an ubuntu machine I had this problem: > > > > > > > *[100%] Built target ITKv3ThinPlateSplineWarp/bin/sh: 1: > DOXYGEN_EXECUTABLE-NOTFOUND: not foundmake[2]: *** > [Utilities/Doxygen/CMakeFiles/Documentation] Errore 127make[1]: *** > [Utilities/Doxygen/CMakeFiles/Documentation.dir/all] Errore 2make: *** > [all] Errore* > But doxygen exist and stay in my */usr/bin* directory > > How can I to force ITK to search doxygen in that directory? > > thanks a lot > > Gg > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141003/ec1ddfe8/attachment-0001.html > > > > ------------------------------ > > Message: 9 > Date: Mon, 6 Oct 2014 09:58:09 +0200 > From: Arnaud Gelas > To: insight-users > Cc: Mathieu Malaterre > Subject: [ITK-users] How to remove a tag from MetaDataDictionary? > Message-ID: > < > CAK3qF+8e1kg7bN4EcM2FUYy_e3AYz-M3ZrGGwkssWz0Kvz4y2Q at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I am trying to write a DICOM file in which, the orientation (among others) > has changed in my pipeline... > > 1- After having a look > > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > It appears to me that if the orientation is in the MetaDataDictionary, it > is saved anyway into the DICOM image, there is no way to force the ImageIO > to recompute it from the image and save it ??? > If there is, can anyone give me a pointer? > > 2- Since I can't find a way to update the image orientation in > itk::GDCMImageIO, I have been looking at removing the corresponding tag > from the MetaDataDictionary. I could not find any method or any way to do > it??? > If there is, can anyone give me a pointer? > > I wish I would not have to copy the dictionary and add if statement to > avoid copying the direction... > > Thanks in advance, > Arnaud > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/51ca077c/attachment-0001.html > > > > ------------------------------ > > Message: 10 > Date: Mon, 6 Oct 2014 12:31:03 +0100 > From: Emma Saunders > To: "insight-users at itk.org Users" > Subject: [ITK-users] Overlap_image registration metrics > Message-ID: > 1as4oZLo5UXQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello all, > > When computing metrics for image registration, does ITK calculated the > metric for only the regions in the image that overlap? > > If so is this performed on just the initial regions that overlap or will > this region of overlap increase during registration and thus require the > region in which the metric is calculated to alter? > > Thanks for any help > > Emma > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/639045b5/attachment-0001.html > > > > ------------------------------ > > Message: 11 > Date: Mon, 6 Oct 2014 06:20:27 -0700 (MST) > From: Marco Ulge > To: insight-users at itk.org > Subject: [ITK-users] Texture Features extraction > Message-ID: <1412601627242-34642.post at n7.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Hello, > > i'm currently working on texture feature extraction and I'm following this > examle: > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > It works fine and basically it's all i need. The only problem is that i > need > to able to specify an arbitrary window size (which is 3 in this example) > but > as soon as i try to assign it a different value this won't work anymore and > i can't figure out why. > > Can anyone help me with this please? > > Thanks. > > Marco > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html > Sent from the ITK - Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 12 > Date: Mon, 06 Oct 2014 15:47:12 +0200 > From: Dominique T?pfer > To: Marco Ulge , insight-users at itk.org > Subject: Re: [ITK-users] Texture Features extraction > Message-ID: <54329D60.9030004 at toepfer-web.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Marco, > > you probably forgot to adjust the range of the for-loops. They are > running from 1 to size-2 so that the window will not "leave" the image > at its boundaries. > > HTH > Dominique > > > On 06.10.2014 15:20, Marco Ulge wrote: > > Hello, > > > > i'm currently working on texture feature extraction and I'm following > this > > examle: > > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > > > > It works fine and basically it's all i need. The only problem is that i > need > > to able to specify an arbitrary window size (which is 3 in this example) > but > > as soon as i try to assign it a different value this won't work anymore > and > > i can't figure out why. > > > > Can anyone help me with this please? > > > > Thanks. > > > > Marco > > > > > > > > -- > > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html > > Sent from the ITK - Users mailing list archive at Nabble.com. > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > ------------------------------ > > Message: 13 > Date: Mon, 6 Oct 2014 07:18:26 -0700 (MST) > From: Marco Ulge > To: insight-users at itk.org > Subject: Re: [ITK-users] Texture Features extraction > Message-ID: <1412605106652-34644.post at n7.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Thanks for your reply, so if i wanted to specify a window size of 5 (for > example) i should iterate from 1 to size - 4? > > Thanks. > > Marco > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.html > Sent from the ITK - Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 14 > Date: Mon, 6 Oct 2014 10:27:10 -0400 > From: Jiahui Wang > To: insight-users at itk.org > Subject: [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer > Message-ID: > UPK2wK-ksA6v1vKak75aE1f3ea-de7sLQSTrGiQwxEpQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > I modified ImageRegistration8.cxx to run my own rigid registration. > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > > Thanks, > > JW > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/40c2b5ce/attachment-0001.html > > > > ------------------------------ > > Message: 15 > Date: Mon, 6 Oct 2014 11:08:10 -0400 > From: Matt McCormick > To: Arnaud Gelas > Cc: insight-users , Mathieu Malaterre > > Subject: Re: [ITK-users] How to remove a tag from MetaDataDictionary? > Message-ID: > < > CALzTN-TjoXUpe16JNsViVH0srU_q1oTJpVYG94G3S6a0mUD3Eg at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Arnaud, > > > > I am trying to write a DICOM file in which, the orientation (among > others) > > has changed in my pipeline... > > > > 1- After having a look > > > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > > > It appears to me that if the orientation is in the MetaDataDictionary, > it is > > saved anyway into the DICOM image, there is no way to force the ImageIO > to > > recompute it from the image and save it ??? > > If there is, can anyone give me a pointer? > > If there is a Direction on the input image, it should use it [1]. But > the DICOM tag 0020|0037 cannot be present. > > > > 2- Since I can't find a way to update the image orientation in > > itk::GDCMImageIO, I have been looking at removing the corresponding tag > from > > the MetaDataDictionary. I could not find any method or any way to do > it??? > > If there is, can anyone give me a pointer? > > > > I wish I would not have to copy the dictionary and add if statement to > avoid > > copying the direction... > > This is the method I usually apply... > > Sorry for the lack of new tricks! > Matt > > [1] > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828 > > > ------------------------------ > > Message: 16 > Date: Mon, 6 Oct 2014 11:12:52 -0400 > From: Matt McCormick > To: Emma Saunders > Cc: "insight-users at itk.org Users" > Subject: Re: [ITK-users] Overlap_image registration metrics > Message-ID: > < > CALzTN-SrbFWD0R7-GAPxxT0ssf2fzLN_bATjtHB+ZAyHYZjk+w at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Emma, > > > When computing metrics for image registration, does ITK calculated the > > metric for only the regions in the image that overlap? > > Yes. See, for example, [1]. > > > If so is this performed on just the initial regions that overlap or > will > > this region of overlap increase during registration and thus require the > > region in which the metric is calculated to alter? > > Yes. Ideally, as the registration progresses, the overlap increases, > and the registration becomes progressively better. > > HTH, > Matt > > [1] > http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312 > > > ------------------------------ > > Message: 17 > Date: Mon, 6 Oct 2014 15:44:08 +0000 > From: Andras Lasso > To: Jiahui Wang , "insight-users at itk.org" > > Subject: Re: [ITK-users] [ITK] Speed of ITKv4 based Gradient Descent > Optimizer > Message-ID: > < > B6FC5543F5C41E479B8B89158B0C58FF179374D9 at MP-DUP-MBX-02.AD.QUEENSU.CA> > Content-Type: text/plain; charset="utf-8" > > See this long thread about this issue: > > http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html > > Short summary: There were some performance regressions in mutual > information metric computation, threading, etc. that have been recently > fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more > accurate optimizer, but if you adjust the number of samples and stopping > condition then usually the registration time only increases by about 30-50% > (and you might get better quality results). > > You can see all the changes that have been done in 3D Slicer and BRAINS > repositories to go from a 10x-100x slowdown to an approximately equivalent > registration speed with ITKv4 compared to ITKv3. > > Andras > > From: Community [mailto:community-bounces at itk.org] On Behalf Of Jiahui > Wang > Sent: Monday, October 06, 2014 10:27 AM > To: insight-users at itk.org > Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer > > Dear All, > I modified ImageRegistration8.cxx to run my own rigid registration. > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > Thanks, > JW > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/230f318a/attachment-0001.html > > > > ------------------------------ > > Message: 18 > Date: Tue, 7 Oct 2014 15:13:06 +0800 > From: Fabian Torres > To: insight-users at itk.org > Subject: [ITK-users] Polygon inside point > Message-ID: > KP5XsjnYeFWGwWbifQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. I > want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/152068ea/attachment-0001.html > > > > ------------------------------ > > Message: 19 > Date: Tue, 7 Oct 2014 15:38:49 +0800 > From: Fabian Torres > To: insight-users > Subject: [ITK-users] region inside points > Message-ID: > < > CALD_Ep+OEAE8Jik0hsy8PWYGBmxTHYWoRZOoFQaP2OqT1P_GyQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. I > want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/2f835b53/attachment-0001.html > > > > ------------------------------ > > Message: 20 > Date: Tue, 7 Oct 2014 07:40:40 +0000 > From: Gib Bogle > To: Fabian Torres , insight-users > > Subject: Re: [ITK-users] region inside points > Message-ID: > < > BD80F91C3E2E394894ED4780703D7F9E826C670A at uxcn10-tdc06.UoA.auckland.ac.nz> > > Content-Type: text/plain; charset="iso-8859-1" > > Maybe you could do something with BinaryImageDilateFilter. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > Sent: Tuesday, 7 October 2014 8:38 p.m. > To: insight-users > Subject: [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, > dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/4f28baa5/attachment-0001.html > > > > ------------------------------ > > Message: 21 > Date: Tue, 7 Oct 2014 07:46:17 +0000 > From: Gib Bogle > To: Fabian Torres , insight-users > > Subject: Re: [ITK-users] region inside points > Message-ID: > < > BD80F91C3E2E394894ED4780703D7F9E826C671B at uxcn10-tdc06.UoA.auckland.ac.nz> > > Content-Type: text/plain; charset="iso-8859-1" > > Sorry, I misread your post Fabian - I read it as you wanting the region > _surrounding_ the white pixels. But dilate might be usable to fill the > gaps, followed by skeletonization. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib > Bogle [g.bogle at auckland.ac.nz] > Sent: Tuesday, 7 October 2014 8:40 p.m. > To: Fabian Torres; insight-users > Subject: Re: [ITK-users] region inside points > > Maybe you could do something with BinaryImageDilateFilter. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > Sent: Tuesday, 7 October 2014 8:38 p.m. > To: insight-users > Subject: [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, > dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/4dee4e3f/attachment-0001.html > > > > ------------------------------ > > Message: 22 > Date: Tue, 7 Oct 2014 16:05:24 +0800 > From: Fabian Torres > To: Gib Bogle > Cc: insight-users > Subject: Re: [ITK-users] region inside points > Message-ID: > < > CALD_Ep+NkNKwMdz18XLQ3ygxBAdCwK0AGFBZcNPT3MfUpC_ARA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Gib. > > Thanks for the quick response. The problem of using dilation and > skeletonization is that some times the gap between pixels is big, and I > will have to work with different and big structural elements to be sure > that all the gaps were eliminated. > > I was hoping to find a class that works similar to a convex hull (it does > not have to be convex) algorithm and then find the region surrounded by the > hull. > > Thanks > > On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > > > Sorry, I misread your post Fabian - I read it as you wanting the region > > _surrounding_ the white pixels. But dilate might be usable to fill the > > gaps, followed by skeletonization. > > ------------------------------ > > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib > > Bogle [g.bogle at auckland.ac.nz] > > *Sent:* Tuesday, 7 October 2014 8:40 p.m. > > *To:* Fabian Torres; insight-users > > *Subject:* Re: [ITK-users] region inside points > > > > Maybe you could do something with BinaryImageDilateFilter. > > ------------------------------ > > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of > Fabian > > Torres [dae.wong at gmail.com] > > *Sent:* Tuesday, 7 October 2014 8:38 p.m. > > *To:* insight-users > > *Subject:* [ITK-users] region inside points > > > > Hi all. > > > > I have an image that represents some pixels over the surface of an > > object. Pixels in the surface have value of 1 while any other pixel has > > value of 0. > > The pixels are not a continuous line, there are some gaps between pixels. > > I want to know the region surrounded by the white pixels in my image. > > > > I will be working with 2D and 3D data. Is there any class implemented in > > ITK that I can use? > > > > Thanks > > -- > > Fabi?n Torres Robles > > Maestria en Ciencias en Ingenier?a Electr?nica > > Ingenier?a en Sistemas Electr?nicos > > tel. 58081280, 0445534661338 > > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > > > > > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/6202b2cc/attachment.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Insight-users mailing list > Insight-users at itk.org > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > > End of Insight-users Digest, Vol 126, Issue 2 > ********************************************* > -------------- next part -------------- An HTML attachment was scrubbed... URL: From 65104355 at qq.com Tue Oct 7 10:06:17 2014 From: 65104355 at qq.com (=?ISO-8859-1?B?SmVycnk=?=) Date: Tue, 7 Oct 2014 22:06:17 +0800 Subject: [ITK-users] Detect tube and ball typed objects in airway CT image. Message-ID: I am developing a segmentation algorithm that requires detect tube and ball typed airways in CT image. I tried canny, log, hessian etc. None of them looks promising. Any advice will be appreicated. Regards, Jerry -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: B3AB03A0 at 8E359815.59F33354.jpg Type: image/jpeg Size: 79219 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tubecircle.jpg Type: application/octet-stream Size: 79219 bytes Desc: not available URL: From blowekamp at mail.nih.gov Tue Oct 7 10:18:10 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 7 Oct 2014 10:18:10 -0400 Subject: [ITK-users] [ITK] Detect tube and ball typed objects in airway CT image. In-Reply-To: References: Message-ID: <6FF244AB-597A-4CFB-8644-3E918F42F938@mail.nih.gov> Interesting. Have you considered looking at the ratio of a gaussian and a laplacian at certain scales to detect the feature you are interested in? Brad Brad On Oct 7, 2014, at 10:06 AM, Jerry <65104355 at qq.com> wrote: > I am developing a segmentation algorithm that requires detect tube and ball typed airways in CT image. I tried canny, log, hessian etc. None of them looks promising. Any advice will be appreicated. > > Regards, > > Jerry > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Oct 7 10:28:40 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 10:28:40 -0400 Subject: [ITK-users] Segmentation fault when using BSplineScatteredDataPointSetToImageFilter for 3D image In-Reply-To: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> References: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> Message-ID: Hi Fran?ois, Yes, it should work on a 3D Image -- itkBSplineScatteredDataPointSetToImageFilterTest4.cxx is for ParametericDimension = 3. HTH, Matt On Tue, Oct 7, 2014 at 4:11 AM, francois rousseau wrote: > Hi everyone, > > I?m trying to use the BSplineScatteredDataPointSetToImageFilter. No problem > when applying it on 2D images (using > itkBSplineScatteredDataPointSetToImageFilterTest.cxx). > However, after setting const unsigned int ParametricDimension = 3; it > crashes when I try to apply it on 3D image (segmentation fault). Can this > code be used for 3D images? > > Thank you > Fran?ois > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From matt.mccormick at kitware.com Tue Oct 7 10:43:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 10:43:55 -0400 Subject: [ITK-users] Detect tube and ball typed objects in airway CT image. In-Reply-To: References: Message-ID: Hi Jerry, The LesionSizingToolkit [1], and TubeTK [2], both based on ITK, may be helpful here. The LesionSizeToolkit is available as a Remote Module. It can be built by setting Module_LesionSizingToolkit=ON in your CMake configuration. HTH, Matt [1] http://public.kitware.com/LesionSizingKit/index.php/Main_Page [2] http://tubetk.org/ On Tue, Oct 7, 2014 at 10:06 AM, Jerry <65104355 at qq.com> wrote: > I am developing a segmentation algorithm that requires detect tube and > ball typed airways in CT image. I tried canny, log, hessian etc. None of > them looks promising. Any advice will be appreicated. > > Regards, > > Jerry > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: B3AB03A0 at 8E359815.59F33354.jpg Type: image/jpeg Size: 79219 bytes Desc: not available URL: From matt.mccormick at kitware.com Tue Oct 7 11:52:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 11:52:56 -0400 Subject: [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From wjhzwy at gmail.com Tue Oct 7 13:44:47 2014 From: wjhzwy at gmail.com (Jiahui Wang) Date: Tue, 7 Oct 2014 13:44:47 -0400 Subject: [ITK-users] [ITK] Speed of ITKv4 based Gradient Descent Optimizer In-Reply-To: References: Message-ID: Thank you very much, Andras. Jiahui On Mon, Oct 6, 2014 at 11:44 AM, Andras Lasso wrote: > See this long thread about this issue: > > > http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html > > > > Short summary: There were some performance regressions in mutual > information metric computation, threading, etc. that have been recently > fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more > accurate optimizer, but if you adjust the number of samples and stopping > condition then usually the registration time only increases by about 30-50% > (and you might get better quality results). > > > > You can see all the changes that have been done in 3D Slicer and BRAINS > repositories to go from a 10x-100x slowdown to an approximately equivalent > registration speed with ITKv4 compared to ITKv3. > > > > Andras > > > > *From:* Community [mailto:community-bounces at itk.org] *On Behalf Of *Jiahui > Wang > *Sent:* Monday, October 06, 2014 10:27 AM > *To:* insight-users at itk.org > *Subject:* [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent > Optimizer > > > > Dear All, > > I modified ImageRegistration8.cxx to run my own rigid registration. > > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > > Thanks, > > JW > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dae.wong at gmail.com Wed Oct 8 06:51:51 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Wed, 8 Oct 2014 18:51:51 +0800 Subject: [ITK-users] region inside points In-Reply-To: References: Message-ID: Hi all. Just wanted to let you know I solved the problem for 2D by doing the next: Arrange the white pixels in clockwise order 1. Calculate the centroid of the region define by the white pixels 2. Calculate the angle between the white pixels and the centroid using atan2( ) 3. Sort the white pixels in clockwise order. Draw a line between the pixels to fill the gap between points to obtain a closed contour 1. Using LineIterator to draw lines between the clockwise ordered points Fill the region inside the close contour. 1. Using GrayScaleFillholeImageFilter. I don?t know if this is a nice solution but it works for now. I will try to use this approach for 3D images, processing them slice by slice. I think I can use the itkSliceBySliceImageFilter, since I create an itk filter that outputs the closed contour image, but I don?t know if this is going to work. If any one have any advice on this matter it would be appreciated. Greetings On Tue, Oct 7, 2014 at 4:08 PM, Gib Bogle wrote: > Maybe there is a way to use a rolling ball. Richard Beare has some > morphological filters that might be applicable, but I think it will always > be a bit complicated. > ------------------------------ > *From:* Fabian Torres [dae.wong at gmail.com] > *Sent:* Tuesday, 7 October 2014 9:05 p.m. > *To:* Gib Bogle > *Cc:* insight-users > > *Subject:* Re: [ITK-users] region inside points > > Hi Gib. > > Thanks for the quick response. The problem of using dilation and > skeletonization is that some times the gap between pixels is big, and I > will have to work with different and big structural elements to be sure > that all the gaps were eliminated. > > I was hoping to find a class that works similar to a convex hull (it > does not have to be convex) algorithm and then find the region surrounded > by the hull. > > Thanks > > On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > >> Sorry, I misread your post Fabian - I read it as you wanting the region >> _surrounding_ the white pixels. But dilate might be usable to fill the >> gaps, followed by skeletonization. >> ------------------------------ >> *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib >> Bogle [g.bogle at auckland.ac.nz] >> *Sent:* Tuesday, 7 October 2014 8:40 p.m. >> *To:* Fabian Torres; insight-users >> *Subject:* Re: [ITK-users] region inside points >> >> Maybe you could do something with BinaryImageDilateFilter. >> ------------------------------ >> *From:* Insight-users [insight-users-bounces at itk.org] on behalf of >> Fabian Torres [dae.wong at gmail.com] >> *Sent:* Tuesday, 7 October 2014 8:38 p.m. >> *To:* insight-users >> *Subject:* [ITK-users] region inside points >> >> Hi all. >> >> I have an image that represents some pixels over the surface of an >> object. Pixels in the surface have value of 1 while any other pixel has >> value of 0. >> The pixels are not a continuous line, there are some gaps between pixels. >> I want to know the region surrounded by the white pixels in my image. >> >> I will be working with 2D and 3D data. Is there any class implemented >> in ITK that I can use? >> >> Thanks >> -- >> Fabi?n Torres Robles >> Maestria en Ciencias en Ingenier?a Electr?nica >> Ingenier?a en Sistemas Electr?nicos >> tel. 58081280, 0445534661338 >> e-mail fabian.trobles at gmail.com, dae.wong at gmail.com >> > > > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From alfonso.castro at udc.es Wed Oct 8 14:13:43 2014 From: alfonso.castro at udc.es (Alfonso Castro) Date: Wed, 08 Oct 2014 20:13:43 +0200 Subject: [ITK-users] Problem compiling ITK 4.6.1 Message-ID: <2757769.bt995I62FB@hinata> Hi. I'm trying to compile ITK 4.6.1 on OpenSuSE 13.1 with CUDA 6.5 from NVIDIA. Whwn I turn on the option of Module_SmoothingRecursiveYvvGaussianFilter and Module_VariationalRegistration with ITK_USE_GPU option. Make gives the follow errors: Building CXX object Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/CMakeFiles/SmoothingRecursiveYvvGaussianFilter.dir/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx.o In file included from /usr/local/cuda-6.5/include/CL/opencl.h:44:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkOpenCLUtil.h:36, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/include/itkGPUSmoothingRecursiveYvvGaussianImageFilter.h:29, from /opt/mia/itk/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx:1: /usr/local/cuda-6.5/include/CL/cl_gl_ext.h:44:4: warning: "/*" within comment [-Wcomment] * /* cl_VEN_extname extension */ ^ In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.h:284:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUKernelManager.h:30, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImageToImageFilter.h:22, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/include/itkGPUSmoothingRecursiveYvvGaussianImageFilter.h:30, from /opt/mia/itk/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx:1: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.hxx: In member function ?virtual void itk::GPUImage::Graft(const itk::DataObject*)?: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.hxx:188:56: warning: typedef ?GPUImageDataSuperclassPointer? locally defined but not used [-Wunused-local-typedefs] typedef typename GPUImageDataSuperclass::Pointer GPUImageDataSuperclassPointer; ^ Linking CXX static library ../../../../lib/libSmoothingRecursiveYvvGaussianFilter.a [100%] Built target SmoothingRecursiveYvvGaussianFilter Scanning dependencies of target SplitComponents-all [100%] Built target SplitComponents-all Scanning dependencies of target VariationalRegistration-all [100%] Built target VariationalRegistration-all Scanning dependencies of target VariationalRegistration [100%] Building CXX object Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFilter.h:24:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationMultiResolutionFilter.h:24, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/src/VariationalRegistrationMain.cxx:60: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFunction.h:156:11: error: duplicate ?virtual? virtual virtual void InitializeIteration(); ^ make[2]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o] Erro 1 make[1]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/all] Erro 2 make: *** [all] Erro 2 If I deactivated the GPU option only, I obtained: [ 18%] Building CXX object Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFilter.h:24:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationMultiResolutionFilter.h:24, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/src/VariationalRegistrationMain.cxx:60: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFunction.h:156:11: error: duplicate ?virtual? virtual virtual void InitializeIteration(); ^ make[2]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o] Erro 1 make[1]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/all] Erro 2 make: *** [all] Erro 2 If I deactivated GPU and Module_VariationalRegistration, ITK compile without problem. Is there some solution or walk around for those errors? Thanks. Alfonso Faculty of Computer Science University of A Coruna From curiale at gmail.com Thu Oct 9 10:43:03 2014 From: curiale at gmail.com (=?iso-8859-1?Q?Ariel_Hern=E1n_Curiale?=) Date: Thu, 9 Oct 2014 16:43:03 +0200 Subject: [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: Message-ID: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Hi Matt, Is there any chance to see the video of the meeting on you tube, for example ? Cheers __________________________________ | Ariel Hern?n Curiale Ph.D Candidate | ETSI Telecomunicaci?n | Universidad de Valladolid | Campus Miguel Delibes | 47011 Valladolid, Spain | Phone: 983-423000 ext. 5590 | Web: www.curiale.com.ar |_________________________________ On 07/10/2014, at 17:52, Matt McCormick wrote: > On Friday, 11:00 AM Eastern USA time, an ITK development conference, > > https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 > > > To get regular invites to these events, join the ITK Bar Camp G+ Community: > > https://plus.google.com/u/0/communities/111375098792764998322 > > > All are welcome. Hope to talk to you then! > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From handongfeng at gmail.com Thu Oct 9 15:54:20 2014 From: handongfeng at gmail.com (Dongfeng Han) Date: Thu, 9 Oct 2014 15:54:20 -0400 Subject: [ITK-users] TransformMatrix order in MHD file Message-ID: Dear ITK users, Now I have a 3x3 TransformMatrix , when I write to mhd file, it just one line. I should write as row order or column order? thanks dongfeng - -------------- next part -------------- An HTML attachment was scrubbed... URL: From fbudin at email.unc.edu Fri Oct 10 08:35:04 2014 From: fbudin at email.unc.edu (Budin, Francois) Date: Fri, 10 Oct 2014 12:35:04 +0000 Subject: [ITK-users] itkTransformFileReaderTemplate In-Reply-To: <4FAFFD37-9479-4FF9-ACB7-27C50195B685@unc.edu> References: <4FAFFD37-9479-4FF9-ACB7-27C50195B685@unc.edu> Message-ID: Hello, I use to read transform files with itkTransformFileReader, but I discovered the new class in itk4.5 and above called itkTransformFileReaderTemplate. This class seems very convenient as it converts my transforms from let?s say float to double automatically if my transform file is a float transform, but if my reader is instantiated as double. However, I was wondering if there is a way to know the original type in which the transform in the file is encoded. I would like to be able to know if my file contains a float or a double transform (without manually reading the transform file myself). Sincerely, Francois From hans-johnson at uiowa.edu Fri Oct 10 08:37:26 2014 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Fri, 10 Oct 2014 12:37:26 +0000 Subject: [ITK-users] itkTransformFileReaderTemplate Message-ID: Ali Ghayoor in my lab did this work. I?ll allow him to respond appropriately today. Hans On 10/10/14, 7:35 AM, "Budin, Francois" wrote: >Hello, > >I use to read transform files with itkTransformFileReader, but I >discovered the new class in itk4.5 and above called >itkTransformFileReaderTemplate. This class seems very convenient as it >converts my transforms from let?s say float to double automatically if my >transform file is a float transform, but if my reader is instantiated as >double. However, I was wondering if there is a way to know the original >type in which the transform in the file is encoded. I would like to be >able to know if my file contains a float or a double transform (without >manually reading the transform file myself). >Sincerely, > >Francois >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the ITK FAQ at: >http://www.itk.org/Wiki/ITK_FAQ > >Follow this link to subscribe/unsubscribe: >http://public.kitware.com/mailman/listinfo/insight-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ From alii.ghayoor at gmail.com Fri Oct 10 14:40:55 2014 From: alii.ghayoor at gmail.com (Ali Ghayoor) Date: Fri, 10 Oct 2014 13:40:55 -0500 Subject: [ITK-users] itkTransformFileReaderTemplate In-Reply-To: References: Message-ID: Well, I am not sure whether there is a way to know about the original precision type of transform parameters before reading them in ITK. Based on the reader class implementation, the parameters precision types are casted to the request type (float or double) instantly while reading the parameters from the transform buffer, so we don?t need any knowledge about their current type. Ali On 10/10/14, 7:37 AM, "Johnson, Hans J" wrote: >Ali Ghayoor in my lab did this work. I?ll allow him to respond >appropriately today. > >Hans > > >On 10/10/14, 7:35 AM, "Budin, Francois" wrote: > >>Hello, >> >>I use to read transform files with itkTransformFileReader, but I >>discovered the new class in itk4.5 and above called >>itkTransformFileReaderTemplate. This class seems very convenient as it >>converts my transforms from let?s say float to double automatically if my >>transform file is a float transform, but if my reader is instantiated as >>double. However, I was wondering if there is a way to know the original >>type in which the transform in the file is encoded. I would like to be >>able to know if my file contains a float or a double transform (without >>manually reading the transform file myself). >>Sincerely, >> >>Francois >>_____________________________________ >>Powered by www.kitware.com >> >>Visit other Kitware open-source projects at >>http://www.kitware.com/opensource/opensource.html >> >>Kitware offers ITK Training Courses, for more information visit: >>http://www.kitware.com/products/protraining.php >> >>Please keep messages on-topic and check the ITK FAQ at: >>http://www.itk.org/Wiki/ITK_FAQ >> >>Follow this link to subscribe/unsubscribe: >>http://public.kitware.com/mailman/listinfo/insight-users > > > >________________________________ >Notice: This UI Health Care e-mail (including attachments) is covered by >the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >confidential and may be legally privileged. If you are not the intended >recipient, you are hereby notified that any retention, dissemination, >distribution, or copying of this communication is strictly prohibited. >Please reply to the sender that you have received the message in error, >then delete it. Thank you. >________________________________ >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the ITK FAQ at: >http://www.itk.org/Wiki/ITK_FAQ > >Follow this link to subscribe/unsubscribe: >http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sun Oct 12 22:49:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 12 Oct 2014 22:49:24 -0400 Subject: [ITK-users] vector image registration In-Reply-To: References: Message-ID: Hi Lianli, No, ITK does not have any vector image registration methods yet. There could be many approaches here that are often problem specific. Extracting a scalar pixel value from the vectors for application in the metric is a workable approach. Hope this helps, Matt On Thu, Oct 2, 2014 at 8:40 PM, Lianli Liu wrote: > Hi all, > > I wonder if ITK is supporting vector image registration now? If not, any > suggestions to achieve this goal? > > Thanks! > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From stnava at gmail.com Sun Oct 12 22:59:29 2014 From: stnava at gmail.com (brian avants) Date: Sun, 12 Oct 2014 22:59:29 -0400 Subject: [ITK-users] vector image registration In-Reply-To: References: Message-ID: Both: itkMultiGradientImageToImageMetricv4RegistrationTest.cxx and itkMeanSquaresImageToImageMetricv4VectorRegistrationTest.cxx can achieve some form of vector image registration. but it depends on what you mean by *vector*. brian On Sun, Oct 12, 2014 at 10:49 PM, Matt McCormick wrote: > Hi Lianli, > > No, ITK does not have any vector image registration methods yet. > There could be many approaches here that are often problem specific. > Extracting a scalar pixel value from the vectors for application in > the metric is a workable approach. > > Hope this helps, > Matt > > On Thu, Oct 2, 2014 at 8:40 PM, Lianli Liu wrote: > > Hi all, > > > > I wonder if ITK is supporting vector image registration now? If not, any > > suggestions to achieve this goal? > > > > Thanks! > > Lianli > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Oct 13 11:11:20 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 13 Oct 2014 11:11:20 -0400 Subject: [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> References: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Message-ID: Hi Ariel, I'll see if we can record and upload the audio next time. Thanks, Matt On Thu, Oct 9, 2014 at 10:43 AM, Ariel Hern?n Curiale wrote: > Hi Matt, > Is there any chance to see the video of the meeting on you tube, for example > ? > > Cheers > __________________________________ > | Ariel Hern?n Curiale Ph.D Candidate > | ETSI Telecomunicaci?n > | Universidad de Valladolid > | Campus Miguel Delibes > | 47011 Valladolid, Spain > | Phone: 983-423000 ext. 5590 > | Web: www.curiale.com.ar > |_________________________________ > > On 07/10/2014, at 17:52, Matt McCormick wrote: > > On Friday, 11:00 AM Eastern USA time, an ITK development conference, > > https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 > > > To get regular invites to these events, join the ITK Bar Camp G+ Community: > > https://plus.google.com/u/0/communities/111375098792764998322 > > > All are welcome. Hope to talk to you then! > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > From matt.mccormick at kitware.com Mon Oct 13 11:20:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 13 Oct 2014 11:20:13 -0400 Subject: [ITK-users] TransformMatrix order in MHD file In-Reply-To: References: Message-ID: Hi Dongfeng, Column order. See itkImageIODirection3DTest [1] [2] for reference. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/test/itkImageIODirection3DTest.cxx;h=dc0f351944bc9dc293d95cf6ffb01bb832059bf8;hb=HEAD [2] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/test/CMakeLists.txt;h=1f8c20ec0ade96b860d000e3a777ee0d613cc467;hb=HEAD#l217 On Thu, Oct 9, 2014 at 3:54 PM, Dongfeng Han wrote: > Dear ITK users, > > Now I have a 3x3 TransformMatrix , when I write to mhd file, it just one > line. > I should write as row order or column order? > > thanks > > dongfeng > - > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From noreply at insightsoftwareconsortium.org Mon Oct 13 14:29:18 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 14:29:18 -0400 (EDT) Subject: [ITK-users] New Submission: Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS) Message-ID: <20141013182918.87F7E3D6C171@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS) Authors: Bernard O., Heyde B., Alessandrini M., Barbosa D., Camarasu-Pop S., Cervenansky F., Valette S., Mirea O., Galli E., Geleijnse M., Papachristidis A., Bosch J.G., D'hooge J. Abstract: Real-time 3D echocardiography has already been shown to be an accurate tool for left ventricular (LV) volume assessment. However, LV border identification remains a challenging task, mainly because of the low contrast of the images combined with drop-out artifacts. Many (semi-)automatic algorithms have been proposed to segment the LV border, but a systematic and fair comparison between such methods has so far been impossible due to a lack of publicly available common database. The aim of this MICCAI challenge was to gather researchers around the field of LV segmentation in 3D cardiac ultrasound by providing a common database to compare algorithms directly. The proposed platform will allow a consistent evaluation and ranking of the current state-of-the-art segmentation solutions and will contribute to a faster clinical translation of groundbreaking technical advances. The purpose of this paper is to describe the technical aspects of the generation of the database, give an ov erview of the ranking strategy and the outline of the challenge itself. Download and review this publication at: http://hdl.handle.net/10380/3479 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 15:20:14 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:20:14 -0400 (EDT) Subject: [ITK-users] New Submission: Clinical Expert Delineation of 3D Left Ventricular Echocardiograms for the CETUS Segmentation Challenge Message-ID: <20141013192014.688FB3D6C4F4@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Clinical Expert Delineation of 3D Left Ventricular Echocardiograms for the CETUS Segmentation Challenge Authors: Papachristidis A., Geleijnse M.L., Galli E., Heyde B., Alessandrini M., Barbosa D., Monaghan M.J., Bernard O., D'hooge J., Bosch J.G. Abstract: Within the framework of the CETUS challenge, forty-five 3D echocardiographic datasets have been acquired and segmented independently by three clinical experts from different hospitals. The goal was to generate a well-established ground truth of validated expert contours on this broad range of images from different ultrasound vendors, for a number of common pathologies. Image data were acquired and segmented according to a specifically designed protocol. Since there is no clear standard or guideline for segmentation for 3DUS, we defined a tracing consensus which results in clinically acceptable and reproducible contours. Tracing was performed in four longitudinal and five transversal 3D-derived 2D planes in ED and ES. 3D contours were constructed from these tracings. If the contours or their clinical parameters differed by more than a predefined level, the tracings were compared and the experts would reach a consensus interpretation on the best segmentation. One or more experts would then adapt their tracings. Final distance differences in contours were 0.77??0.18mm for the training set and 0.82??0.27mmfor the testing set. For the training set, 69% of contours were retraced. For the testing set, 76% of contours were retraced. The used protocol resulted in well-established ground truth contours. Download and review this publication at: http://hdl.handle.net/10380/3480 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 15:40:38 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:40:38 -0400 (EDT) Subject: [ITK-users] New Submission: Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching Message-ID: <20141013194038.520803D6C2EB@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching Authors: Barbosa D., Friboulet D., D'hooge J., Bernard O. Abstract: We present a novel method for segmentation and tracking of the left ventricle (LV) in 4D ultrasound sequences using a combination of automatic segmentation at the end-diastolic frame and tracking using both a global optical flow-based tracker and local block matching. The core novelty of the proposed algorithm relies on the recursive formulation of the block-matching problem, which introduces temporal consistency on the patterns being tracked. The proposed method offers a competitive solution, with average segmentation errors of 2.29 and 2.26mm in the training (#=15) and testing (#=15) datasets respectively. Download and review this publication at: http://hdl.handle.net/10380/3481 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 15:47:08 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:47:08 -0400 (EDT) Subject: [ITK-users] New Submission: Automatized Evaluation of the Left Ventricular Ejection Fraction from Echocardiographic Images Using Graph Cut Message-ID: <20141013194708.C4BD63D6C4EC@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Automatized Evaluation of the Left Ventricular Ejection Fraction from Echocardiographic Images Using Graph Cut Authors: Bernier M., Jodoin P., Lalande A. Abstract: In this paper, we present a fast and interactive graph cut method for 3D segmentation of the endocardial wall of the left ventricle (LV) given 3D echocardiographic images. This is a challenging task due to the poor contrast and the low signal-to-noise ratio typical of echocardiographic images. The method is carried out in 3 steps. First, 3D sampling of the LV cavity is made in a spherical-cylindrical coordinate system. Then, a gradient-based energy term is assigned to each voxel, some of which being given an infinite energy to make sure the resulting volume passes through key anatomical points. Then, a graph-cut procedure provides delineation of the endocardial surface. Results obtained on 30 exams from the 2014 CETUS MICCAI challenge dataset reveal that our method takes between 5 and 10 seconds to segment a 3D volume with an overall mean surface distance lower than 2.3 mm and an ejection fraction error of less than 5% compared to a manual tracing by an expert. Download and review this publication at: http://hdl.handle.net/10380/3482 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 15:56:17 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:56:17 -0400 (EDT) Subject: [ITK-users] New Submission: Endocardial Segmentation using Structured Random Forests in 3D Echocardiography Message-ID: <20141013195617.B23403D6C4DA@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Endocardial Segmentation using Structured Random Forests in 3D Echocardiography Authors: Domingos J.S., Stebbing R.V., Noble A.J. Abstract: Segmentation of the left ventricle endocardium in 3D echocardiography is a critical step for the diagnosis of heart disease. Although recent work has shown effective endocardial edge detection, these techniques still preserve spurious anatomical edge responses that undermine overall ventricle segmentation. In this paper we propose a robust semiautomatic framework based on 2D structured learning that facilitates full 3D model-based endocardial segmentation. This method is evaluated on 30 publicly available datasets from different brands of ultrasound machines. Results show that the proposed method accurately finds the endocardium and effectively converges an explicit and continuous surface model to it. Download and review this publication at: http://hdl.handle.net/10380/3483 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 16:25:11 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:25:11 -0400 (EDT) Subject: [ITK-users] New Submission: Endocardial 3D Ultrasound Segmentation using Autocontext Random Forests Message-ID: <20141013202511.6AA1B3D6C291@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Endocardial 3D Ultrasound Segmentation using Autocontext Random Forests Authors: Keraudren K., Oktay O., Shi W., Hajnal J.V., Rueckert D. Abstract: In this paper, we present the use of a generic image segmentation method, namely a succession of Random Forest classifiers in an autocontext framework, for the MICCAI 2014 Challenge on Endocardial 3D Ultrasound Segmentation (CETUS). The proposed method segments each frame independently in 90 sec, without requiring temporal information such as end-diastolic or end-systolic time points nor any registration. For better segmentation accuracy, non-local means denoising can be applied to the images at the cost of an increased run-time. The mean Dice score on the testing dataset was 84.4% without denoising and 86.4% with denoising. The originality of our approach lies in the introduction of two classes, the myocardium and the mitral valve, in addition to the left ventricle and the background classes, in order to gain contextual information for the segmentation task. Download and review this publication at: http://hdl.handle.net/10380/3484 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 16:30:11 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:30:11 -0400 (EDT) Subject: [ITK-users] New Submission: Left Ventricle Segmentation in Cardiac Ultrasound Using Hough-Forests With Implicit Shape and Appearance Priors Message-ID: <20141013203011.25A3E3D6C3C2@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Left Ventricle Segmentation in Cardiac Ultrasound Using Hough-Forests With Implicit Shape and Appearance Priors Authors: Milletari F., Yigitsoy M., Navab N., Ahmadi S. Abstract: We propose a learning based approach to perform automatic segmentation of the left ventricle in 3D cardiac ultrasound images. The segmentation contour is estimated through the use of a variant of Hough forests whose object localization capabilities are coupled with a patch-wise, appearance driven, contour estimation strategy. The performance of the proposed method is evaluated on a dataset of 30 images acquired from 15 patients using different equipment and settings. Download and review this publication at: http://hdl.handle.net/10380/3485 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 16:34:43 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:34:43 -0400 (EDT) Subject: [ITK-users] New Submission: Learning Shape Representations for Multi-Atlas Endocardium Segmentation in 3D Echo Images Message-ID: <20141013203443.D24FA3D6C55B@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Learning Shape Representations for Multi-Atlas Endocardium Segmentation in 3D Echo Images Authors: Oktay O., Shi W., Keraudren K., Caballero J., Rueckert D. Abstract: As part of the CETUS challenge, we present a multi-atlas segmentation framework to delineate the left-ventricle endocardium in echocardiographic images. To increase the robustness of the registration step, we introduce a speckle reduction step and a new shape representation based on sparse coding and manifold approximation in dictionary space. The shape representation, unlike intensity values, provides consistent shape information across different images. The validation results on the test set show that registration based on our shape representation significantly improves the performance of multi-atlas segmentation compared to intensity based registration. To our knowledge it is the first time that multi-atlas segmentation achieves state-of-the-art results for echocardiographic images. Download and review this publication at: http://hdl.handle.net/10380/3486 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 16:38:35 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:38:35 -0400 (EDT) Subject: [ITK-users] New Submission: Real-time Tracking of the Left Ventricle in 3D Ultrasound Using Kalman Filter and Mean Value Coordinates Message-ID: <20141013203835.114943D6C407@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Real-time Tracking of the Left Ventricle in 3D Ultrasound Using Kalman Filter and Mean Value Coordinates Authors: Smistad E., Lindseth F. Abstract: A method for real-time automatic tracking of the left ventricle (LV) in 3D ultrasound is presented. A mesh model of the LV is deformed using mean value coordinates enabling large variations. Kalman filtering and edge detection is used to track the mesh in each frame. The method is evaluated using the framework of the Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS). The results show that the method is able to robustly track the LV in all sequences with a mean mesh difference of about 2.5 mm Download and review this publication at: http://hdl.handle.net/10380/3487 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 16:45:33 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:45:33 -0400 (EDT) Subject: [ITK-users] New Submission: Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models Message-ID: <20141013204533.E60203D6C46C@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models Authors: Van Stralen M., Haak A., Leung E.K., Van Burken G., Bosch J.G. Abstract: Segmentation of 3D echocardiograms (3DEs) is still a challenging task due to the low signal-to-noise ratio, the limited field of view, and typical ultrasound artifacts. We propose to segment the left ventricular endocardial surface by using Active Appearance Models (AAMs). Separate end-diastolic (ED) and end-systolic (ES) AAMs were built from presegmented 3DEs of the CETUS training data and 25 previously acquired 3DEs, imaged using various 3DE equipment. The AAMs fully automatically segmented the 15 training sets in a leave-one-out cross validation, comparing two training populations and various initialization strategies. All segmentations took about 15 seconds per patient. The comparison on the CETUS training data shows that the AAM benefits from additional training data and more accurate initialization. The results on the CETUS training and testing data confirm good ED and ES segmentation accuracy on multi-center, multi-vendor, multi-pathology data, and corresponding EF e stimation. Selection from different initialization strategies, based on the minimal residual error, and propagation of detected ED contours to initialize ES detection, contributed to more accurate segmentations in this heterogeneous population. Download and review this publication at: http://hdl.handle.net/10380/3488 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 13 16:51:08 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:51:08 -0400 (EDT) Subject: [ITK-users] New Submission: Model-based left ventricle segmentation in 3D ultrasound using phase image Message-ID: <20141013205108.426C23D6C7AE@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Model-based left ventricle segmentation in 3D ultrasound using phase image Authors: Wang C., Smedby O. Abstract: In this paper, we propose a semi-automatic method for left ventricle segmentation. The proposed method utilizes a multi-scale quadrature filter method to enhance the 3D volume, followed by a model-based level set method to segment the endocardial surface of the left ventricle. The phase map from the quadrature filters is also used to weight the influence of contour points when updating the statistical model. Download and review this publication at: http://hdl.handle.net/10380/3489 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From davis.vigneault at gmail.com Tue Oct 14 11:31:09 2014 From: davis.vigneault at gmail.com (DVigneault) Date: Tue, 14 Oct 2014 08:31:09 -0700 (PDT) Subject: [ITK-users] Operator overloading in ITK objects. Message-ID: <1413300669946-7586346.post@n2.nabble.com> All-- I've defined an ITK object inheriting from itk::DataObject (full header file copied below). The object has two properties: Index and Value. I've tried to overload the == and < operators (basing my syntax off of itk::Point) so that the two objects would be equal if they have the same index, and one would be less than the other if one's value is less than the other's: bool operator==(const Self & pt) const { return this->GetIndex() == pt->GetIndex(); } bool operator<(const Self & pt) const { return this->GetValue() < pt->GetValue(); } However, the less than operator isn't functioning as intended: typedef IndexValuePair< IndexType, PixelType > PairType; typename PairType::Pointer pair1 = PairType::New(); IndexType index1; pair1->SetIndex( index1.Fill( 0 ) ); pair1->SetValue( 1 ); typename PairType::Pointer pair2 = PairType::New(); IndexType index2; pair2->SetIndex( index2.Fill( 1 ) ); pair2->SetValue( 0 ); std::cout << (pair1 == pair2) << std::endl; // 0 std::cout << (pair1 == pair1) << std::endl; // 1 std::cout << (pair1 < pair2) << std::endl; // 1 Interestingly, the results do not change if I comment out the overloading operators in the header file, or if I change the values of the pairs, suggesting that the program is comparing the objects based on some other criteria. Any ideas what I'm doing wrong? Apologies in advance if this is more of a c++ question and less of an ITK question--I'm sometimes not sure whether my problem is due to my misunderstanding the language or the library. Best, --Davis Best, and thanks, --Davis *** Header ** #ifndef __itkIndexValuePair_h #define __itkIndexValuePair_h #include "itkDataObject.h" namespace itk { template < typename IndexType, typename ValueType > class IndexValuePair:public DataObject { public: /** Standard class typedefs. */ typedef IndexValuePair Self; typedef DataObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkNewMacro(Self); /** Standard part of every itk Object. */ itkTypeMacro(IndexValuePair, DataObject); itkSetMacro( Index, IndexType ); itkGetMacro( Index, IndexType ); itkSetMacro( Value, ValueType ); itkGetMacro( Value, ValueType ); /** Compare two points for equality. */ bool operator==(const Self & pt) const { return this->GetIndex() == pt->GetIndex(); } /** Less than. */ bool operator<(const Self & pt) const { return this->GetValue() < pt->GetValue(); } protected: /** Constructor for use by New() method. */ IndexValuePair() {} ~IndexValuePair() {} // virtual void PrintSelf(std::ostream & os, Indent indent) const; IndexType m_Index; ValueType m_Value; private: IndexValuePair(const Self &); //purposely not implemented void operator=(const Self &); //purposely not implemented }; } #endif -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Operator-overloading-in-ITK-objects-tp7586346.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From blowekamp at mail.nih.gov Tue Oct 14 11:38:49 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 14 Oct 2014 11:38:49 -0400 Subject: [ITK-users] Operator overloading in ITK objects. In-Reply-To: <1413300669946-7586346.post@n2.nabble.com> References: <1413300669946-7586346.post@n2.nabble.com> Message-ID: <47CDDE20-C688-4DA0-A28B-AAEE0BBAC93A@mail.nih.gov> Hello, I think the issue is that the variables pair1 and pair2 are SmartPointers not the derived data object type, so your operators are working on a different object type than you expected. ITK was not designed for use with overloaded operators with it's data objects and process objects. You could likely hack it by doing (*pair1) == (*pair2), if you really want to use overloaded operators. Otherwise a conventional member function could just as easily be used. Brad On Oct 14, 2014, at 11:31 AM, DVigneault wrote: > All-- > > I've defined an ITK object inheriting from itk::DataObject (full header file > copied below). The object has two properties: Index and Value. I've tried > to overload the == and < operators (basing my syntax off of itk::Point) so > that the two objects would be equal if they have the same index, and one > would be less than the other if one's value is less than the other's: > > bool operator==(const Self & pt) const { > return this->GetIndex() == pt->GetIndex(); } > > bool operator<(const Self & pt) const { > return this->GetValue() < pt->GetValue(); } > > However, the less than operator isn't functioning as intended: > > typedef IndexValuePair< IndexType, PixelType > PairType; > typename PairType::Pointer pair1 = PairType::New(); > IndexType index1; > pair1->SetIndex( index1.Fill( 0 ) ); > pair1->SetValue( 1 ); > > typename PairType::Pointer pair2 = PairType::New(); > IndexType index2; > pair2->SetIndex( index2.Fill( 1 ) ); > pair2->SetValue( 0 ); > > std::cout << (pair1 == pair2) << std::endl; // 0 > std::cout << (pair1 == pair1) << std::endl; // 1 > std::cout << (pair1 < pair2) << std::endl; // 1 > > Interestingly, the results do not change if I comment out the overloading > operators in the header file, or if I change the values of the pairs, > suggesting that the program is comparing the objects based on some other > criteria. Any ideas what I'm doing wrong? Apologies in advance if this is > more of a c++ question and less of an ITK question--I'm sometimes not sure > whether my problem is due to my misunderstanding the language or the > library. > > Best, > > --Davis > > Best, and thanks, > > --Davis > > *** Header ** > > #ifndef __itkIndexValuePair_h > #define __itkIndexValuePair_h > > #include "itkDataObject.h" > > namespace itk > { > > template < typename IndexType, typename ValueType > > class IndexValuePair:public DataObject > { > > public: > > /** Standard class typedefs. */ > typedef IndexValuePair Self; > typedef DataObject Superclass; > typedef SmartPointer< Self > Pointer; > typedef SmartPointer< const Self > ConstPointer; > > /** Method for creation through the object factory. */ > itkNewMacro(Self); > > /** Standard part of every itk Object. */ > itkTypeMacro(IndexValuePair, DataObject); > > itkSetMacro( Index, IndexType ); > itkGetMacro( Index, IndexType ); > > itkSetMacro( Value, ValueType ); > itkGetMacro( Value, ValueType ); > > > /** Compare two points for equality. */ > bool > operator==(const Self & pt) const > { > return this->GetIndex() == pt->GetIndex(); > } > > /** Less than. */ > bool > operator<(const Self & pt) const > { > return this->GetValue() < pt->GetValue(); > } > > protected: > /** Constructor for use by New() method. */ > IndexValuePair() {} > ~IndexValuePair() {} > // virtual void PrintSelf(std::ostream & os, Indent indent) const; > > IndexType m_Index; > ValueType m_Value; > > private: > IndexValuePair(const Self &); //purposely not implemented > void operator=(const Self &); //purposely not implemented > > }; > > } > > #endif > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Operator-overloading-in-ITK-objects-tp7586346.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From gabrielgimenez85 at gmail.com Tue Oct 14 19:51:39 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Tue, 14 Oct 2014 16:51:39 -0700 (PDT) Subject: [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform Message-ID: <1413330699438-7586348.post@n2.nabble.com> Hello everyone, I modified the example 8 for use OnePlusOneEvolutionaryOptimizer and itkMattesMutualInformationImageToImageMetric, this worked for me. Now, i try to use itkRegistrationParameterScalesFromPhysicalShift for to estimate the parameters of scale. I adapted my code to use the ITKv4, but, but I have this error: *Optimizer stop condition: OnePlusOneEvolutionaryOptimizerv4: Fnorm (0.000777958) is less than Epsilon (1 at iteration #0* I found almost no documentation of ITK version 4, why ?In Manuals not found anything. This is the part of code to configure the estimation scale (based on examples found in the DoxyGen): typedef itk::RegistrationParameterScalesFromPhysicalShift ScalesEstimatorType; ScalesEstimatorType::Pointer scalesEstimator = ScalesEstimatorType::New(); scalesEstimator->SetMetric( metric ); scalesEstimator->SetTransformForward( true ); scalesEstimator->SetSmallParameterVariation( 1.0 ); optimizer->SetScalesEstimator( scalesEstimator ); optimizer->SetDoEstimateScales(true); Hopefully someone can help me with something, thanks. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From j.plumat at auckland.ac.nz Tue Oct 14 21:42:19 2014 From: j.plumat at auckland.ac.nz (Jerome Plumat) Date: Wed, 15 Oct 2014 14:42:19 +1300 Subject: [ITK-users] how to visualise deformed volume along registration process Message-ID: <543DD0FB.1040609@auckland.ac.nz> Hello everyone, I'm facing to a problem and I hope some may have ideas to help me. I'm using Multi Resolution Symmetric Log-Domain Diffeomorphic Demons Algorithm (http://www.insight-journal.org/browse/publication/644) to register volumes. The current results are not very good and I would like to observe them along the registration process. My current solution uses object to display metrics and information along pyramid levels: template class ShowProgressObject { public: ShowProgressLevelObject(TRegistration* o) { m_Process = o; } void ShowProgress() { std::cout << "Level: " << m_Process->GetCurrentLevel() << " "; std::cout << "Progress: " << m_Process->GetProgress() << " "; std::cout << "Starting Metric: " << m_Process->GetRegistrationFilter()->GetMetric() << " "; std::cout << std::endl; } typename TRegistration::Pointer m_Process; }; .... typedef ShowProgressObject ProgressType; ProgressType progressWatch(registrator); itk::SimpleMemberCommand::Pointer command; command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(&progressWatch, &ProgressType::ShowProgress); I would like to use this object to display the current deformed image at each level of the pyramid. My current (not so good) idea is to use fixed and moving images and current deformation field. I'm using warper to deform the moving image in the ShowProgressObject::ShowProgress function: warper->SetInput( m_originalMoving ); warper->SetInterpolator( interpolator ); warper->SetOutputSpacing( m_fixed->GetSpacing() ); warper->SetOutputOrigin( m_fixed->GetOrigin() ); warper->SetOutputDirection( m_fixed->GetDirection() ); warper->SetDisplacementField( m_Process->GetRegistrationFilter()->GetDeformationField() ); warper->Update(); Then the result would be display with QuickView. But ... it appears that using fixed and moving images in this process makes them unavailable for the registration. I can make copies of them but this seems very inefficient. Any recommendations or advices to achieve to display deformed image along process? Thanks a lot. -- Jerome ------- School of Medical Sciences University of Auckland If I am not for myself, who will be for me? And if I am only for myself, then what an I? And if not now when? ? Hillel HaZaken From shinya.onogi at live.jp Wed Oct 15 05:45:39 2014 From: shinya.onogi at live.jp (Shinya Onogi) Date: Wed, 15 Oct 2014 02:45:39 -0700 (MST) Subject: [ITK-users] ITK build failed in using ITK_USE_FLOAT_SPACE_PRECISION Message-ID: <1413366339221-34689.post@n7.nabble.com> Hi, When ITK_USE_FLOAT_SPACE_PRECISION is TRUE, Compilation error occurs in itkTransformFactoryBase.cxx at L274 and L275. I could not find the issue in Google; therefore, I will note it here for anyone. L274: TransformFactory< GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >::RegisterTransform (); L275 TransformFactory< GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >::RegisterTransform (); My env is followings. OS: Windows 8.1 Platform: Visual Studio 2013 ITK: ITK-4.6.1 -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-build-failed-in-using-ITK-USE-FLOAT-SPACE-PRECISION-tp34689.html Sent from the ITK - Users mailing list archive at Nabble.com. From blowekamp at mail.nih.gov Wed Oct 15 08:32:47 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 08:32:47 -0400 Subject: [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413330699438-7586348.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> Message-ID: <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> Hello, > > *Optimizer stop condition: OnePlusOneEvolutionaryOptimizerv4: Fnorm > (0.000777958) is less than Epsilon (1 at iteration #0* This message may mean that the scales are not correctly set, and the the initial search area failed to yield a significant change. Things that can impact the scales include the metric used and the spacing of your image. This can some times be a difficult thing to track down. Would the spacing of you image happen to be very large or very small? Also keep in mind that the Versor transforms are not Euclidean spaces and a best suited for use with the regular step gradient descent optimizers as only that optimizer takes into consideration the correct normalization of the versor space. In short I think you have picked three challenging components that may just now work well together. Brad > > I found almost no documentation of ITK version 4, why ?In Manuals not found > anything. > > This is the part of code to configure the estimation scale (based on > examples found in the DoxyGen): > > typedef itk::RegistrationParameterScalesFromPhysicalShift > ScalesEstimatorType; > ScalesEstimatorType::Pointer scalesEstimator = > ScalesEstimatorType::New(); > scalesEstimator->SetMetric( metric ); > scalesEstimator->SetTransformForward( true ); > scalesEstimator->SetSmallParameterVariation( 1.0 ); > > optimizer->SetScalesEstimator( scalesEstimator ); > optimizer->SetDoEstimateScales(true); > > Hopefully someone can help me with something, thanks. > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From emmasaunders123 at gmail.com Wed Oct 15 08:56:33 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Wed, 15 Oct 2014 13:56:33 +0100 Subject: [ITK-users] Metric Distance on Manifold Message-ID: Hello all, ITK offers numerous diffeomorphic registration algorithms, is there a mechanism within ITK to calculate the distance each transformation has moved along the diffeomorphic manifold? If not is it possible to perform such a calculation on the displacement fields themselves. Thanks for any help Emma -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Oct 15 09:14:25 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 09:14:25 -0400 Subject: [ITK-users] ITK build failed in using ITK_USE_FLOAT_SPACE_PRECISION In-Reply-To: <1413366339221-34689.post@n7.nabble.com> References: <1413366339221-34689.post@n7.nabble.com> Message-ID: Hello, I tried compiling with this options with gcc 4.8.2 on Linux and I am getting a large number of compilation errors too. Looks like it would requite a bit of work to get this working again. Perhaps This option worked with the ITK 4.5 release? Brad On Oct 15, 2014, at 5:45 AM, Shinya Onogi wrote: > Hi, > > When ITK_USE_FLOAT_SPACE_PRECISION is TRUE, Compilation error occurs in > itkTransformFactoryBase.cxx at L274 and L275. I could not find the issue in > Google; therefore, I will note it here for anyone. > > L274: > TransformFactory< > GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >> ::RegisterTransform (); > > L275 > TransformFactory< > GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >> ::RegisterTransform (); > > > My env is followings. > OS: Windows 8.1 > Platform: Visual Studio 2013 > ITK: ITK-4.6.1 > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/ITK-build-failed-in-using-ITK-USE-FLOAT-SPACE-PRECISION-tp34689.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From gabrielgimenez85 at gmail.com Wed Oct 15 10:26:00 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Wed, 15 Oct 2014 07:26:00 -0700 (PDT) Subject: [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> Message-ID: <1413383160042-7586354.post@n2.nabble.com> Hello Brad ,thanks for answering, I need the definition of scales Optimizer (translation and rotation) to be dynamic, not hard, so I use the RegistrationParameterScalesFromPhysicalShift class. Any other alternatives for my problem?. Nor do I find much information about how to define these scales and even less dynamically. Theoretically ITK architecture is fully modular and low-coupling, then, should be no problem to combine different types of optimizers, transformations, etc, or am I wrong? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586354.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From blowekamp at mail.nih.gov Wed Oct 15 10:43:45 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 10:43:45 -0400 Subject: [ITK-users] [ITK] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413383160042-7586354.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> Message-ID: <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> Hello, The scales are going to be for the serializable optimization parameters for the Transform defined in the doxygen[1]. You may wish to try the other scales estimators: RegistrationPatameterScalesFromIndexShift, RegistrationParameterScalesFromJacobian Also the other parameters for your optimizer may need to be adjusted such as InitialRadius, ShrinkFactor and the GrowthFactor. I have not investigated if these optimizer parameters are correctly scales into the parameter space when applied, but they should be. As you are doing you can theoretically plug any combination of components together. However the results may not be robust or stable. Again I will urge caution with using the Versor transforms with an optimizer other than the RegularStepGradientDescent as there is some coupling of these two to do the correct normalization in the versor space. Brad [1] http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html On Oct 15, 2014, at 10:26 AM, Gabriel A. Gim?nez wrote: > Hello Brad ,thanks for answering, > > I need the definition of scales Optimizer (translation and rotation) to be > dynamic, not hard, so I use the RegistrationParameterScalesFromPhysicalShift > class. Any other alternatives for my problem?. Nor do I find much > information about how to define these scales and even less dynamically. > > > Theoretically ITK architecture is fully modular and low-coupling, then, > should be no problem to combine different types of optimizers, > transformations, etc, or am I wrong? > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586354.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From llliu at umich.edu Wed Oct 15 18:13:19 2014 From: llliu at umich.edu (Lianli Liu) Date: Wed, 15 Oct 2014 18:13:19 -0400 Subject: [ITK-users] get B spline coefficients Message-ID: Hi all, I have a deformation field (m*n*k*3 vector image) obtained from B spline registration and I want to get the B spline coefficient from the deformation field. Here are my questions: Shall I use the itkBSplineDecompositionImageFilter to do this? If so, do I need to decompose it along each dimension all just input the entire vector image? Do I need to down sample the image first before decomposition? How should I save my decomposition results? Thanks! Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabrielgimenez85 at gmail.com Wed Oct 15 21:40:06 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Wed, 15 Oct 2014 18:40:06 -0700 (PDT) Subject: [ITK-users] [ITK] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> Message-ID: <1413423606327-7586357.post@n2.nabble.com> thank you very much Brad! Some documentation on how to configure these scales (translation and rotation) manually? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586357.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From matt.mccormick at kitware.com Thu Oct 16 00:05:07 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:05:07 -0400 Subject: [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cg7hf091i0k638gm43n3ktkfic0 On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/c3fr7aeqa06lhp2j1r601586o1s For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From matt.mccormick at kitware.com Thu Oct 16 00:25:03 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:25:03 -0400 Subject: [ITK-users] [ITK] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413423606327-7586357.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> <1413423606327-7586357.post@n2.nabble.com> Message-ID: Hi Gabriel, Documentation on the ITKv4 registration scale estimation can be found in the Nightly build of the ITK Software Guide. There is is usually a link to the Nightly PDF builds of the ITK Software Guide on the dashboard [1], but it is currently not available due to some build issues. The code for the examples in the software guide can be found in the Examples/Registrationv4/ direction of ITK Git master [2]. Hope this helps, Matt [1] http://open.cdash.org/index.php?project=Insight [2] http://www.itk.org/Wiki/ITK/Git On Wed, Oct 15, 2014 at 9:40 PM, Gabriel A. Gim?nez wrote: > thank you very much Brad! > Some documentation on how to configure these scales (translation and > rotation) manually? > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586357.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Oct 16 00:34:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:34:11 -0400 Subject: [ITK-users] how to visualise deformed volume along registration process In-Reply-To: <543DD0FB.1040609@auckland.ac.nz> References: <543DD0FB.1040609@auckland.ac.nz> Message-ID: Hi Jerome, Writing out the Transform as the program progresses may work. Then, use a separate program to generate the resampled images from the input images and the transform. Also, the Transform Visualizer [1] available in the current Slicer Nightly build [2] (soon to be 4.4.0), is a great tool. Hope this helps, Matt [1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/TransformVisualizer [2] http://download.slicer.org/ On Tue, Oct 14, 2014 at 9:42 PM, Jerome Plumat wrote: > Hello everyone, > I'm facing to a problem and I hope some may have ideas to help me. > > I'm using Multi Resolution Symmetric Log-Domain Diffeomorphic Demons > Algorithm (http://www.insight-journal.org/browse/publication/644) to > register volumes. The current results are not very good and I would like to > observe them along the registration process. > > My current solution uses object to display metrics and information along > pyramid levels: > > template > class ShowProgressObject > { > public: > ShowProgressLevelObject(TRegistration* o) > { > m_Process = o; > } > > void ShowProgress() > { > std::cout << "Level: " << m_Process->GetCurrentLevel() << " "; > std::cout << "Progress: " << m_Process->GetProgress() << " "; > std::cout << "Starting Metric: " << > m_Process->GetRegistrationFilter()->GetMetric() << " "; > std::cout << std::endl; > > } > > typename TRegistration::Pointer m_Process; > }; > > .... > > typedef ShowProgressObject ProgressType; > ProgressType progressWatch(registrator); > > itk::SimpleMemberCommand::Pointer command; > command = itk::SimpleMemberCommand::New(); > command->SetCallbackFunction(&progressWatch, &ProgressType::ShowProgress); > > > I would like to use this object to display the current deformed image at > each level of the pyramid. My current (not so good) idea is to use fixed and > moving images and current deformation field. I'm using warper to deform the > moving image in the ShowProgressObject::ShowProgress function: > warper->SetInput( m_originalMoving ); > warper->SetInterpolator( interpolator ); > warper->SetOutputSpacing( m_fixed->GetSpacing() ); > warper->SetOutputOrigin( m_fixed->GetOrigin() ); > warper->SetOutputDirection( m_fixed->GetDirection() ); > warper->SetDisplacementField( > m_Process->GetRegistrationFilter()->GetDeformationField() ); > warper->Update(); > > Then the result would be display with QuickView. > > But ... it appears that using fixed and moving images in this process makes > them unavailable for the registration. I can make copies of them but this > seems very inefficient. > > Any recommendations or advices to achieve to display deformed image along > process? > > Thanks a lot. > > -- > > Jerome > ------- > > School of Medical Sciences > University of Auckland > > If I am not for myself, who will be for me? And if I am only for myself, > then what an I? And if not now when? ? Hillel HaZaken > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Oct 16 15:30:10 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 15:30:10 -0400 Subject: [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Message-ID: Based on feedback at the Code Review Hangout today, to respect the privacy of participants, we are not going to record the audio tomorrow. Matt On Mon, Oct 13, 2014 at 11:11 AM, Matt McCormick wrote: > Hi Ariel, > > I'll see if we can record and upload the audio next time. > > Thanks, > Matt > > On Thu, Oct 9, 2014 at 10:43 AM, Ariel Hern?n Curiale wrote: >> Hi Matt, >> Is there any chance to see the video of the meeting on you tube, for example >> ? >> >> Cheers >> __________________________________ >> | Ariel Hern?n Curiale Ph.D Candidate >> | ETSI Telecomunicaci?n >> | Universidad de Valladolid >> | Campus Miguel Delibes >> | 47011 Valladolid, Spain >> | Phone: 983-423000 ext. 5590 >> | Web: www.curiale.com.ar >> |_________________________________ >> >> On 07/10/2014, at 17:52, Matt McCormick wrote: >> >> On Friday, 11:00 AM Eastern USA time, an ITK development conference, >> >> https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 >> >> >> To get regular invites to these events, join the ITK Bar Camp G+ Community: >> >> https://plus.google.com/u/0/communities/111375098792764998322 >> >> >> All are welcome. Hope to talk to you then! >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> From boll0107 at umn.edu Thu Oct 16 16:00:17 2014 From: boll0107 at umn.edu (Evan Bollig PhD) Date: Thu, 16 Oct 2014 15:00:17 -0500 Subject: [ITK-users] SimpleITK python3.4 OSX egg/homebrew Message-ID: Can someone generate a SimpleITK egg for python3.4 on OSX? easy_install SimpleITK comes back with 0 hits for me, and I'd rather not try to figure out how to reproduce your builds. By the way, you should also consider writing a Homebrew recipe to build and install the library as well. I can provide an example recipe for another CMake project that provides Python (SWIG wrapped) libraries if you're interested. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan at msi.umn.edu boll0107 at umn.edu From gabrielgimenez85 at gmail.com Thu Oct 16 20:36:42 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Thu, 16 Oct 2014 17:36:42 -0700 (PDT) Subject: [ITK-users] [ITK] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> <1413423606327-7586357.post@n2.nabble.com> Message-ID: <1413506202830-7586363.post@n2.nabble.com> Thanks Matt, I sure will be very useful! I'm working on my thesis, I would like to implement a GA optimizer for ITK. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586363.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From blowekamp at mail.nih.gov Fri Oct 17 08:12:16 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 17 Oct 2014 08:12:16 -0400 Subject: [ITK-users] SimpleITK python3.4 OSX egg/homebrew In-Reply-To: References: Message-ID: Hello, There are quite a large number of different binary distributions of Python and not all of them can be supported. Currently the the binaries are compatible with OSX's system python. It is not too hard to build SimpleITK itself for you custom installation. Information on how to do that can be found here [1]. If you are familiar with Homebrew then it should not be too hard to write a recipe for that packaging system. Contributing this to the community would be very welcomed and appreciated by many. There is a recipe for the anaconda python distribution that may be a good basis for Homebrew[2]. Brad [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself [2] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh On Oct 16, 2014, at 4:00 PM, Evan Bollig PhD wrote: > Can someone generate a SimpleITK egg for python3.4 on OSX? > easy_install SimpleITK comes back with 0 hits for me, and I'd rather > not try to figure out how to reproduce your builds. > > By the way, you should also consider writing a Homebrew recipe to > build and install the library as well. I can provide an example recipe > for another CMake project that provides Python (SWIG wrapped) > libraries if you're interested. > > Cheers, > -Evan Bollig > Research Associate | Application Developer | User Support Consultant > Minnesota Supercomputing Institute > 599 Walter Library > 612 624 1447 > evan at msi.umn.edu > boll0107 at umn.edu > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From joel.schaerer at laposte.net Fri Oct 17 12:03:49 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Fri, 17 Oct 2014 18:03:49 +0200 Subject: [ITK-users] Possible missing method in itkImageSource Message-ID: <54413DE5.1050108@laposte.net> Hi all, I've run into a problem with named outputs, which I believe could be a bug in ITK. When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. . These methods are declared and defined first in itkProcessObject: .h: * ... * ProcessObject::MakeOutput. Note that MakeOutput always returns a * itkSmartPointer to a DataObject. ImageSource and MeshSource override * this method to create the correct type of image and mesh respectively. * If a filter has multiple outputs of different types, then that * filter must provide an implementation of MakeOutput(). */ virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); .cxx DataObject::Pointer ProcessObject ::MakeOutput( const DataObjectIdentifierType & name ) { itkDebugMacro("MakeOutput(" << name << ")"); if( this->IsIndexedOutputName(name) ) { return this->MakeOutput( this->MakeIndexFromOutputName(name) ); } return static_cast(DataObject::New().GetPointer()); } DataObject::Pointer ProcessObject ::MakeOutput(DataObjectPointerArraySizeType) { return static_cast(DataObject::New().GetPointer()); } For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. template< typename TOutputImage > ProcessObject::DataObjectPointer ImageSource< TOutputImage > ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) { return TOutputImage::New().GetPointer(); } So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. Any reason for this behavior? Is this an oversight? Thanks, Jo?l From millerjv at gmail.com Fri Oct 17 17:01:57 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 17 Oct 2014 17:01:57 -0400 Subject: [ITK-users] Possible missing method in itkImageSource In-Reply-To: <54413DE5.1050108@laposte.net> References: <54413DE5.1050108@laposte.net> Message-ID: <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> At first glance it looks like an oversight. I would expect, however, that we should be seeing warnings about the named version of MakeOutput in ProcessObject being hidden. Jim > On Oct 17, 2014, at 12:03 PM, Jo?l Schaerer wrote: > > Hi all, > > I've run into a problem with named outputs, which I believe could be a bug in ITK. > > When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. > . > These methods are declared and defined first in itkProcessObject: > > .h: > * ... > * ProcessObject::MakeOutput. Note that MakeOutput always returns a > * itkSmartPointer to a DataObject. ImageSource and MeshSource override > * this method to create the correct type of image and mesh respectively. > * If a filter has multiple outputs of different types, then that > * filter must provide an implementation of MakeOutput(). */ > virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); > virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); > > .cxx > DataObject::Pointer > ProcessObject > ::MakeOutput( const DataObjectIdentifierType & name ) > { > itkDebugMacro("MakeOutput(" << name << ")"); > if( this->IsIndexedOutputName(name) ) > { > return this->MakeOutput( this->MakeIndexFromOutputName(name) ); > } > return static_cast(DataObject::New().GetPointer()); > } > > DataObject::Pointer > ProcessObject > ::MakeOutput(DataObjectPointerArraySizeType) > { > return static_cast(DataObject::New().GetPointer()); > } > > > For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. > > template< typename TOutputImage > > ProcessObject::DataObjectPointer > ImageSource< TOutputImage > > ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) > { > return TOutputImage::New().GetPointer(); > } > > So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. > > Any reason for this behavior? Is this an oversight? > > Thanks, > > Jo?l > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From gralewskik at email.chop.edu Sun Oct 19 20:13:09 2014 From: gralewskik at email.chop.edu (Kevin) Date: Sun, 19 Oct 2014 17:13:09 -0700 (MST) Subject: [ITK-users] Error running Exmaple code -- ICP2.cxx Message-ID: <1413763989914-34707.post@n7.nabble.com> Hello, Just started working with ITK and could use help from this nice community getting up to speed. As the subject reads, I'm currently trying to run iterativeclosestpoint2.cxx from the example source code to register 2 volume meshes. Below is the copied error message I keep getting (ClosestPoint3D is the executable name, obviously): /ClosestPoint3D(15746,0x7fff79138310) malloc: *** error for object 0x7f818d00e328: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6/ I haven't coded in about 10 years and was never great at debugging so I'm at a bit of a loss. I'm running the official release 4.6.1 on OS X 10.9.5 with clang, Apple LLVM 6.0 (based on 3.5). Here are a few more details/curious notes: when I would pass it the mesh files in either .STL or .vtk format the code would get stuck in the indexing function (I just dropped and returned an counter in the while loop). It never kicked out even after running for iterations orders of magnitude more than the points (and edges for that matter). I then passed it a point cloud file as both a .txt and .xyz (a 3D point plot from MeshLab 1.3.3). This is when I get the checksum error. The code indexed and returned the points tally fine, and initiated a matrix transform, but would the abort. Even more oddly, when I run the executable again (with the same files) to make sure I got the error message right it returned a solution with the .txt, along with the checksum error, but not the .xyz point cloud. Lastly, I lowered the convergence criterion, epsilon, to .001 thinking maybe it wasn't converging before the number of iterations was hit, but that didn't alleviate the issue. In fact, it wouldn't return the initial identity matrix. -- View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707.html Sent from the ITK - Users mailing list archive at Nabble.com. From matt.mccormick at kitware.com Sun Oct 19 23:47:47 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 19 Oct 2014 23:47:47 -0400 Subject: [ITK-users] Error running Exmaple code -- ICP2.cxx In-Reply-To: <1413763989914-34707.post@n7.nabble.com> References: <1413763989914-34707.post@n7.nabble.com> Message-ID: Hi Kevin, Welcome to ITK! Please send your CMakeLists.txt, code, data, and the command that you run so that others may understand the problem. Thanks, Matt On Sun, Oct 19, 2014 at 8:13 PM, Kevin wrote: > Hello, > > Just started working with ITK and could use help from this nice community > getting up to speed. > > As the subject reads, I'm currently trying to run iterativeclosestpoint2.cxx > from the example source code to register 2 volume meshes. Below is the > copied error message I keep getting (ClosestPoint3D is the executable name, > obviously): > > /ClosestPoint3D(15746,0x7fff79138310) malloc: *** error for object > 0x7f818d00e328: incorrect checksum for freed object - object was probably > modified after being freed. > *** set a breakpoint in malloc_error_break to debug > Abort trap: 6/ > > I haven't coded in about 10 years and was never great at debugging so I'm > at a bit of a loss. I'm running the official release 4.6.1 on OS X 10.9.5 > with clang, Apple LLVM 6.0 (based on 3.5). > > Here are a few more details/curious notes: when I would pass it the mesh > files in either .STL or .vtk format the code would get stuck in the indexing > function (I just dropped and returned an counter in the while loop). It > never kicked out even after running for iterations orders of magnitude more > than the points (and edges for that matter). > > I then passed it a point cloud file as both a .txt and .xyz (a 3D point plot > from MeshLab 1.3.3). This is when I get the checksum error. The code indexed > and returned the points tally fine, and initiated a matrix transform, but > would the abort. Even more oddly, when I run the executable again (with the > same files) to make sure I got the error message right it returned a > solution with the .txt, along with the checksum error, but not the .xyz > point cloud. > > Lastly, I lowered the convergence criterion, epsilon, to .001 thinking maybe > it wasn't converging before the number of iterations was hit, but that > didn't alleviate the issue. In fact, it wouldn't return the initial identity > matrix. > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From gralewskik at email.chop.edu Mon Oct 20 21:43:38 2014 From: gralewskik at email.chop.edu (Kevin) Date: Mon, 20 Oct 2014 18:43:38 -0700 (MST) Subject: [ITK-users] Error running Exmaple code -- ICP2.cxx In-Reply-To: References: <1413763989914-34707.post@n7.nabble.com> Message-ID: <1413855818662-34709.post@n7.nabble.com> Thanks, Matt. And thanks for the quick reply. Attached are the requested files: CMakeLists.txt IterativeClosestPoint2.cxx (directly from source package) Data_1.txt Data_2.txt Again, I'm running OS x and follow the method outlined in the manual to configure, compile and run. The line commands are: ccmake ../(directory containing CMakelists.txt and code) make ./(executable name) (file 1) (file 2) -- View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707p34709.html Sent from the ITK - Users mailing list archive at Nabble.com. From lefebvre at imnc.in2p3.fr Tue Oct 21 12:18:02 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Tue, 21 Oct 2014 18:18:02 +0200 Subject: [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt Message-ID: <5446873A.7070500@imnc.in2p3.fr> Hi, ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. I get the following link error : 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) I didn't get this error when compiling with itk4.3 . Any hint ? Thank you for your help, F. Lefebvre From blowekamp at mail.nih.gov Tue Oct 21 13:18:05 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 21 Oct 2014 13:18:05 -0400 Subject: [ITK-users] [ITK] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <5446873A.7070500@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> Message-ID: <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> Did you try the latest 4.6.1 release? Brad On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre wrote: > > Hi, > > ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. > > I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. > > I get the following link error : > > 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) > > I didn't get this error when compiling with itk4.3 . > > Any hint ? > > Thank you for your help, > > F. Lefebvre > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From marina.bendersky at gmail.com Tue Oct 21 18:05:00 2014 From: marina.bendersky at gmail.com (Marina Bendersky) Date: Tue, 21 Oct 2014 15:05:00 -0700 Subject: [ITK-users] Find corresponding slices in two different volumes Message-ID: Hi all, I need to find corresponding slices in 2 different volumes. I used the ImageRegistration20.cxx example to register "volumeSource" and "volumeTarget". My question is, then, to which slice in "volumeTarget" does ?slice 10? in "volumeSource" correspond? Is there an ITK example/hints that could guide me in the right direction? I?ve just started using ITK and would be grateful for any help. Thank you very much! Marina -------------- next part -------------- An HTML attachment was scrubbed... URL: From rsvpitt at gmail.com Tue Oct 21 18:06:54 2014 From: rsvpitt at gmail.com (Vikas) Date: Tue, 21 Oct 2014 18:06:54 -0400 Subject: [ITK-users] Problem applying landmarks in FEM registration Message-ID: Hi, I am having issues applying landmarks to FEM registration and would appreciate any help to resolve it. I am following the example in RegistrationITKv4/DeformableRegistration11 with the following modification: //Add landmartks RegistrationType::PointType SourceLandmark; RegistrationType::PointType TargetLandmark; SourceLandmark[0] = 23;SourceLandmark[1] = 12;SourceLandmark[2] = 41; TargetLandmark[0] = 26;TargetLandmark[1] = 16;TargetLandmark[2] = 45; registrationFilter->AddLandmark(SourceLandmark,TargetLandmark); registrationFilter->SetUseLandmarks(true); I get a run time error: "Vector subscript out of range". The call stack is as follows: > msvcp90d.dll!std::_Debug_message(const wchar_t * message=0x000000013fa48fc8, const wchar_t * file=0x000000013fa49010, unsigned int line=779) Line 24 C++ HybridRegistration.exe!std::vector >::operator[](unsigned __int64 _Pos=0) Line 780 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::ApplyLoads(itk::Size<3> ImgSz={...}, double * scaling=0x0000000000000000) Line 410 + 0x35 bytes C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::MultiResSolve() Line 1173 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::RunRegistration() Line 169 C++ HybridRegistration.exe!main(int argc=1, char * * argv=0x0000000002546b40) Line 225 C++ HybridRegistration.exe!__tmainCRTStartup() Line 586 + 0x19 bytes C HybridRegistration.exe!mainCRTStartup() Line 403 C Thanks Vikas -------------- next part -------------- An HTML attachment was scrubbed... URL: From lefebvre at imnc.in2p3.fr Wed Oct 22 03:23:48 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Wed, 22 Oct 2014 09:23:48 +0200 Subject: [ITK-users] [ITK] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> Message-ID: <54475B84.5020906@imnc.in2p3.fr> Yes I did. Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : > Did you try the latest 4.6.1 release? > > Brad > > On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre wrote: > >> Hi, >> >> ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. >> >> I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. >> >> I get the following link error : >> >> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >> >> I didn't get this error when compiling with itk4.3 . >> >> Any hint ? >> >> Thank you for your help, >> >> F. Lefebvre >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community -- Fran?oise LEFEBVRE IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) Campus d'Orsay - B?t 440 91405 ORSAY Cedex 01 69 15 51 87 From blowekamp at mail.nih.gov Wed Oct 22 09:44:15 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 22 Oct 2014 09:44:15 -0400 Subject: [ITK-users] Possible missing method in itkImageSource In-Reply-To: <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> References: <54413DE5.1050108@laposte.net> <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> Message-ID: <0023FC88-13F9-4ED2-9767-FB324A2EE0CB@mail.nih.gov> Hello, I'm going to take a look at this issue. Brad On Oct 17, 2014, at 5:01 PM, Jim Miller wrote: > At first glance it looks like an oversight. I would expect, however, that we should be seeing warnings about the named version of MakeOutput in ProcessObject being hidden. > > Jim > >> On Oct 17, 2014, at 12:03 PM, Jo?l Schaerer wrote: >> >> Hi all, >> >> I've run into a problem with named outputs, which I believe could be a bug in ITK. >> >> When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. >> . >> These methods are declared and defined first in itkProcessObject: >> >> .h: >> * ... >> * ProcessObject::MakeOutput. Note that MakeOutput always returns a >> * itkSmartPointer to a DataObject. ImageSource and MeshSource override >> * this method to create the correct type of image and mesh respectively. >> * If a filter has multiple outputs of different types, then that >> * filter must provide an implementation of MakeOutput(). */ >> virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); >> virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); >> >> .cxx >> DataObject::Pointer >> ProcessObject >> ::MakeOutput( const DataObjectIdentifierType & name ) >> { >> itkDebugMacro("MakeOutput(" << name << ")"); >> if( this->IsIndexedOutputName(name) ) >> { >> return this->MakeOutput( this->MakeIndexFromOutputName(name) ); >> } >> return static_cast(DataObject::New().GetPointer()); >> } >> >> DataObject::Pointer >> ProcessObject >> ::MakeOutput(DataObjectPointerArraySizeType) >> { >> return static_cast(DataObject::New().GetPointer()); >> } >> >> >> For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. >> >> template< typename TOutputImage > >> ProcessObject::DataObjectPointer >> ImageSource< TOutputImage > >> ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) >> { >> return TOutputImage::New().GetPointer(); >> } >> >> So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. >> >> Any reason for this behavior? Is this an oversight? >> >> Thanks, >> >> Jo?l >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From nikita at iitj.ac.in Wed Oct 22 18:33:23 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Wed, 22 Oct 2014 18:33:23 -0400 Subject: [ITK-users] Data Structure to save Vectors obtained from Demons Registration. Message-ID: Hello All I'm using itk:DemonsRegistrationFilter to apply registration on each successive frame that I obtain from Video .Please tell me how can I save the vector obtained from registration, what is the data structure I should use for saving the vector field. If it is saved automatically let me know how can I retrieve it . Also ,Please suggest me how to visualize these vectors as well. Thanks for the help in advance. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: From lasso at queensu.ca Wed Oct 22 18:56:44 2014 From: lasso at queensu.ca (Andras Lasso) Date: Wed, 22 Oct 2014 22:56:44 +0000 Subject: [ITK-users] [ITK] Data Structure to save Vectors obtained from Demons Registration. In-Reply-To: References: Message-ID: If you save the transform as a displacement field (in a nrrd or mha file) then you can load it into 3D Slicer as a transform and visualize it in 2D and 3D (as glyphs, deformed grid, or contour lines) overlaid with your images, segmentation results, landmarks, etc. See more info and some examples here: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms Andras ________________________________ From: Nikita Chopra Sent: ?2014-?10-?22 18:33 To: insight-users at itk.org Subject: [ITK] [ITK-users] Data Structure to save Vectors obtained from Demons Registration. Hello All I'm using itk:DemonsRegistrationFilter to apply registration on each successive frame that I obtain from Video .Please tell me how can I save the vector obtained from registration, what is the data structure I should use for saving the vector field. If it is saved automatically let me know how can I retrieve it . Also ,Please suggest me how to visualize these vectors as well. Thanks for the help in advance. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Oct 23 00:54:06 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 23 Oct 2014 00:54:06 -0400 Subject: [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cn4gsqfr90k9ssa0jogal8vobco On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/c2qo0onsh06h3adslvkcj66nr7k? For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From g.lemaitre58 at gmail.com Thu Oct 23 04:43:23 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Thu, 23 Oct 2014 10:43:23 +0200 Subject: [ITK-users] Issue installing SimpleITK via conda-recipe Message-ID: Hi all, First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== import: u'SimpleITK' Traceback (most recent call last): File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in import SimpleITK File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in from .SimpleITK import * File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in _SimpleITK = swig_import_helper() File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper _mod = imp.load_module('_SimpleITK', fp, pathname, description) ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference TESTS FAILED: simpleitk-0.8.0.post29-py27_0 I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. My system is: Ubuntu 14.04 Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 Cheers, -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: From rsvpitt at gmail.com Thu Oct 23 07:04:10 2014 From: rsvpitt at gmail.com (Vikas) Date: Thu, 23 Oct 2014 07:04:10 -0400 Subject: [ITK-users] Problem applying landmarks in FEM registration Message-ID: Hi, I am having issues applying landmarks to FEM registration and would appreciate any help to resolve it. I am following the example in RegistrationITKv4/DeformableRegistration11 with the following modification: //Add landmartks RegistrationType::PointType SourceLandmark; RegistrationType::PointType TargetLandmark; SourceLandmark[0] = 23;SourceLandmark[1] = 12;SourceLandmark[2] = 41; TargetLandmark[0] = 26;TargetLandmark[1] = 16;TargetLandmark[2] = 45; registrationFilter->AddLandmark(SourceLandmark,TargetLandmark); registrationFilter->SetUseLandmarks(true); I get a run time error: "Vector subscript out of range". The call stack is as follows: > msvcp90d.dll!std::_Debug_message(const wchar_t * message=0x000000013fa48fc8, const wchar_t * file=0x000000013fa49010, unsigned int line=779) Line 24 C++ HybridRegistration.exe!std::vector >::operator[](unsigned __int64 _Pos=0) Line 780 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::ApplyLoads(itk::Size<3> ImgSz={...}, double * scaling=0x0000000000000000) Line 410 + 0x35 bytes C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::MultiResSolve() Line 1173 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::RunRegistration() Line 169 C++ HybridRegistration.exe!main(int argc=1, char * * argv=0x0000000002546b40) Line 225 C++ HybridRegistration.exe!__tmainCRTStartup() Line 586 + 0x19 bytes C HybridRegistration.exe!mainCRTStartup() Line 403 C Thanks Vikas -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Oct 23 08:52:07 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 08:52:07 -0400 Subject: [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: Message-ID: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Hello, Can you please send me you CMakeCache.txt file from the build directory. The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. Brad [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: > Hi all, > > First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial > I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: > > ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== > import: u'SimpleITK' > Traceback (most recent call last): > File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in > import SimpleITK > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in > from .SimpleITK import * > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in > _SimpleITK = swig_import_helper() > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference > TESTS FAILED: simpleitk-0.8.0.post29-py27_0 > > I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. > > My system is: > Ubuntu 14.04 > Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > > Cheers, > > -- > LEMA?TRE Guillaume > PhD Candiate > MSc Erasmus Mundus ViBOT (Vision-roBOTic) > MSc Business Innovation and Technology Management > > g.lemaitre58 at gmail.com > > > ViCOROB - Computer Vision and Robotic Team > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > LE2I - Le Creusot > IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.lemaitre58 at gmail.com Thu Oct 23 09:00:13 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Thu, 23 Oct 2014 15:00:13 +0200 Subject: [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: Hi Brad, Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build In this file it seems that, ITK_USE_SYSTEM_TIFF:BOOL=ON Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. Thanks, On 23 October 2014 14:52, Bradley Lowekamp wrote: > Hello, > > Can you please send me you CMakeCache.txt file from the build directory. > > The simplest thing to do may be to remote using the anaconda "system" tiff > library and just use the one ITK has. This can be done by modifying the > conda recipe build script here [1]. > > Most likely there is some confusion which occurs during the CMake > configuration about which tiff library to use. > > Brad > > [1] > https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 > > On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre > wrote: > > Hi all, > > First, I am a newbie in Python and anaconda and sorry in advance if things > seems trivial > I tried to install SimpleITK through conda-recipe. The installation by > itself seems to be fined but the test is failling: > > ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== > import: u'SimpleITK' > Traceback (most recent call last): > File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line > 25, in > import SimpleITK > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", > line 1, in > from .SimpleITK import * > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", > line 28, in > _SimpleITK = swig_import_helper() > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", > line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: > /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: > symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file > libtiff.so.5 with link time reference > TESTS FAILED: simpleitk-0.8.0.post29-py27_0 > > I got that the issue is linked with the libtiff but I believed that > anaconda would manage the installation of the dependencies needed. > > My system is: > Ubuntu 14.04 > Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > > Cheers, > > -- > > > > > *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT > (Vision-roBOTic)MSc Business Innovation and Technology Management* > g.lemaitre58 at gmail.com > > > *ViCOROB - Computer Vision and Robotic Team* > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > > *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la > Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- # This is the CMakeCache file. # For build in directory: /home/lemaitre/anaconda/conda-bld/work/build # It was generated by CMake: /home/lemaitre/anaconda/envs/_build/bin/cmake # You can edit this file to change values found and used by cmake. # If you do not want to change any of the values, simply exit the editor. # If you do want to change a value, simply edit, save, and exit the editor. # The syntax for the file is as follows: # KEY:TYPE=VALUE # KEY is the name of a variable in the cache. # TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!. # VALUE is the current value for the KEY. ######################## # EXTERNAL cache entries ######################## //path to the bison executable BISON_EXECUTABLE:FILEPATH=/usr/bin/bison //Flags used by bison BISON_FLAGS:STRING= //Enable Building of the SimpleITK Examples as a separate project. BUILD_EXAMPLES:BOOL=ON //Build SimpleITK ITK with shared libraries. This does not effect // wrapped languages. BUILD_SHARED_LIBS:BOOL=OFF //Turn on Testing for SimpleITK BUILD_TESTING:BOOL=OFF //Path to a program. CMAKE_AR:FILEPATH=/usr/bin/ar //No help, variable specified on the command line. CMAKE_BUILD_TYPE:STRING=RELEASE //Enable/Disable color output during build. CMAKE_COLOR_MAKEFILE:BOOL=ON //CXX compiler. CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++ //No help, variable specified on the command line. CMAKE_CXX_FLAGS:STRING=-fvisibility=hidden -fvisibility-inlines-hidden //Flags used by the compiler during debug builds. CMAKE_CXX_FLAGS_DEBUG:STRING=-g //Flags used by the compiler during release builds for minimum // size. CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG //Flags used by the compiler during release builds. CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG //Flags used by the compiler during release builds with debug info. CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG //C compiler. CMAKE_C_COMPILER:FILEPATH=/usr/bin/cc //No help, variable specified on the command line. CMAKE_C_FLAGS:STRING=-fvisibility=hidden //Flags used by the compiler during debug builds. CMAKE_C_FLAGS_DEBUG:STRING=-g //Flags used by the compiler during release builds for minimum // size. CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG //Flags used by the compiler during release builds. CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG //Flags used by the compiler during release builds with debug info. CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG //Flags used by the linker. CMAKE_EXE_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Enable/Disable output of compile commands during generation. CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF //Where all the prerequisite libraries go CMAKE_INSTALL_PREFIX:PATH=/home/lemaitre/anaconda/conda-bld/work/build //No help, variable specified on the command line. CMAKE_INSTALL_PREFIX=:PATH=/home/lemaitre/anaconda/envs/_build //Path to a program. CMAKE_LINKER:FILEPATH=/usr/bin/ld //Path to a program. CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/make //Flags used by the linker during the creation of modules. CMAKE_MODULE_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Path to a program. CMAKE_NM:FILEPATH=/usr/bin/nm //Path to a program. CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy //Path to a program. CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump //No help, variable specified on the command line. CMAKE_OSX_DEPLOYMENT_TARGET:STRING= //Value Computed by CMake CMAKE_PROJECT_NAME:STATIC=SuperBuildSimpleITK //Path to a program. CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib //Flags used by the linker during the creation of dll's. CMAKE_SHARED_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING= //If set, runtime paths are not added when installing shared libraries, // but are added when building. CMAKE_SKIP_INSTALL_RPATH:BOOL=NO //If set, runtime paths are not added when using shared libraries. CMAKE_SKIP_RPATH:BOOL=NO //Flags used by the linker during the creation of static libraries. CMAKE_STATIC_LINKER_FLAGS:STRING= //Flags used by the linker during debug builds. CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Path to a program. CMAKE_STRIP:FILEPATH=/usr/bin/strip //If true, cmake will use relative paths in makefiles and projects. 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variable: RUBY_RUBY_LIB_DIR RUBY_RUBY_LIB_DIR-ADVANCED:INTERNAL=1 //ADVANCED property for variable: RUBY_SITEARCH_DIR RUBY_SITEARCH_DIR-ADVANCED:INTERNAL=1 //ADVANCED property for variable: RUBY_SITELIB_DIR RUBY_SITELIB_DIR-ADVANCED:INTERNAL=1 //ADVANCED property for variable: RUBY_VENDORARCH_DIR RUBY_VENDORARCH_DIR-ADVANCED:INTERNAL=1 //ADVANCED property for variable: RUBY_VENDORLIB_DIR RUBY_VENDORLIB_DIR-ADVANCED:INTERNAL=1 //ADVANCED property for variable: RUBY_VERSION_MAJOR RUBY_VERSION_MAJOR-ADVANCED:INTERNAL=1 //ADVANCED property for variable: RUBY_VERSION_MINOR RUBY_VERSION_MINOR-ADVANCED:INTERNAL=1 //ADVANCED property for variable: RUBY_VERSION_PATCH RUBY_VERSION_PATCH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: R_COMMAND R_COMMAND-ADVANCED:INTERNAL=1 //ADVANCED property for variable: R_INCLUDE_DIR R_INCLUDE_DIR-ADVANCED:INTERNAL=1 //ADVANCED property for variable: R_LIBRARY_BASE R_LIBRARY_BASE-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TCL_INCLUDE_PATH TCL_INCLUDE_PATH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TCL_LIBRARY TCL_LIBRARY-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TCL_TCLSH TCL_TCLSH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_INCLUDE_PATH TK_INCLUDE_PATH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_LIBRARY TK_LIBRARY-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_WISH TK_WISH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: USE_SYSTEM_ITK USE_SYSTEM_ITK-ADVANCED:INTERNAL=1 //ADVANCED property for variable: USE_SYSTEM_SWIG USE_SYSTEM_SWIG-ADVANCED:INTERNAL=1 From blowekamp at mail.nih.gov Thu Oct 23 09:21:31 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 09:21:31 -0400 Subject: [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: Hello, Yes, Changing the problematic USE_SYSTEM cmake options to OFF should fix this issue. Unfortunately, the variables I was looking for were not in that CMakeCache.txt file. They would be in the CMakeCache.txt file in the ITK-buiild subdirectory. Could you please e-mail that one off list? Thanks, Brad On Oct 23, 2014, at 9:00 AM, Guillaume Lema?tre wrote: > Hi Brad, > > Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build > In this file it seems that, > ITK_USE_SYSTEM_TIFF:BOOL=ON > > Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. > > Thanks, > > On 23 October 2014 14:52, Bradley Lowekamp wrote: > Hello, > > Can you please send me you CMakeCache.txt file from the build directory. > > The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. > > Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. > > Brad > > [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 > > On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: > >> Hi all, >> >> First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial >> I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: >> >> ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== >> import: u'SimpleITK' >> Traceback (most recent call last): >> File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in >> import SimpleITK >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in >> from .SimpleITK import * >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in >> _SimpleITK = swig_import_helper() >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >> ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference >> TESTS FAILED: simpleitk-0.8.0.post29-py27_0 >> >> I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. >> >> My system is: >> Ubuntu 14.04 >> Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) >> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 >> >> Cheers, >> >> -- >> LEMA?TRE Guillaume >> PhD Candiate >> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >> MSc Business Innovation and Technology Management >> >> g.lemaitre58 at gmail.com >> >> >> ViCOROB - Computer Vision and Robotic Team >> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >> http://vicorob.udg.es/ >> LE2I - Le Creusot >> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >> http://le2i.cnrs.fr >> >> https://sites.google.com/site/glemaitre58/ >> Vice - Chairman of A.S.C. Fours UFOLEP >> Chairman of A.S.C. Fours FFC >> Webmaster of http://ascfours.free.fr >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > > > > -- > LEMA?TRE Guillaume > PhD Candiate > MSc Erasmus Mundus ViBOT (Vision-roBOTic) > MSc Business Innovation and Technology Management > > g.lemaitre58 at gmail.com > > > ViCOROB - Computer Vision and Robotic Team > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > LE2I - Le Creusot > IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Oct 23 09:57:01 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 09:57:01 -0400 Subject: [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: <3CA52435-26B7-46DA-B0CD-3ADF369F23F6@mail.nih.gov> Hello, Thank you for sending me the file off list. I asked that just because of the potential size of the file. It's best to keep the conversation on the list so that all can benefit. It does appear that there is a problem with the SimpleITK using system libraries not picking up the anaconda dependencies but instead the system ones. For example here in the ITK CMakeCache.txt file we have: TIFF_INCLUDE_DIR:PATH=/usr/include/x86_64-linux-gnu TIFF_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libtiff.so PNG_PNG_INCLUDE_DIR:PATH=/usr/include and simular things for jpeg and zlib. I'd recommend turning them all off until a better solution is found. I have a pull request for this change here: https://github.com/conda/conda-recipes/pull/201 Thanks, Brad On Oct 23, 2014, at 9:21 AM, Bradley Lowekamp wrote: > Hello, > > Yes, Changing the problematic USE_SYSTEM cmake options to OFF should fix this issue. > > Unfortunately, the variables I was looking for were not in that CMakeCache.txt file. They would be in the CMakeCache.txt file in the ITK-buiild subdirectory. Could you please e-mail that one off list? > > Thanks, > Brad > > On Oct 23, 2014, at 9:00 AM, Guillaume Lema?tre wrote: > >> Hi Brad, >> >> Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build >> In this file it seems that, >> ITK_USE_SYSTEM_TIFF:BOOL=ON >> >> Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. >> >> Thanks, >> >> On 23 October 2014 14:52, Bradley Lowekamp wrote: >> Hello, >> >> Can you please send me you CMakeCache.txt file from the build directory. >> >> The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. >> >> Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. >> >> Brad >> >> [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 >> >> On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: >> >>> Hi all, >>> >>> First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial >>> I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: >>> >>> ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== >>> import: u'SimpleITK' >>> Traceback (most recent call last): >>> File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in >>> import SimpleITK >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in >>> from .SimpleITK import * >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in >>> _SimpleITK = swig_import_helper() >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >>> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >>> ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference >>> TESTS FAILED: simpleitk-0.8.0.post29-py27_0 >>> >>> I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. >>> >>> My system is: >>> Ubuntu 14.04 >>> Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) >>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 >>> >>> Cheers, >>> >>> -- >>> LEMA?TRE Guillaume >>> PhD Candiate >>> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >>> MSc Business Innovation and Technology Management >>> >>> g.lemaitre58 at gmail.com >>> >>> >>> ViCOROB - Computer Vision and Robotic Team >>> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >>> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >>> http://vicorob.udg.es/ >>> LE2I - Le Creusot >>> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >>> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >>> http://le2i.cnrs.fr >>> >>> https://sites.google.com/site/glemaitre58/ >>> Vice - Chairman of A.S.C. Fours UFOLEP >>> Chairman of A.S.C. Fours FFC >>> Webmaster of http://ascfours.free.fr >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> >> -- >> LEMA?TRE Guillaume >> PhD Candiate >> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >> MSc Business Innovation and Technology Management >> >> g.lemaitre58 at gmail.com >> >> >> ViCOROB - Computer Vision and Robotic Team >> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >> http://vicorob.udg.es/ >> LE2I - Le Creusot >> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >> http://le2i.cnrs.fr >> >> https://sites.google.com/site/glemaitre58/ >> Vice - Chairman of A.S.C. Fours UFOLEP >> Chairman of A.S.C. Fours FFC >> Webmaster of http://ascfours.free.fr >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From lefebvre at imnc.in2p3.fr Thu Oct 23 12:20:03 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Thu, 23 Oct 2014 18:20:03 +0200 Subject: [ITK-users] [ITK] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <54475B84.5020906@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> Message-ID: <54492AB3.2030006@imnc.in2p3.fr> Hi, I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same link error. FL Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : > Yes I did. > > Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >> Did you try the latest 4.6.1 release? >> >> Brad >> >> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >> wrote: >> >>> Hi, >>> >>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>> parameters and the Module_ITKReview on. >>> >>> I am now trying to compile a program developed in C++ using Qt5.1.1 >>> and Microsoft Visual C++ express 2010 on Windows 7. >>> >>> I get the following link error : >>> >>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe >>> non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction >>> "public: static class itksys::Encoding::CommandLineArguments __cdecl >>> itksys::Encoding::CommandLineArguments::Main(int,char const * const >>> *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>> >>> I didn't get this error when compiling with itk4.3 . >>> >>> Any hint ? >>> >>> Thank you for your help, >>> >>> F. Lefebvre >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Thu Oct 23 17:37:02 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 23 Oct 2014 17:37:02 -0400 Subject: [ITK-users] [ITK] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <54492AB3.2030006@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> Message-ID: Hi, Are you using CMake to configure your project? Matt On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre wrote: > Hi, > > I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same > link error. > > FL > > > Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : > >> Yes I did. >> >> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>> >>> Did you try the latest 4.6.1 release? >>> >>> Brad >>> >>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>> wrote: >>> >>>> Hi, >>>> >>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>> parameters and the Module_ITKReview on. >>>> >>>> I am now trying to compile a program developed in C++ using Qt5.1.1 and >>>> Microsoft Visual C++ express 2010 on Windows 7. >>>> >>>> I get the following link error : >>>> >>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" >>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>> >>>> I didn't get this error when compiling with itk4.3 . >>>> >>>> Any hint ? >>>> >>>> Thank you for your help, >>>> >>>> F. Lefebvre >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From lefebvre at imnc.in2p3.fr Fri Oct 24 04:00:59 2014 From: lefebvre at imnc.in2p3.fr (=?UTF-8?B?RnJhbsOnb2lzZSBMZWZlYnZyZQ==?=) Date: Fri, 24 Oct 2014 10:00:59 +0200 Subject: [ITK-users] [ITK] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> Message-ID: <544A073B.4080905@imnc.in2p3.fr> No, I'm not. I have always used a .pro file and qmake. Le 23/10/2014 23:37, Matt McCormick a ?crit : > Hi, > > Are you using CMake to configure your project? > > Matt > > On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre > wrote: >> Hi, >> >> I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same >> link error. >> >> FL >> >> >> Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : >> >>> Yes I did. >>> >>> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>>> Did you try the latest 4.6.1 release? >>>> >>>> Brad >>>> >>>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>>> parameters and the Module_ITKReview on. >>>>> >>>>> I am now trying to compile a program developed in C++ using Qt5.1.1 and >>>>> Microsoft Visual C++ express 2010 on Windows 7. >>>>> >>>>> I get the following link error : >>>>> >>>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" >>>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>>> >>>>> I didn't get this error when compiling with itk4.3 . >>>>> >>>>> Any hint ? >>>>> >>>>> Thank you for your help, >>>>> >>>>> F. Lefebvre >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users -- Fran?oise LEFEBVRE IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) Campus d'Orsay - B?t 440 91405 ORSAY Cedex 01 69 15 51 87 From abdul.sw84 at gmail.com Fri Oct 24 04:30:29 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 10:30:29 +0200 Subject: [ITK-users] ImageFileReader Update() Message-ID: Hello, I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. For instance: typedef itk::ImageFileReader ReaderType; ReaderType::Pointer imageReader = ReaderType::New(); imageReader->SetFileName( argv[1] ); * imageReader->Update();* Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Fri Oct 24 04:32:33 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 10:32:33 +0200 Subject: [ITK-users] Numeric traits Message-ID: Hello, I came across the following statement: PixelType label = itk::NumericTraits::One; It seems to be related to numric traits, which I have visited its documentation website, here , but, yet, didn't get the idea of the statement. Can you kindly just describe to me what the statement means? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Fri Oct 24 05:00:42 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:00:42 +0200 Subject: [ITK-users] ImageRegionIteratorWithIndex Message-ID: Hello, What is the purpose of ImageRegionIteratorWithIndex ? I didn't get the whole point from the documentation. Can you kindly just clarify it a bit? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Fri Oct 24 05:04:01 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:04:01 +0200 Subject: [ITK-users] ItI in itk Message-ID: Hello, I came across this code: itk::ImageRegionIteratorWithIndex *ItI*( imageReader->GetOutput(), imageReader->GetOutput()->GetLargestPossibleRegion() ); What does "ItI" mean? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Fri Oct 24 05:11:02 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:11:02 +0200 Subject: [ITK-users] Shouldn't they be swapped? Message-ID: Hello, I came across the following code: PixelType maxValue = itk::NumericTraits::NonpositiveMin(); PixelType minValue = itk::NumericTraits::max(); Shouldn't the above statements be swapped? That is, minValue for the first, and ,maxValue for the second? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Fri Oct 24 05:16:40 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 24 Oct 2014 11:16:40 +0200 Subject: [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: Hi Abdul, A good starting point is the software guide: http://www.itk.org/ItkSoftwareGuide.pdf Best Arnaud On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > Hello, > > I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. > > For instance: > > typedef itk::ImageFileReader ReaderType; > ReaderType::Pointer imageReader = ReaderType::New(); > imageReader->SetFileName( argv[1] ); > imageReader->Update(); > > Thanks. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Fri Oct 24 05:54:53 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:54:53 +0200 Subject: [ITK-users] Pointers and New() Message-ID: Hello, I noticed that when we want to use "New()" in itk with some type, we use "Pointer" with that type. Like for instance: SomeType::Pointer st = SomeType::New(); In "itk", is this always the case? Is it because in order to access the "functions" with a a type in itk, this can only be done through pointers? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Fri Oct 24 06:10:45 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 12:10:45 +0200 Subject: [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: Hi Arnaud, Thanks for your kind reply. That is very helpful. I got the following from the guide regarding "Update()": *The pipeline update mechanism ensures that the reader only executes when a data request is made to the reader and the reader has not read any data.* But, it is yet not very clear. Can you kindly describe it a bit? Thanks. On Fri, Oct 24, 2014 at 11:16 AM, Arnaud Gelas wrote: > Hi Abdul, > > A good starting point is the software guide: > > http://www.itk.org/ItkSoftwareGuide.pdf > > Best > Arnaud > > On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > > Hello, > > I'm new to ITK, and just want to ask about what "Update()" means when used > with ImageFileReader. > > For instance: > > typedef itk::ImageFileReader ReaderType; > ReaderType::Pointer imageReader = ReaderType::New(); > imageReader->SetFileName( argv[1] ); > * imageReader->Update();* > > Thanks. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Fri Oct 24 07:03:46 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 24 Oct 2014 13:03:46 +0200 Subject: [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: <8261ECB7-BEFC-4841-9A95-E9F3BD9C612F@gmail.com> please read section 3.5 Data Processing Pipeline On Oct 24, 2014, at 12:10 PM, Abdul Abdul wrote: > Hi Arnaud, > > Thanks for your kind reply. That is very helpful. I got the following from the guide regarding "Update()": > > The pipeline update mechanism ensures that the reader only executes when a data request is made to the reader and the reader has not read any data. > > But, it is yet not very clear. > > Can you kindly describe it a bit? > > Thanks. > > On Fri, Oct 24, 2014 at 11:16 AM, Arnaud Gelas wrote: > Hi Abdul, > > A good starting point is the software guide: > > http://www.itk.org/ItkSoftwareGuide.pdf > > Best > Arnaud > > On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > >> Hello, >> >> I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. >> >> For instance: >> >> typedef itk::ImageFileReader ReaderType; >> ReaderType::Pointer imageReader = ReaderType::New(); >> imageReader->SetFileName( argv[1] ); >> imageReader->Update(); >> >> Thanks. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From millerjv at gmail.com Fri Oct 24 07:31:24 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:31:24 -0400 Subject: [ITK-users] Numeric traits In-Reply-To: References: Message-ID: This statement assigns the value of 1 to variable "label". The value of NumericTraits::One is specific to the datatype PixelType. For instance, For an integer type, NumericTraits::One will be 1. For a floating point type, it will be 1.0. Techniques like this are used in Generic Programming to initialize or assign a variable a value of the appropriate type (and avoid compiler warnings and performance associated with casting between types). On Fri, Oct 24, 2014 at 4:32 AM, Abdul Abdul wrote: > Hello, > > I came across the following statement: > > PixelType label = itk::NumericTraits::One; > > It seems to be related to numric traits, which I have visited its > documentation website, here > , but, > yet, didn't get the idea of the statement. > > Can you kindly just describe to me what the statement means? > > Thanks. > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From millerjv at gmail.com Fri Oct 24 07:33:26 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:33:26 -0400 Subject: [ITK-users] ImageRegionIteratorWithIndex In-Reply-To: References: Message-ID: Image Iterators allow you to visit every pixel in an image (or image region) with a prescribed pattern of access. We use Image Iterators to write generic code that can operate on 1D, 2D, 3D, and 4D images without requiring the algorithm code to understand the dimension of the image. The WithIndex variants of the Image Iterators are optimized to be able to report the pixel position (Index) of the iterator. On Fri, Oct 24, 2014 at 5:00 AM, Abdul Abdul wrote: > Hello, > > What is the purpose of ImageRegionIteratorWithIndex > ? > I didn't get the whole point from the documentation. Can you kindly just > clarify it a bit? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From millerjv at gmail.com Fri Oct 24 07:34:54 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:34:54 -0400 Subject: [ITK-users] ItI in itk In-Reply-To: References: Message-ID: Itl is this case is a variable of type ImageRegionIteratorWithIndex. Its constructor is being called with the output of the ImageReader and the iterator will walk the LargestPossibleRegion of the ImageReader's output. On Fri, Oct 24, 2014 at 5:04 AM, Abdul Abdul wrote: > Hello, > > I came across this code: > > itk::ImageRegionIteratorWithIndex *ItI*( > imageReader->GetOutput(), > imageReader->GetOutput()->GetLargestPossibleRegion() ); > > What does "ItI" mean? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From millerjv at gmail.com Fri Oct 24 07:36:52 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:36:52 -0400 Subject: [ITK-users] Shouldn't they be swapped? In-Reply-To: References: Message-ID: Most likely you are looking at code that is just before a loop that is searching to find the min and max values within an image. It is common practice to initialize the current values of min and max in this manner so that you can write code like if (value > maxValue) { value = maxValue; } On Fri, Oct 24, 2014 at 5:11 AM, Abdul Abdul wrote: > Hello, > > I came across the following code: > > PixelType maxValue = itk::NumericTraits::NonpositiveMin(); > PixelType minValue = itk::NumericTraits::max(); > > Shouldn't the above statements be swapped? That is, minValue for the > first, and ,maxValue for the second? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From anton.delehony at gmail.com Fri Oct 24 09:56:56 2014 From: anton.delehony at gmail.com (Anton Delehony) Date: Fri, 24 Oct 2014 09:56:56 -0400 Subject: [ITK-users] Liver lobes atlas Message-ID: Hi All, I'm looking for a liver atlas that I can use to segment the different lobes of the liver from MR images. Does something like this exist? Anton -------------- next part -------------- An HTML attachment was scrubbed... URL: From norman-k-williams at uiowa.edu Fri Oct 24 10:06:41 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 24 Oct 2014 14:06:41 +0000 Subject: [ITK-users] ImageRegionIteratorWithIndex In-Reply-To: References: Message-ID: Normally, to visit every pixel in an Image, you?d use an ImageRegionIterator, or ImageRegionConstIterator. The latter you?d use when you don?t want to or cannot modify the image. ImageRegionIteratorWithIndex (and ImageRegionConstIteratorWithIndex) are, as Jim Miller said, optimized for reporting the index of the voxel currently referenced by the iterator. A very common use would be to iterate through an image, but use the index to access another image?s voxels as well. Generally, you?d use an iterator for each image but there are cases ? like when you only occasionally use the index to access another image ? where it makes sense not to bother with the second iterator. From: Abdul Abdul > Date: Friday, October 24, 2014 at 4:00 AM To: Insight > Subject: [ITK-users] ImageRegionIteratorWithIndex Hello, What is the purpose of ImageRegionIteratorWithIndex? I didn't get the whole point from the documentation. Can you kindly just clarify it a bit? Thanks. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From sami.koho at gmail.com Fri Oct 24 10:36:01 2014 From: sami.koho at gmail.com (Sami Koho) Date: Fri, 24 Oct 2014 17:36:01 +0300 Subject: [ITK-users] Example medical images for teaching Image Segmentation Message-ID: Hello, This is not directly related to ITK, but I will ask anyway, out of curiosity. This fall I have been teaching Digital Image Processing to Biomedical imaging students. The next subject will be Image Segmentation (Edge detection models, / thresholding). Would any of you have some favorite medical images to demonstrate these subjects? I can of course use any pictures, but having examples relevant to the students would be nice. I have my own libraries as well, but they are mostly of cells and their internals (microscopy lab). Feel free to send any links/files, if something comes to mind. Best, Sami -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Oct 24 10:56:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 10:56:17 -0400 Subject: [ITK-users] Pointers and New() In-Reply-To: References: Message-ID: Hi Abdul, Welcome to ITK! Yes, we always want to use ::New(), which returns ITK SmartPointer's [1] since this is used by the reference count kept in all ITK Object's [2]. This is described in more detail in the ITK Software Guide [3]. Hope this helps, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1SmartPointer.html [2] http://www.itk.org/Doxygen/html/classitk_1_1Object.html [3] http://itk.org/ItkSoftwareGuide.pdf On Fri, Oct 24, 2014 at 5:54 AM, Abdul Abdul wrote: > Hello, > > I noticed that when we want to use "New()" in itk with some type, we use > "Pointer" with that type. Like for instance: > > SomeType::Pointer st = SomeType::New(); > > In "itk", is this always the case? Is it because in order to access the > "functions" with a a type in itk, this can only be done through pointers? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From matt.mccormick at kitware.com Fri Oct 24 10:57:29 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 10:57:29 -0400 Subject: [ITK-users] [ITK] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <544A073B.4080905@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> <544A073B.4080905@imnc.in2p3.fr> Message-ID: Hi Fran?oise, CMake is recommended -- it will avoid this problem and others. It works well with Qt. Thanks, Matt On Fri, Oct 24, 2014 at 4:00 AM, Fran?oise Lefebvre wrote: > > No, I'm not. I have always used a .pro file and qmake. > > Le 23/10/2014 23:37, Matt McCormick a ?crit : > >> Hi, >> >> Are you using CMake to configure your project? >> >> Matt >> >> On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre >> wrote: >>> >>> Hi, >>> >>> I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the >>> same >>> link error. >>> >>> FL >>> >>> >>> Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : >>> >>>> Yes I did. >>>> >>>> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>>>> >>>>> Did you try the latest 4.6.1 release? >>>>> >>>>> Brad >>>>> >>>>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>>>> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>>>> parameters and the Module_ITKReview on. >>>>>> >>>>>> I am now trying to compile a program developed in C++ using Qt5.1.1 >>>>>> and >>>>>> Microsoft Visual C++ express 2010 on Windows 7. >>>>>> >>>>>> I get the following link error : >>>>>> >>>>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const >>>>>> *)" >>>>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>>>> >>>>>> I didn't get this error when compiling with itk4.3 . >>>>>> >>>>>> Any hint ? >>>>>> >>>>>> Thank you for your help, >>>>>> >>>>>> F. Lefebvre >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> _______________________________________________ >>>>>> Community mailing list >>>>>> Community at itk.org >>>>>> http://public.kitware.com/mailman/listinfo/community >>>> >>>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users > > > -- > Fran?oise LEFEBVRE > IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) > Campus d'Orsay - B?t 440 > 91405 ORSAY Cedex > 01 69 15 51 87 > From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: "selector" for each filter may not be most desirable solution. A different approach could be to provide a mechanism for assembling parametric pipeline fragments, say using a parametric StaticPipelineChunk<> class and then generating a "selector" for each such chunk. A StaticPipelineChunk correspons to pipeline fragments where image type could not randomly change. As before, the selector would handle instantiating StaticPipelineChunk with proper data representation types at runtime. This could be a solution simpler to implement and maintain but may be more difficult to handle on the user side. In general, there should always be a possibility of directly using parametric filter. With same care parametric and non parametric code could be mixed. There may be a need to modify existing parametric filters and the pipeline in general. For instance, many filters take output image type as a parameter. In non-parametric pipeline, as in example above, the output image type is decided by the filter based on the input image type and type of processing. Another example, efficient streaming support may require addition of messages that would indicate beginning (before first piece is in) and end of streaming (after last piece is out) to prevent unneeded re-instantiations of template-filters. Just some thoughts, hope that you will find them helpful. I wonder what you were thinking about. Jarek __________________________________________________ Do You Yahoo!? Yahoo! - Official partner of 2002 FIFA World Cup http://fifaworldcup.yahoo.com From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: by A->SetInput( B->GetOutput() ) calls, and the invoke "Update()" in the last filter of the pipeline. Please let us know if you have further questions, Thanks Luis ================================= zhao wrote: > Hi Luis, > > By reading the source code of WaterShedSegmentation example, I got a taste of the pipeline architecture used in ITK. In this example, there are three filters (except for image read and write filters): Anisotropic Diffusion Filter, Gradient Magnitude Filter, and Watershed Segmentation Filter. I know the output of one filter is the input of it's subsequent filter, and thus a processing pipeline is constructed. It seems that it's the Write() member function of ImageFileWriter object that triggers the whole processing procedure. Now, I got two question to ask: > > (1) How does the later Filter trigger the former Filter's execution? ( e.g. Watershed trigers Gradient, and Gradient triggers Diffusion ). > (2) How does a Process Object (i.e. a filter) begin it's own processing? (e.g. I think the processing subroutine of GradientMagnitudeImageFilter should be ThreadedGenerateData, but I can't find explicitly where GradientMagnitudeImageFilter evoke it. ) > > Maybe it's too complex to give a clear explanation. Any reply will be appreciated. Thanks in advance!! > > Zhao > > > Zhao ChenGuang > P.O.Box:010, > Dept. BME > Shanghai Jiao Tong University, > 1954# Hua Shan Road, > Shanghai,P.R.China, > 200030 > > > _______________________________________________ > Insight-users mailing list > Insight-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users > > From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: segmentations to subdivide the image until each voronoi region was "homogenous", using the classical definition of homogeneous from other split and merge segmentation techniques. So what I expected to see was a partitioning of the entire image where each voronoi region was "well" approximated as constant intensity (with extensions to piecewise linear and piecewise quadratic intensity surfaces). Instead, the algorithm labels each voronoi region as either "interior", "exterior", or "boundary" and subdivides the "boundary" voronoi regions down to a specified resolution. The definition of "interior" is not a homogeneity measure but rather a "compatibility" measure with a seed region (where the sample mean and sample variance of the voronoi region agree with the estimates from the seed region using an ad-hoc criterion). I am going to try to subclass the VoronoiSegmentationImageFilterBase class and construct an algorithm to produce the partitioning or oversegmentation of the scene that I am interested in. I think I can reuse the voronoi engine and use my own TestHomogeneity() method and use a virtual function to replace the "interior", "exterior", "boundary" designations that only allow the boundary regions to be subdivided with code that will subdivide any region that is not homogeneous enough. This will give us two types of voronoi segmentation algorithms, one that roughly segments a region that intensity value "consistent" or "compatible" with a seed region and one that partitions the image into homogeneous regions. I am thinking of calling the new filter VoronoiPartitioningImageFilter. Jim > -----Original Message----- > From: Celina Imielinska [mailto:ci42 at columbia.edu] > Sent: Monday, October 21, 2002 6:19 PM > To: Yinpeng Jin > Cc: Seungbum Koo; insight-users at public.kitware.com > Subject: Re: Re: [Insight-users] using > itkVoronoiSegmentationImageFilter > ? > > > > Seungbum, > > as Yinpeng said, the Voronoi Diagram classifier segments > globally all the > tissue in the image that is characterized by the homogeneity operator > (derived from the fuzzy connectendness method). If you are > interested in > picking one connected component from all the segmented > regions, you may > use the DeformableMeshFilter (DM) to do the selection (and > smoothing/improvement of the final segmentation as well). > > You can't use the DeformableMeshFilter without a prior, > since this is a > boundary-based segmentation method that has to be initialized near the > solution. For example, you can use as a prior the Markov Random Field > (MRF)/Gibbs Prior, the itkGibbsPriorFilter (or > itkRGBGibbsPriorFilter), > and follow with DM, then repeat iteratively MRF and DM, and > so on. There is > a new version of the DM method that can be explained, in > details, by Ting > Chen (chenting at graphics.cis.upenn.edu). > > You may try also, a stand-alone, vectorial relative fuzzy > connectedness > method, the VectorFuzzyconnectednessImageFilter, to segment a region. > > The "Hybrid Segmentation Engine" consists of four > components: Deformable > Model (DM), Gibbs Prior/Markov Random Field (MRF), Voroni Diagram > Clssifier (VD), and Fuzzy Connectedness (FC). We have explored some > hybrid "mixtures" derived from the engine: e.g. FC/VD/DM, MRF/DM, > vectorial relatice FC... but other combinations could be > tested as well. > > Please let us know if need more detailed explanation. > > good luck, > > Celina Imielinska > > On Mon, 21 Oct 2002, Yinpeng Jin wrote: > > > VoronoiSegmenationImageFilter is a region-based classification, > > split-and-merge like algorithm. > > you are perfectly right, it picks up all the similar color > regions in whole > > image. It works well if you have multiple objects in the image to > > segment, it was used because SimpleFuzzyConnectedness can > only pick up > > one connected component. > > there is another version of FuzzyConnectedness, which is > able to claim > > multiple objects (VectoriorFuzzyConnectedness) > > And to use Deformable Models is definitedly a good idea, > actually, all > > those three methods had been tested for combining together > to build a > > hybrid segmentation framework. > > I bet Celina, Jay and Dimitris can explain the idea > > better, for your reference, please look at following paper > in MICCAI 2001: > > C. Imielinska, D. Metaxas, J. Udupa, Y.Jin and T. Chen, "Hybrid > > Segmentation Methods of Anatomical Data." Proceedings of The Fourth > > International Conference on Medical Image Computing and Computer > > Assisted Interventions (MICCAI 2001), pp. 1058-1066, > October 2001, Utrecht > > Netherlands. > > > > > > ----- Original Message ----- > > From: Seungbum Koo > > To: Yinpeng Jin > > Cc: insight-users at public.kitware.com > > Sent: Monday, October 21, 2002 4:51 PM > > Subject: Re: Re: [Insight-users] using > itkVoronoiSegmentationImageFilter ? > > > > > > Hi, > > Thanks for the help. It worked and segmented but not as I > expected. I don't understand well about > VoronoiSegmentationImageFilter but it seems to segment all > similar color regions in whole image as the seed region. I > just wanted to find more exact boundary of that found using > FuzzyConnectednessScalarFilter. > > Anyway I think the VoronoiSegmentationImageFilter worked > fine. What do you think about using DeformableMeshFilter > instead of VoronoiSegmentationImageFilter? > > > > regards > > Seungbum Koo > > > > > Title : Re: [Insight-users] using > itkVoronoiSegmentationImageFilter ? > > > Date : Sun, 20 Oct 2002 13:34:32 -0400 > > > From : "Yinpeng Jin" > > > To : Seungbum Koo, > > > > > > if you use takeaprior, then you don't want to setMean > and setVar, those two parameters will be calculated from the > binary mask. > > > and > > > try to use > > > m_voronoiFilter->SetMeanPercentError(PERCENT); > > > m_voronoiFilter->SetVarPercentError(VARPERCENT); > > > in stead of > > > m_voronoiFilter->SetMeanTolerance(10); > > > m_voronoiFilter->SetVarTolerance(20); > > > > > > they are trying to manipulate the same parameter, but > usually are more intuitive to figure. > > > the MeanPercentError could usually be set between 0.1 to 0.3 > > > and the VarPercentError could be between 1 to 3. they > don't depends on your pixel intensity range, while the > MeanTolerance and VarTolerance usually do. > > > Also, you can first output your m_binaryImage to see if > it is something reasonable. the > VoronoisegmentationImagefilter will need something at least represents > > > parts of your target object as the a prior. > > > Try the above, and let me know what happens. > > > Yinpeng. > > > > > > > > > > > > ----- Original Message ----- > > > From: Seungbum Koo > > > To: insight-users at public.kitware.com > > > Sent: Sunday, October 20, 2002 12:45 AM > > > Subject: [Insight-users] using > itkVoronoiSegmentationImageFilter ? > > > > > > > > > Hi, > > > > > > I'm trying to use itkVoronoiSegmentationImageFilter > combined with itkSimpleFuzzyConnectednessScalarImageFilter. > > > > > > I made a binary image from > itkSimpleFuzzyConnectednessScalarImageFilter but I couldn't > figure out how to set itkVoronoiSegmentationImageFilter > variables. Here is my source code. > > > > > > ============================================================= > > > m_voronoiFilter->SetInput(m_rawImageSource->GetOutput()); > > > m_voronoiFilter->TakeAPrior(m_binaryImage); > > > m_voronoiFilter->SetMean(520); > > > m_voronoiFilter->SetVar(20); > > > m_voronoiFilter->SetMeanTolerance(10); > > > m_voronoiFilter->SetVarTolerance(20); > > > // m_voronoiFilter->SetNumberOfSeeds(400); // ?? > > > m_voronoiFilter->SetSteps(5); > > > m_voronoiFilter->Update(); > > > ============================================================= > > > > > > m_binaryImage is calculated from m_rawImageSource and > as I expected. > > > But this code just makes a black image... all zeros. > > > > > Seungbum Koo > > > > > > > > > > > > "?i,(r) AIAI3Y, Daum" http://www.daum.net !o AEo>y3/42?A > 1<*a CN,?AI3Y !> > > > > ou,??U! AEiCI?U! Daum,?1/2AAu > > ,AAI,AAI 3/42?i ?e1/2AAO? Daum??AIA > DaumE,?oAC CE1/4oC?! ?A?ACA AO?iAC CyAA~ > > > > > > > > _______________________________________________ > Insight-users mailing list > Insight-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users > From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: Is there an optimal combination of registration parameters for the satellite images (optimizer, transform, interpolator and metric) or does the combination depend on the individual images? My code is heavily based on the Image Registration example (filtered out all of the FLTK from it) in the Examples directory and I used some of the tricks I learned from the examples in the Algorithms Tests directory. Thanks, Nino From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: a range of physical file formats - raw image, meta image, dicom image etc. This is very elegant. Now in principle this means that any itk application that accesses an image can auto-detect the format of the specified file and automatically use the appropriate class to read it. The application just uses a pointer to the base class of course. To do this requires static functions that can figure out what format a file is in (of course for raw image this would not work as you still need the dimensionality) and this is not always a totally trivial exercise. This all then gets packaged up so the application programmer just calls one function and get back a pointer which has created the correct derived class object. So there are three basic models for accessing images . Transparent native access to all supported file formats for all applications . There is a native itk format, and foreign formats are filled or converted to this format in an extra step. All applications then operate on the native format. . Each application reads a specific format only which has to be documented. So my question is, what model does itk follow (or perhaps another ?) ? The reason i ask really is that i downloaded some BrainWeb data (meta image and raw image) and tried a couple of the example programs on it. They failed with a variety of i/o errors or segmentation failures (urk). Really, all i want to be able to do to start with is read an image and print out some numbers or display it (but i haven't got vtk to build yet...) to make sure things are working. The test programs ran ok, and the example program MetaImageReadWrite happily did its thing. A second question is, if there is a native itk image storage format, is it tiled for efficiency ? thanks Neil From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: way, regardless of cells etc. See PointSet::SetPoint() and PointSet::SetPoints(). All that happens there is PointSet calling Modified(). The first adapter calls Modified() when it's destroyed, and thus guarantees that afterwards all the necessary notifications were sent. Still, you can modify the non-const vector that you obtained from the Adapter and try to access the cells without the PointSet::Modified(). That is not so wise, bu it's possible. However, as long as you separate vector modification from accessing the cells by at least a {block}, Modified() wil be called automatically. As for the const reference, it's possible to follow your direction. I added the STLConstVectorAdapter for consistency with the STLVectorAdapter. But it's possible, and maybe simpler, to do without. Luis Ibanez wrote: > Hi Ofri, > > The code of the STL adpator looks good. > > It seems however that we could take better advantage > of the natural derivation of the VectorContainer from > the std::vector. > > In principle a simple casting to > > const std::vector & > > could provide the same functionality. > > Something like adding the following to the > VectorContainer class: > > typedef std::vector< TElement > STLContainerType; > > const STLContainerType & GetSTLContainer() const { > return static_cast( *this ); > } > > With this lines you can now do: > > typedef itk::VectorContainer< > unsigned int, > double > VectorContainerType; > > VectorContainerType::Pointer vector = VectorContainerType::New(); > > const std::vector & vectorref = vector->GetSTLContainer(); > > and now use the "vectorref" as to access the content > of the itk::VectorContainer. > > Note that only the "const" access is allowed here. The reason > is that the itk container should maintain the association between > identifiers and elements. This is quite important in the Mesh > class for example since the identifiers to points are supplied > to the cells. Allowing access to the std::vector under the > PointsContainer could facilitate the removal or insertion of a > point and this will corrupt all the identifiers stored in the > Mesh cells. > > Do you see use cases in the proposed adaptor that > may not be covered by the casting above ? > > Thanks > > Luis > > ================================================================== > > Ofri Sadowsky wrote: > > > I added the following code in the public section of my copy of itkVectorContainer.h > > > > <<< BEGIN >>> > > /* forward declaration */ > > class STLVectorAdapter; > > class STLConstVectorAdapter; > > > > /** \class STLVectorAdapter > > * An adapter object that casts a VectorContainer into std::vector > > * and enables access to the underlying data structure. When the STLVectorAdapter > > * is destroyed, it automatically calls VectorContainer::Modified(). > > * Here's a usage example of STLVectorAdapter > > * VectorContainer::STLVectorAdapter vecAdapter = > > aContainer.GetStlVectorAdapter(); > > * std::vector & vec = vecAdapter.GetStlVectorRef(); > > * // do things with vec ... > > * // upon return from function, vecAdapter is destroyed and aContainer is > > Modified() > > */ > > class STLVectorAdapter > > { > > public: > > VectorType & GetStlVectorRef() > > { > > return (VectorType &)m_VectorRef; > > } > > > > ~STLVectorAdapter() > > { > > m_VectorRef.Modified(); > > } > > > > /** public copy ctor to enable > > * VectorContainer::STLVectorAdapter vecAdapter = > > aContainer.GetStlVectorAdapter(); > > */ > > STLVectorAdapter(const STLVectorAdapter & r) > > : m_VectorRef(r.m_VectorRef) {} > > private: > > VectorContainer & m_VectorRef; > > friend class VectorContainer; > > friend class STLConstVectorAdapter; > > > > /* hide ctor */ > > STLVectorAdapter(VectorContainer & vc) > > : m_VectorRef(vc) {} > > > > /* hide and avoid operator= */ > > const STLVectorAdapter & operator=(const STLVectorAdapter & r); > > }; > > > > > > /** Create a STLVectorAdapter that adapts this object to std::vector > > */ > > STLVectorAdapter GetStlVectorAdapter() > > { > > return STLVectorAdapter(*this); > > } > > > > /** \class STLConstVectorAdapter > > * An adapter object that casts a VectorContainer into const std::vector > > * and enables access to the underlying data structure. STLConstVectorAdapter > > * does not call VectorContainer::Modified(), because it is cast to const. > > * Here's a usage example of STLConstVectorAdapter > > * VectorContainer::STLConstVectorAdapter vecAdapter = > > * aContainer.GetConstStlVectorAdapter(); > > * const std::vector & vec = vecAdapter.GetStlConstVectorRef(); > > * // do things with vec ... but it can't be modified. > > */ > > class STLConstVectorAdapter > > { > > public: > > const VectorType & GetStlConstVectorRef() const > > { > > return (const VectorType &)m_VectorRef; > > } > > > > /* no need to declare dtor, as the Adapter is const */ > > > > /* public copy ctor. See StlVectorAdapter */ > > STLConstVectorAdapter(const STLConstVectorAdapter & r) > > : m_ConstVectorRef(r.m_ConstVectorRef) {} > > > > /* "copy" ctor from the non-const STLVectorAdapter */ > > STLConstVectorAdapter(const STLVectorAdapter & r) > > : m_ConstVectorRef(r.m_VectorRef) {} > > > > private: > > const VectorContainer & m_ConstVectorRef; > > friend class VectorContainer; > > > > /* hide main ctor */ > > STLConstVectorAdapter(const VectorContainer & vc) > > : m_ConstVectorRef(vc) {} > > > > /* hide and avoid operator= */ > > const STLConstVectorAdapter & operator=(const STLConstVectorAdapter & r); > > }; > > > > STLConstVectorAdapter GetStlConstVectorAdapter() const > > { > > return STLConstVectorAdapter(*this); > > } > > > > <<< END >>> > > From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: > I am working on MRI Registration.I have made my own project using MRI > Registration example available in ITK examples.It is working well for > some MRI images.But,It is throwing exception at StartRegistration() for > some imagess.I have hard coded the Parameters which I have to set > before calling StartRegistration().Plese, help me in solving my > problem and give me some information on setting parameter values. Here > I am enclosing the code and parameters details.I am also enclosing the > exception message thrown by startregistration(). > > //Exception message > itk::ERROR: MutualInformationImageToImageMetric(003C6D20): All the > sampled point mapped to outside of the moving image Now, I have exactly the same error as you had that time. And your code looks very similar to my code. Did you find a solution to this problem? Or, do you know why you had this error? Hope you can help me, Thanks and Regards, Jorn. From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: code leaves its scope and then so does the output image data. How can I get around that without copying the data from the itk image into another chunk of memory (which is a waste of time and memory)? Thanks david __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: It means that whenever I upgrade ITK, those Auxilliary classes may well change in the ITK distribution and I will have to remember to copy them somewhere. To do this properly, I suppose they should be distributed separately in a separate 'Auxilliary' package, with its own CMakeLists.txt file, but I am sure that is not very high on the project's priorities. More interestingly, the following is probably a bug... What I did was rebuild ITK telling it use the INSTALLED VTK but not to build any examples or tests. Now, when I came to build my application, the build command was % g++-3.1.1 -Wno-deprecated -I/nfs/mid/NKILLEEN/medim/source/code/apps/metaView -I/usr/local/include/InsightToolkit -I/usr/local/include/InsightToolkit/Numerics/vxl -I/usr/local/include/InsightToolkit/Numerics/vxl/vcl -I/usr/local/include/InsightToolkit/Algorithms -I/usr/local/include/InsightToolkit/BasicFilters -I/usr/local/include/InsightToolkit/Common -I/usr/local/include/InsightToolkit/IO -I/usr/local/include/InsightToolkit/Numerics/FEM -I/usr/local/include/InsightToolkit/Numerics -I/usr/local/include/InsightToolkit/Numerics/Statistics -I/usr/local/include/InsightToolkit/SpatialObject -I/usr/local/include/InsightToolkit/Utilities/GlutMaster -I/usr/local/include/InsightToolkit/Utilities/MetaIO -I/usr/local/include/InsightToolkit/Utilities/png -I/usr/local/include/InsightToolkit/Utilities/zlib -I/usr/local/include/InsightToolkit/Auxiliary/FltkImageViewer -I/usr/local/include/InsightToolkit/Auxiliary/VtkFltk -I/usr/local/include/InsightToolkit/Auxiliary/vtk -I/usr/local/include/vtk -I/usr/openwin/include -c /nfs/mid/NKILLEEN/medim/source/code/apps/metaView/MetaImageViewer.cxx -o MetaImageViewer.o you can see that it has specified the include directory -I/usr/local/include/InsightToolkit/Auxiliary/vtk amongst others. The way I have specified the INCLUDE directories in my CMakeLists.txt file is just via INCLUDE_DIRECTORIES(${ITK_INCLUDE_DIRS}) so the ITK configuration process has itself thought that these Auxilliary files should land up in the ITK install tree. So I suggest that a) The README in the Auxilliary directory describes how you intend these files should be used (the present one does not) b) the above problem should be attended to, because in the absence of a) it makes you think the Auxilliary files should have been installed in the tree ! cheers Neil From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: platforms. Just add SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") and it will always add the debugging flags to the generated makefiles. This is not recommended, though. -Brad From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: the info of my vtkImageData object and interface with itk::VTKImageImport. This would allow me to interface itk with the vtk pipeline. However, the documentation does not seem to be suffcient for me to get it to work. I do not know what member functions to use and what pointer to pass as arguments. I was therefore wondering if someone could draft a C++ code snippet as an example how to use vtkImageExport with itk::VTKImageImport and itk::VTKImageExport with vtkImageImport. Thanks a lot in advance !! Christof Christof Karmonik, PhD Baylor College of Medicine/The Methodist Hospital Mailstation M217 6565 Fannin Houston, TX 77030 Pager: (713) 708-2232 Fax: (713) 790-4688 From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: T =3D T_overall + R(MR_center(physical)) - PET_center(physical)=20 ----------------------- By the way I think the program also dumped the last/final parameters - what did you get for those? There should be 7 numbers, the first four represents a unit quaternion and the last 3 numbers should be "T". - Lydia > -----Original Message----- > From: David Wikler [mailto:dwikler at ulb.ac.be] > Sent: Friday, March 14, 2003 1:16 AM > To: Lydia Ng > Cc: insight-users at public.kitware.com; luis.ibanez at kitware.com > Subject: RE: [Insight-users] MI Registration example translation > parameters >=20 > Dear Lydia, >=20 > >Actually, the MultiResMIRegistration application actually doesn't use > >image origin information. The first preprocessing step it does is to > >artificially place the origin in the center of each of the images. This > >is equivalent to align the images at their center. Additionally any > >rotation is with respect to the center of the image. > > >=20 > I have seen this in the code and that was the substrate for my > correction of the physical translation parameters using the > relative distance between the image centers. Does your remark > make this computation irrelevant or just makes Luis proposal > to tweak the original images origins impossible with this code ? >=20 > >You should also note that the "final quaternion parameters" are respect > >to the origin at the image center - but the display of the overall > >matrix and translation is reposition so that the image origin for both > >images is at the [0,0,0] pixel. > > > >Since the output matrix has some rotation in it - the position of the > >center of rotation comes into play and hence the output translation is a > >mixture of your introduced translation and the center of rotation. >=20 > Could we formalize it with a formula to add the rotation contribution > to the translations numbers ? > using > 1. the rotation matrix > 2. the volume center coordinates >=20 > We would end with someting like >=20 > T(mm) =3D T(physical) - D - d >=20 > where D =3D (PET_volume_center(physical)-MR_volume_center(physical))/2 > which is the relative distance between the centers of images > where d =3D PET_volume_center(physical) - RotationMatrix * > PET_volume_center(physical) >=20 > [d would be zero for a null rotation whicj makes sense] >=20 > For my case, I would end with >=20 > For Z: 86.6143 - (63*2.4- 50*1.3)/2 - dz =3D 43.5 mm - dz > For Y: 31.1387 - (128*2.57- 256*1.05)/2 - dy =3D 1.06 mm - dy > For X: 36.6828 - (128*2.57- 256*1.05)/2 - dx =3D 6.6 mm - dx >=20 > with dx =3D 0.6885, dy =3D -0.7060, dz =3D 0.0495 >=20 > and I would end with a translation of >=20 > (6.55, 1,766, 42.81) >=20 > which still makes sense according to my visual evaluation but as > my rotation quasi null, I can't be 100% sure of my formulas. > I don't currently have a dataset with more rotation to check this > better. Can you tell me whether you think my math development > looks allright according to your comments. >=20 > Thank you all. >=20 > David >=20 > >> -----Original Message----- > >> From: Luis Ibanez [mailto:luis.ibanez at kitware.com] > >> Sent: Thursday, March 13, 2003 11:01 AM > >> To: David Wikler > >> Cc: insight-users at public.kitware.com > >> Subject: Re: [Insight-users] MI Registration example translation > >> parameters > >> > >> Hi David, > >> > >> The origin of the physical coordinate system > >> for the volumes should be taken into account > >> during the registration process. > >> > >> Your analysis looks right. It makes sense to > >> first discount the relative distance between > >> the image centers. > >> > >> In general, simply creating a diagram of the > >> images in a common coordinate system in physical > >> space should clarify the discrepancy. > >> > >> In any case, if the resampled images are aligned > >> correctly, you can be confident that the only > >> difficulty is the intrepretation of the transform > >> in a common coordinate system. > >> > >> -- > >> > >> If the resampled images are not aligned correctly, > >> then we could suspect that the registration method > >> didn't converge as expected. > >> > >> --- > >> > >> An easy and quick test is to tweak the origin > >> values of your images and verify that the > >> changes are reflected in the final registration. > >> For example, if you add (13,17,19) to x,y,z of one > >> of the images origin, the registration should > >> report a variation of (13,17,19) in the translation > >> offset. > >> > >> > >> > >> Luis > >> > >> > >> --------------------- > >> David Wikler wrote: > >> > Dear Luis, > >> > > >> > I think your comments helped me to understand > >> > my numbers a bit better. I focused on my numeral (3) > >> > > >> > > >> >>3. The registration result I get with datasets oriented > >> >>Head to Feet along the z axis is > >> >> > >> >>Overall transform matrix: > >> >>0.999868 -0.0144369 0.00750628 > >> >>0.0144862 0.999874 -0.00655476 > >> >>-0.0074107 0.00666263 0.99995 > >> >> > >> >>Overall transform offset: > >> >>36.6828 31.1387 86.6143 > >> > > >> > > >> > What I actually did was flip the images along the Z axis > >> > so the head goes to feet and vice-versa. I actually also > >> > did flip Anterio-posterior but this is not relevant for > >> > the following. > >> > > >> > I said to you that I estimated the Z translation to > >> > about 40.8 mm. Actually I can also estimate X and Y > >> > translation being of the order of less than 10mm. > >> > > >> > After reading your comments about physical space vs > >> > voxels space, I imagined the dicrepancy could come > >> > from the centers of volumes translations when going > >> > from voxel space to physical space. > >> > We could then write > >> > > >> > Tz(slices) =3D slicethickness *( Tz(physical) - D) > >> > and > >> > Tz(mm) =3D Tz(physical) - D > >> > > >> > where D =3D (PET_volume_Zcenter(physical)-MR_volume_Zcenter(physical)) > >/2 > >> > which is the translation in physical space between volume centers > >> > (for Z coordinate) > >> > > >> > In my case: > >> > > >> > For Z: 86.6143 - (63*2.4- 50*1.3)/2 =3D 43.5 mm > >> > For Y: 31.1387 - (128*2.57- 256*1.05)/2 =3D 1.06 mm > >> > For X: 36.6828 - (128*2.57- 256*1.05)/2 =3D 6.6 mm > >> > > >> > which is now compatible with my estimation. > >> > I still have got to check with other cases but > >> > I think it could be the solution, what is your > >> > impression ? > >> > > >> > Thank a lot for your quick help. > >> > > >> > David > >> > > >> > David Wikler, Ir > >> > ULB - Erasme Hospital - PET Scan > >> > 808 route de Lennik - B1070 Brussels - Belgium > >> > Phone: 32 2 5556603 - Fax: 32 25556631 > >> > Email: dwikler at ulb.ac.be > >> > _______________________________________________ > >> > Insight-users mailing list > >> > Insight-users at public.kitware.com > >> > http://public.kitware.com/mailman/listinfo/insight-users > >> > > >> > >> > >> > >> > >> _______________________________________________ > >> Insight-users mailing list > >> Insight-users at public.kitware.com > >> http://public.kitware.com/mailman/listinfo/insight-users > > > > >=20 >=20 > David Wikler, Ir > ULB - Erasme Hospital - PET Scan > 808 route de Lennik - B1070 Brussels - Belgium > Phone: 32 2 5556603 - Fax: 32 25556631 > Email: dwikler at ulb.ac.be From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: blood vessel from MRA. I think in theory, Level Set method can not extract one voxel wide or two voxel wide small blood vessel, is that right? And are there some effect can solve this problem in the level set framework? Thanks for any advice. Fucang _________________________________________________________________ From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: MET_CHAR,=20 MET_UCHAR,=20 MET_SHORT, MET_USHORT, MET_INT,=20 MET_UINT,=20 MET_FLOAT,=20 MET_DOUBLE, You might also want to look at the following MetoIO documentation http://tolkien.rad.unc.edu/technologies/MetaImage/MetaIO-Introduction.pd f Hope this helps, Lydia > -----Original Message----- > From: George C LaVerde [mailto:gclst6+ at pitt.edu] > Sent: Monday, April 14, 2003 9:00 AM > To: insight-users at public.kitware.com > Subject: [Insight-users] Re: meta image files (fwd) >=20 >=20 > Hi, can anybody help me with this? Thanks, >=20 >=20 > ---------- Forwarded message ---------- > Date: Mon, 14 Apr 2003 10:56:00 -0400 (EDT) > From: George C LaVerde > To: dmshelto at andrew.cmu.edu > Subject: Re: meta image files >=20 >=20 > Damion, > In brainweb165a10f17.mha is: >=20 > NDims =3D 3 > DimSize =3D 181 217 180 > ElementType =3D MET_UCHAR > ElementSpacing =3D 1.0 1.0 1.0 > ElementByteOrderMSB =3D False > ElementDataFile =3D brainweb165a10f17.raw >=20 > I'm trying to convert raw image files to .mha files. I assume that the > above: > ElementType =3D MET_UCHAR > is declaring the pixel type to unsigned char. What is the correct thing > for: >=20 > short int > long int > float > double >=20 > and do I just add the "U" to make them unsigned? >=20 > I looked at the website below, but I couldn't find any info about this. >=20 > The BrainWeb project home page is : >=20 > http://www.bic.mni.mcgill.ca/brainweb >=20 > Thanks, >=20 > George >=20 >=20 > ----------------- > George C. LaVerde > MD/PhD Student > Univ. of Pittsburgh > gclst6+ at pitt.edu > (412)889-2046 >=20 >=20 >=20 >=20 > _______________________________________________ > Insight-users mailing list > Insight-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: "When this filter is updated, NumberOfLevels outputs are produced. The N'th output correspond to the N'th level of the pyramid." So if the filter has 3 levels then the output images are obtained via: ZerothLevelOutput =3D filter->GetOutput(0); FirstLevelOutput =3D filter->GetOutput(1); SecondLevelOutput =3D filter->GetOutput(2); Is this the info you are looking for?=20 - Lydia > -----Original Message----- > From: Peter Lorenzen [mailto:lorenzen at cs.unc.edu] > Sent: Friday, May 23, 2003 2:41 PM > To: Insight-users at public.kitware.com > Subject: [Insight-users] RecursiveMultiResolutionPyramidImageFilter >=20 > Hi All, >=20 > Does anyone know how to use the GenerateOutputRequestedRegion or other > method to extract computed reduced resolution datasets from an > itkRecursiveMultiResolutionPyramidImageFilter? There is plenty of > documentation on how to set the shrink schedule and how to connect this > filter to other filters but not much, that I have found, in the way of > directly accessing the output of this filter. >=20 > Thanks in advance, >=20 > - Peter >=20 > -- > Peter J. Lorenzen > Ph.D. Student > Department of Computer Science > University of North Carolina at Chapel Hill > Sitterson Hall 268, Campus Box 3175 > Chapel Hill, NC 27599-3175 >=20 > TEL (919) 962-1879 > FAX (919) 962-1699 > E-MAIL lorenzen at cs.unc.edu > WEB PAGE http://www.cs.unc.edu/~lorenzen >=20 > _______________________________________________ > Insight-users mailing list > Insight-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: =20 /** Set the pointer from which the image data is imported. "num" is * the number of pixels in the block of memory. If * "LetSourceManageMemory" is false, then the application retains * the responsibility of freeing the memory for this image data. If * "LetSourceManageMemory" is true, then this class will free the * memory when this object is destroyed. */ void SetImportPointer(TPixel *ptr, unsigned long num, bool LetSourceManageMemory); So a value of "true" means the ImportImageFilter will delete the = memory. A value of "false" means the application is responsible for deleting the memory. =20 So I am guessing we may have it backwards in the Software Guide. =20 =20 -----Original Message----- From: Severino Fernandez [mailto:severinofer at recol.es] Sent: Friday, June 06, 2003 7:04 AM To: insight-users at public.kitware.com Subject: [Insight-users] userPromiseToDeleteTheBuffer I call ITK C++ code from a C program. The C program passes buffers with image data to the static library generated using ITK code. I import = these buffers using ImportImageFilter. As I understand from the Software Guide the = userPromiseToDeleteTheBuffer argument to the SetImportPointer method should be true, in order for = the ImportImageFilter not to try to delete the passed buffer. Taking this approach, the code will fail when the C++ code using the = ITK classes exits. On the contrary, if I set the value to false, it seems = to work OK and I can retrieve the values in the buffers from the C = program. It seems that I am misuderstanding the text of the Software Guide or I = do not undersand some part of the mechanisms, or that there is some inconsistency in the Software Guide. Could someone give a short comment on this ? Severino Fernandez Instituto Nacional de Tecnica Aeroespacial Departamento de Observaci=F3n de la Tierra, Teledetecci=F3n y = Aeronom=EDa Carretera de Ajalvir, Km 4 28850 Torrejon de Ardoz Spain Tel +34 91 648 78 00 +34 91 305 16 52 Fax +34 91 677 46 46 Email severinofer at recol.es =20 =20 =20 ------_=_NextPart_001_01C32C4F.FDF436E1 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
From=20 the header file of ImportImageFilter (which is the only=20 truth)
 
 =20 /** Set the pointer from which the image data is imported.  "num"=20 is
   * the number of pixels in the block of memory.=20 If
   * "LetSourceManageMemory" is false, then the = application=20 retains
   * the responsibility of freeing the memory for = this=20 image data.  If
   * "LetSourceManageMemory" is true, = then=20 this class will free the
   * memory when this object is = destroyed.=20 */
  void SetImportPointer(TPixel *ptr, unsigned long=20 num,
          &nbs= p;           &nbs= p;=20 bool LetSourceManageMemory);
So a=20 value of "true" means the ImportImageFilter will delete the = memory.  A=20 value of "false" means the application is responsible for deleting the=20 memory.
 
So I=20 am guessing we may have it backwards in the Software = Guide.
 
 
-----Original Message-----
From: Severino = Fernandez=20 [mailto:severinofer at recol.es]
Sent: Friday, June 06, 2003 = 7:04=20 AM
To: insight-users at public.kitware.com
Subject:=20 [Insight-users] userPromiseToDeleteTheBuffer

I call ITK C++ code from a C = program. The C=20 program passes buffers with image data to the static library = generated using=20 ITK code.  I import these buffers using ImportImageFilter.
As I understand from the=20 Software Guide  the userPromiseToDeleteTheBuffer argument to the = SetImportPointer method should be  true, in order for the ImportImageFilter  not to try to delete = the passed=20 buffer.
Taking this approach, the code will = fail when the=20 C++ code using the ITK classes exits. On the contrary, if I set = the value=20 to false, it seems to = work OK and I=20 can retrieve the values in the buffers from the C = program.
It seems that I am misuderstanding = the text of=20 the Software Guide or I do not undersand some part of the=20 mechanisms,  or that there is some inconsistency in the Software = Guide.
Could someone give a short comment = on this=20 ?
Severino Fernandez
Instituto = Nacional de=20 Tecnica Aeroespacial
Departamento de Observaci=F3n de la Tierra,=20 Teledetecci=F3n y Aeronom=EDa
Carretera de Ajalvir, Km 4
28850 = Torrejon de=20 Ardoz
Spain
Tel   +34 91 648 78=20 00
        +34 91 305 16=20 52
Fax   +34 91 677 46 46
Email severinofer at recol.es  = ;=20
 
 
------_=_NextPart_001_01C32C4F.FDF436E1-- From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: after which I open the file in VC++ and build the toolkit. Is this right ? Thanks Tejas Luis Ibanez wrote: Hi Tejas, Please take some time for reading the installation instructions provided in the SoftwareGuide http://www.itk.org/ItkSoftwareGuide.pdf Chapter 2. The HelloWorld example is described there in detail. ---------------- Since the binary directory that you provided for building ITK was c:\InsightToolkit-1.2.0\Examples\Installation You should now find there a file named ITK.dsw Open this file with VC++, and build the toolkit. When the build is done you should find a number of libraries in c:\InsightToolkit-1.2.0\Examples\Installation\bin\Debug (or ... \bin\Release). Among those libraries you should see ITKCommon.lib ITKIO.lib.... for example. Once you are done with building the ITK libraries, you can then go and configure and build your application. In this case, the HelloWorld example: 1) copy the HelloWorld example in an external directory "XYZ", 2) run CMAke and provide the source directory "XYZ" where you copied the HelloWorld example. Select a binary directory where you want the HelloWorld example to be built. (this is different from the ITK-DIR directory). 3) fill in the CMAke variable ITK-DIR with c:\InsightToolkit-1.2.0\Examples\Installation 4) click Configure and then click Ok 5) Go to the binary directory that you selected for building the HelloWorld example, and open the .dsw with VC++ 6) Build it. ------------ Regards, Luis ---------------------- tejas mehta wrote: > Hi Luis > Thank you for your reply. I am still unsure about how to open the ITK > Workspace and build the toolkit. Do I open the helloworld.cxx file in > VC++ and try to build it ? > > Tejas > > */Luis Ibanez /* wrote: > > > Hi Tejas, > > The ITK-DIR variable should point to > the binary directory where you built ITK. > > When you ran CMake, the first thing you do > is to provide a 'Source' directory and a > 'Binary' directory. The 'Binary' directory > is where the toolkit will be built. > Then you open the ITK workspace with > VisualStudio (it looks like you are doing > this on windows..) and build the toolkit. > > This same ITK 'Binary' directory is the one > you should provide for the ITK-DIR variable > in CMake when you configure an applications > that uses ITK. (e.g. the "Hellow World" example). > > > Regards,. > > > Luis > > > --------------------------------- > tejas mehta wrote: > > > Hi, > > > > I am having problem using CMake. What should the ITK-DIR option > point > > to ? I am unable to find ITKConfig.cmake on my system. > > > > so! urce dir : c:\InsightToolkit-1.2.0\Examples\Installation > > bin dir : c:\InsightToolkit-1.2.0\Examples\Installation > > > > (I am trying to compile the "Hello World" example given in the ITK > > tutorial) > > > > > > Thank you in advance > > > > Tejas > > > ------------------------------------------------------------------------ > > Do you Yahoo!? > > SBC Yahoo! DSL > > > > - Now only $29.95 per month! > > > > > ------------------------------------------------------------------------ > Do you Yahoo!? > SBC Yahoo! DSL > > - Now only $29.95 per month! --------------------------------- Do you Yahoo!? SBC Yahoo! DSL - Now only $29.95 per month! --0-419792898-1056513885=:22634 Content-Type: text/html; charset=us-ascii
Hello Luis,
Thank you for your reply, I have read Ch2 of the Guide and am still having trouble building the itk.dsw workspace using CMake.
 
In CMake I set: 
 
source dir : C:\itk\InsightToolkit-1.2.0
and binary dir : C:\temp
 
I get some error messages when I try to configure (UseITK.cmake.in system error: no such file or dir)
 
From what I understand, I need to create the workspace (itk.dsw) first using CMake
after which I open the file in VC++ and build the toolkit. Is this right ?
 
Thanks
Tejas
 

Luis Ibanez <luis.ibanez at kitware.com> wrote:

Hi Tejas,


Please take some time for reading the installation instructions
provided in the SoftwareGuide

http://www.itk.org/ItkSoftwareGuide.pdf

Chapter 2.

The HelloWorld example is described there in detail.


----------------

Since the binary directory that you provided
for building ITK was

c:\InsightToolkit-1.2.0\Examples\Installation

You should now find there a file named


ITK.dsw

Open this file with VC++, and build the toolkit.

When the build is done you should find a number
of libraries in

c:\InsightToolkit-1.2.0\Examples\Installation\bin\Debug

(or ... \bin\Release).
Among those libraries you should see ITKCommon.lib
ITKIO.lib.... for example.

Once you are done with building the ITK libraries,
you can then go and configure and build your application.
In this case, the HelloWorld example:

1) copy the HelloWorld example in an external directory "XYZ",

2) run CMAke and provide the source directory "XYZ" where
you copied the HelloWorld example. Select a binary directory
where you want the HelloWorld example to be built. (this is
different from the ITK-DIR directory).

3) fill in the CMAke variable ITK-DIR with

c:\InsightToolkit-1.2.0\Examples\Installation

4) click Configure and then click Ok

5) Go to the binary directory that you selected for building the
HelloWorld example, and open the .dsw with VC++

6) Build it.

------------

Regards,


Luis


----------------------
tejas mehta wrote:

> Hi Luis
> Thank you for your reply. I am still unsure about how to open the ITK
> Workspace and build the toolkit. Do I open the helloworld.cxx file in
> VC++ and try to build it ?
>
> Tejas
>
> */Luis Ibanez /* wrote:
>
>
> Hi Tejas,
>
> The ITK-DIR variable should point to
> the binary directory where you built ITK.
>
> When you ran CMake, the first thing you do
> is to provide a 'Source' directory and a
> 'Binary' directory. The 'Binary' directory
> is where the toolkit will be built.
> Then you open the ITK workspace with
> VisualStudio (it looks like you are doing
> this on windows..) and build the toolkit.
>
> This same ITK 'Binary' directory is the one
> you should provide for the ITK-DIR variable
> in CMake when you configure an applications
> that uses ITK. (e.g. the "Hellow World" example).
>
>
> Regards,.
>
>
> Luis
>
>
> ---------------------------------
> tejas mehta wrote:
>
> > Hi,
> >
> > I am having problem using CMake. What should the ITK-DIR option
> point
> > to ? I am unable to find ITKConfig.cmake on my system.
> >
> > so! urce dir : c:\InsightToolkit-1.2.0\Examples\Installation
> > bin dir : c:\InsightToolkit-1.2.0\Examples\Installation
> >
> > (I am trying to compile the "Hello World" example given in the ITK
> > tutorial)
> >
> >
> > Thank you in advance
> >
> > Tejas
> >
> ------------------------------------------------------------------------
> > Do you Yahoo!?
> > SBC Yahoo! DSL
> >
> > - Now only $29.95 per month!
>
>
>
>
> ------------------------------------------------------------------------
> Do you Yahoo!?
> SBC Yahoo! DSL
>
> - Now only $29.95 per month!





Do you Yahoo!?
SBC Yahoo! DSL - Now only $29.95 per month! --0-419792898-1056513885=:22634-- From bogus@does.not.exist.com Fri Oct 24 12:25:09 2014 From: bogus@does.not.exist.com () Date: Fri, 24 Oct 2014 16:25:09 -0000 Subject: No subject Message-ID: a VTK or ITK volume. Nevertheless, I found problems when attempting to convert a gated-SPECT = .dcm file, as it only converts the very first slice but not the rest. Jolinda, any suggestion? I will try DCMTK and see how it goes ...=20 Regards, Sebastian ------=_NextPart_000_0031_01C344A5.DE37D740 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
MRIConvert is a powerful application = developed by=20 Jolinda Smith for = converting DICOM=20 data sets into metafile info volumes.
From this point it is straightforward = to continue=20 working within ITK, as a VTK or ITK volume.
Nevertheless, I found problems when = attempting to=20 convert a gated-SPECT .dcm file, as it only converts the very = first
slice but not the rest. Jolinda, any=20 suggestion?
I will try DCMTK and see how it = goes ...=20
 
Regards,
 
Sebastian
------=_NextPart_000_0031_01C344A5.DE37D740-- From matt.mccormick at kitware.com Fri Oct 24 12:33:41 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 12:33:41 -0400 Subject: [ITK-users] Example medical images for teaching Image Segmentation In-Reply-To: References: Message-ID: Hi Sami, Thanks for helping to educate the next generation on medical computing :-). If you happen to use ITK/SimpleITK in your course, please add a link to the materials in this wiki page [1]. The data used in the examples can be a good resource. Some very nice examples that illustrate level sets segmentation can be found here [2] [3] [4] [5] [6]. Thanks, Matt [1] http://www.itk.org/Wiki/ITK/Documentation [2] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.html [3] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeStaticDense2DLevelSetZeroSet/Documentation.html [4] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeStaticShi2DLevelSetLayers/Documentation.html [5] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.html [6] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html On Fri, Oct 24, 2014 at 10:36 AM, Sami Koho wrote: > Hello, > > This is not directly related to ITK, but I will ask anyway, out of > curiosity. This fall I have been teaching Digital Image Processing to > Biomedical imaging students. The next subject will be Image Segmentation > (Edge detection models, / thresholding). Would any of you have some > favorite medical images to demonstrate these subjects? I can of course use > any pictures, but having examples relevant to the students would be nice. > I have my own libraries as well, but they are mostly of cells and their > internals (microscopy lab). Feel free to send any links/files, if > something comes to mind. > > Best, > > Sami > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From bill.lorensen at gmail.com Fri Oct 24 12:40:06 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 24 Oct 2014 12:40:06 -0400 Subject: [ITK-users] Example medical images for teaching Image Segmentation In-Reply-To: References: Message-ID: You might contact John Galeotti at CMU. He has taught image processing courses using ITK. http://www.cs.cmu.edu/~galeotti/methods_course/books_references.html On Fri, Oct 24, 2014 at 10:36 AM, Sami Koho wrote: > Hello, > > This is not directly related to ITK, but I will ask anyway, out of > curiosity. This fall I have been teaching Digital Image Processing to > Biomedical imaging students. The next subject will be Image Segmentation > (Edge detection models, / thresholding). Would any of you have some > favorite medical images to demonstrate these subjects? I can of course use > any pictures, but having examples relevant to the students would be nice. > I have my own libraries as well, but they are mostly of cells and their > internals (microscopy lab). Feel free to send any links/files, if > something comes to mind. > > Best, > > Sami > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com From llliu at umich.edu Fri Oct 24 13:08:54 2014 From: llliu at umich.edu (Lianli Liu) Date: Fri, 24 Oct 2014 13:08:54 -0400 Subject: [ITK-users] Jacobian in translation transform Message-ID: Hi all, I am quiet new to registration and I am having difficulty understanding the Jacobian matrix calculated in translation transform. From my understanding, the ComputeJacobianWithRespectToParameters should calculate the shift of EACH voxel with respect to parameters, thus the matrix size should be related with number of voxels? But the Jacobian matrix here is only related with image dimensions? (3 by 3 for 3D image). Can anyone help me understand this? And I am confused for other transformation methods such as rigid, where is the Jacobian calculated? Thanks! Best, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Oct 24 14:33:25 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 14:33:25 -0400 Subject: [ITK-users] Jacobian in translation transform In-Reply-To: References: Message-ID: Hi Lianli, The ComputeJacobianWithRespectToParameters takes an input parameter the position in space that the jacobian is to be computed, so it returns the value at that point in space. For the TranslationTransform, it is not that interesting since the jacobian is a uniform identity matrix. Hope this helps, Matt On Fri, Oct 24, 2014 at 1:08 PM, Lianli Liu wrote: > Hi all, > > I am quiet new to registration and I am having difficulty understanding the > Jacobian matrix calculated in translation transform. From my understanding, > the ComputeJacobianWithRespectToParameters should calculate the shift of > EACH voxel with respect to parameters, thus the matrix size should be > related with number of voxels? But the Jacobian matrix here is only related > with image dimensions? (3 by 3 for 3D image). Can anyone help me understand > this? > > And I am confused for other transformation methods such as rigid, where is > the Jacobian calculated? Thanks! > > Best, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From noreply at insightsoftwareconsortium.org Sat Oct 25 15:45:58 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:45:58 -0400 (EDT) Subject: [ITK-users] New Submission: Brain Tumor Progression Modeling - A Data Driven Approach Message-ID: <20141025194558.AB0B13D6C4DD@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Brain Tumor Progression Modeling - A Data Driven Approach Authors: Weber C., G??tz M., Stieltjes B., Polanska J., Binczyk F., Tarnawski R., Bobek-Billewicz B., Maier-Hein K. Abstract: Malignant gliomas are highly heterogeneous brain tumors with complex an- isotropic growth patterns and occult invasion. Computational modeling of cell migration and proliferation has been subject of intensive research aiming at a deeper understanding of the tumor biology and the ability to predict growth and thus improve therapy. However, current modeling techniques follow a generative approach and make strong assumptions about underlying mechanisms. The tumor is so far treated as homogeneous entity with behavioral parameters extrapolated from previous longitudinal image information. We present a novel way of approaching this problem by employing data driven, discrim- inative modeling techniques that learn relevant features from observed growth patterns and are able to make meaningful predictions solely on basis of local and regional tissue characteristics at one given point in time. We demonstrate superior performance of the proposed discriminative method (DICE score 83) compared to the state of the art generative approach (DICE score 72) on six patients and a total of nine different time intervals. Our approach can help estimating occult invasion as well as it can advance our understanding of the tumor biology and lead to valuable predictions of tumor growth patterns that could guide and improve radio therapy. Download and review this publication at: http://hdl.handle.net/10380/3474 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Sat Oct 25 15:47:33 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:47:33 -0400 (EDT) Subject: [ITK-users] New Submission: Visualization of 4D-PET/CT, Target Volumes and Dose Distribution: Applications in Radiotherapy Planning Message-ID: <20141025194733.151A33D6C492@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Visualization of 4D-PET/CT, Target Volumes and Dose Distribution: Applications in Radiotherapy Planning Authors: Schlachter M., Fechter T., Nestle U., B??hler K. Abstract: In radiation treatment (RT) planning medical doctors need to consider a variety of information sources for anatomical and functional target volume delineation. The validation and inspection of the defined target volumes and the resulting RT plan is a complex task, especially in the presence of moving target areas as it is the case for tumors of the chest and the upper abdomen. A 4D-PET/CT visualization system may become a helpful tool for validating RT plans. We define major requirements such a visualization system should fulfill to provide medical doctors with the necessary visual information to validate tumor delineations, and review the dose distribution of a RT plan. We present an implementation of such a system, and present qualitative results of its applications for a lung cancer patient. Download and review this publication at: http://hdl.handle.net/10380/3491 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Sat Oct 25 15:48:24 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:48:24 -0400 (EDT) Subject: [ITK-users] New Submission: Improvements in SlicerRT, the radiation therapy research toolkit for 3D Slicer Message-ID: <20141025194824.224513D6C411@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Improvements in SlicerRT, the radiation therapy research toolkit for 3D Slicer Authors: Pinter C., Lasso A., Wang A., Sharp G.C., Jaffray D., Fichtinger G. Abstract: Purpose: Recent years have seen growing interest in adaptive radiation therapy (RT), but the existing software tools are not ideal for research use, as they are either expensive and closed proprietary applications or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we have developed SlicerRT, an open-source toolkit for RT research, providing fast computations and user-friendly interface for researchers. It is a medium for RT researchers to integrate their workflows in, assists clinical translation of experimental approaches, and enables comparative testing. Methods: SlicerRT builds on the widely used medical image visualization and analysis platform, 3D Slicer (www.slicer.org). In addition to the tools that 3D Slicer offers for visualization, registration and segmentation, the toolkit provides functions specifically designed for RT research. Established development processes as well as testing and validation environment ensure software quality. Standardized software development mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The design and architecture of the toolkit was outlined in [1]. SlicerRT has evolved to contain the most widely used features in the field (see www.slicerrt.org), which have been defined through consensus discussions with a large pool of RT researchers. Results: Numerous modules have been developed for RT-specific features such as DICOM-RT data import and export, as well as dose analysis tools including dose volume histogram, dose accumulation, dose comparison, and isodose line and surface generation. The toolkit also includes contour analysis modules for handling various contour representations, contour morphology, and contour comparison. Advanced registration tools are provided by the included Plastimatch library [2]. The main new features developed in the last year are RT plan and RT image import and the subject hierarchy module, which arranges the loaded data to a structure familiar to clinicians, while providing advanced automation features through the underlying extendible mechanism. The toolkit is being used by several research groups to support and evaluate adaptive radiation therapy workflows. SlicerRT is available for download through the Extension Manager component of 3D Slicer 4.3 or later (see instructions on our websit e). Future work: As SlicerRT has matured to contain most of the planned functions, our focus has shifted from feature development to usability and stability. The subject hierarchy module, and its features such as bulk deformation of studies embodies our efforts toward usability, while the integration of the subject hierarchy and the advanced contour handling mechanism into the 3D Slicer core points towards stability, also benefiting the whole 3D Slicer community. There is ongoing work to evaluate and potentially standardize the way the 2D contours are rasterized into 3D volumes, thus mitigating the great variability between the different solutions for this problem. Current funding ensures continuous development for several years, so SlicerRT is expected to develop further. Acknowledgement: This work was in part funded by Cancer Care Ontario through Applied Cancer Research Unit and Research Chair in Cancer Imaging grants, and the Ontario Consortium for Adaptive Invention in Radiation Oncology (OCAIRO). Download and review this publication at: http://hdl.handle.net/10380/3494 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Sat Oct 25 15:48:55 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:48:55 -0400 (EDT) Subject: [ITK-users] New Submission: Automatic accuracy measurement for multi-modal rigid registration using feature descriptors Message-ID: <20141025194855.F0C933D6C609@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Automatic accuracy measurement for multi-modal rigid registration using feature descriptors Authors: Hauler F., Jurisic M., Furtado H., Sabatini U., Laprie A., Nestle U., Birkfellner W. Abstract: In radiotherapy (RT) for tumor delineation and diagnostics, complementary information of multi-modal images is used. Using high ionizing radiation, the accuracy of registered volume data is crucial; therefore a reliable and robust evaluation method for registered images is needed in clinical practice. Multi-modal image registration aligns images from different modalities like computed tomography (CT) and magnetic resonance imaging (MRI) or cone beam computed tomography (CBCT) into one common frame of reference. The gold standard validation methods are visual inspection by radiation oncology experts and fiducial-based evaluation. However, visual inspection is a qualitative measure with a range of 2-6 mm inaccuracy, it is time consuming and prone to errors. The fiducial-based evaluation is an invasive method when fiducial markers are fixated to bone or implanted in organs. Therefore, in clinical practice a robust non-invasive automated method is needed to validate registratio n of multi-modal images. The aim of this study is to introduce and validate an automatic landmark-based accuracy measure for multi-modal image rigid registration using feature descriptors. A porcine dataset with fixed fiducial markers was used to compare our accuracy measure with the target registration error of fiducial markers.In addition, the robustness of our evaluation method was tested on multi-vendor database consisted of 10 brain and 20 lung cases comparing the automatic landmark accuracy measure based on feature descriptors with manual landmark based evaluation. An automatic, non-invasive method based on feature descriptors for accuracy evaluation of multi-modal rigid registration was introduced. The method can be used to provide accuracy information slice-by slice on CT, CBCT and CT, MR-T1, -T2 weighted, MR-T1 contrast enhanced (ce) multi-modal images. Download and review this publication at: http://hdl.handle.net/10380/3490 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Sat Oct 25 15:49:31 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:49:31 -0400 (EDT) Subject: [ITK-users] New Submission: Gauss-Newton Method for Segmentation assisted Deformable Registration Message-ID: <20141025194931.E2EA03D6C4F0@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Gauss-Newton Method for Segmentation assisted Deformable Registration Authors: Jurisic M., Fechter T., Hauler F., Furtado H., Nestle U., Birkfellner W. Abstract: In this work, we try to develop a fast converging method for segmentation assisted deformable registration. The segmentation step consists of a piece-wise constant Mumford-Shah energy model while reg- istration is driven by the sum of squared distances of both initial images and segmented mask with a diffusion regularization. In order to solve this energy minimization problem, a second order Gauss-Newton opti- mization method is used. For the numerical experiments we used CT data sets from the EMPIRE10 challenge. In this preliminary study, we show high accuracy of our algorithm. Download and review this publication at: http://hdl.handle.net/10380/3492 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Sat Oct 25 15:50:51 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:50:51 -0400 (EDT) Subject: [ITK-users] New Submission: Dose Painting with a Variable Collimator for the Small Animal Radiation Research Platform (SARRP) Message-ID: <20141025195051.C908F3D6C768@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Dose Painting with a Variable Collimator for the Small Animal Radiation Research Platform (SARRP) Authors: Cho N., Wong J., Kazanzides P. Abstract: The goal of radiation treatment is to irradiate cancer cells (i.e., a target region) without destroying adjacent healthy tissue. Thus, it is advantageous to form the beam so that it best approximates the target, thereby reducing the amount of dose absorbed in critical regions outside the target area. While multi-leaf collimators are common in human clinical systems, small animal radiotherapy systems are typically limited to a set of fixed-size collimators. For these systems, dose painting can be used for conformal dose delivery, but is significantly slower than a multi-leaf collimator. As a compromise solution, a variable rectangular collimator has been developed for the Small Animal Radiation Research Platform (SARRP). This enables more efficient dose painting via the decomposition of a 2D target region into a minimum number of rectangles of variable size, which is the topic of this paper. The proposed method consists of several distinct steps and was implemented on the SA RRP Treatment Planning System (TPS). Download and review this publication at: http://hdl.handle.net/10380/3476 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Sat Oct 25 15:51:31 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:51:31 -0400 (EDT) Subject: [ITK-users] New Submission: Deformable Registration with Discontinuity Preservation using Multi-Scale MRF Message-ID: <20141025195131.607C23D6C820@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Deformable Registration with Discontinuity Preservation using Multi-Scale MRF Authors: Seo D., Van Baar J. Abstract: Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate for finer resolutions. However, sliding of organs and breathing motion, exhibit discontinuities. We propose a discrete optimization approach to preserve these discontinuities. Solving continuous deformations using discrete optimization requires a fine distribution of the discrete labels. Coupled with the typical size of medical image datasets, this poses challenges to compute solutions efficiently. In this paper we present a practical, multi-scale formulation. We describe how discontinuities can be preserved, and how the optimization problem is solved. Results on synthetic 2D, and real 3D data show that we can well approximate the smoothness of continuous optimization, while accurately maintaining discontinuities. Download and review this publication at: http://hdl.handle.net/10380/3496 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From noreply at insightsoftwareconsortium.org Mon Oct 27 06:38:02 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 27 Oct 2014 06:38:02 -0400 (EDT) Subject: [ITK-users] New Submission: Deformable Registration with Discontinuity Preservation using Multi-Scale MRF Message-ID: <20141027103802.E13403D6C6A9@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Deformable Registration with Discontinuity Preservation using Multi-Scale MRF Authors: Seo D., Van Baar J. Abstract: Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate for finer resolutions. However, sliding of organs and breathing motion, exhibit discontinuities. We propose a discrete optimization approach to preserve these discontinuities. Solving continuous deformations using discrete optimization requires a fine distribution of the discrete labels. Coupled with the typical size of medical image datasets, this poses challenges to compute solutions efficiently. In this paper we present a practical, multi-scale formulation. We describe how discontinuities can be preserved, and how the optimization problem is solved. Results on synthetic 2D, and real 3D data show that we can well approximate the smoothness of continuous optimization, while accurately maintaining discontinuities. Download and review this publication at: http://hdl.handle.net/10380/3475 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From assil-king at hotmail.fr Mon Oct 27 08:21:31 2014 From: assil-king at hotmail.fr (assil) Date: Mon, 27 Oct 2014 05:21:31 -0700 (PDT) Subject: [ITK-users] ITK Importing Image Data from a Buffer Message-ID: <1414412491137-7586419.post@n2.nabble.com> I have coded a method to create an Itk image from a buffer (in my case it's a Cimg image type). This is the algorithme : void Cimg_To_ITK (CImg img) { const unsigned int Dimension = 2; typedef itk::RGBPixel< unsigned char > RGBPixelType; typedef itk::Image< RGBPixelType, Dimension > RGBImageType; typedef itk::ImportImageFilter< RGBPixelType, Dimension > ImportFilterType; ImportFilterType::Pointer importFilter = ImportFilterType::New(); typedef itk::ImageFileWriter< RGBImageType > WriterType; WriterType::Pointer writer = WriterType::New(); RGBImageType::SizeType imsize; imsize[0] = img.width(); imsize[1] = img.height(); ImportFilterType::IndexType start; start.Fill( 0 ); ImportFilterType::RegionType region; region.SetIndex( start ); region.SetSize( imsize ); importFilter->SetRegion( region ); const itk::SpacePrecisionType origin[ Dimension ] = { 0.0, 0.0 }; importFilter->SetOrigin( origin ); const itk::SpacePrecisionType spacing[ Dimension ] = { 1.0, 1.0 }; importFilter->SetSpacing( spacing ); const unsigned int numberOfPixels = imsize[0] * imsize[1]; const bool importImageFilterWillOwnTheBuffer = true; RGBPixelType * localBuffer = new RGBPixelType[ numberOfPixels ]; memcpy(localBuffer->GetDataPointer(), img.data(), numberOfPixels); importFilter->SetImportPointer( localBuffer, numberOfPixels,importImageFilterWillOwnTheBuffer ); writer->SetInput( importFilter->GetOutput() ); writer->SetFileName( "output.png" ); writer->Update(); } I dont have what i want as a output : input : output : -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From matt.mccormick at kitware.com Mon Oct 27 11:23:53 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 27 Oct 2014 11:23:53 -0400 Subject: [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: <1414412491137-7586419.post@n2.nabble.com> References: <1414412491137-7586419.post@n2.nabble.com> Message-ID: Hi Assil, > > const unsigned int numberOfPixels = imsize[0] * imsize[1]; > const bool importImageFilterWillOwnTheBuffer = true; > > RGBPixelType * localBuffer = new RGBPixelType[ numberOfPixels ]; > memcpy(localBuffer->GetDataPointer(), img.data(), numberOfPixels); This should be numberOfPixels * 3, since there are three unsigned char bytes in for every RGB pixel. HTH, Matt From assil-king at hotmail.fr Mon Oct 27 11:48:40 2014 From: assil-king at hotmail.fr (assil) Date: Mon, 27 Oct 2014 08:48:40 -0700 (PDT) Subject: [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: References: <1414412491137-7586419.post@n2.nabble.com> Message-ID: <1414424920694-7586421.post@n2.nabble.com> Hi Matt, I already did that. my mistake i have plaste the wrong version of the code. Her is what i have : void Cimg_To_ITK (CImg img) { typedef unsigned char PixelType; typedef itk::RGBPixel< PixelType > RGBPixelType; typedef itk::Image< RGBPixelType, 2 > RGBImageType; typedef itk::ImportImageFilter< RGBPixelType, 2 > ImportFilterType; ImportFilterType::Pointer importFilter = ImportFilterType::New(); typedef itk::ImageFileWriter< RGBImageType > WriterType; WriterType::Pointer writer = WriterType::New(); RGBImageType::SizeType imsize; imsize[0] = img.width(); imsize[1] = img.height(); ImportFilterType::IndexType start; start.Fill( 0 ); ImportFilterType::RegionType region; region.SetIndex( start ); region.SetSize( imsize ); importFilter->SetRegion( region ); double origin[ 2 ]; origin[0] = 0.0; // X coordinate origin[1] = 0.0; // Y coordinate importFilter->SetOrigin( origin ); double spacing[ 2 ]; spacing[0] = 1.0; // along X direction spacing[1] = 1.0; // along Y direction importFilter->SetSpacing( spacing ); const unsigned int numberOfPixels = imsize[0] * imsize[1] * 3; const unsigned int numberOfBytes = numberOfPixels * sizeof( PixelType ); const bool importImageFilterWillOwnTheBuffer = true; unsigned char * localBuffer = new unsigned char[ numberOfPixels ]; memcpy(localBuffer, img.data(), numberOfBytes); importFilter->SetImportPointer( localBuffer, numberOfPixels,importImageFilterWillOwnTheBuffer ); importFilter->Update(); writer->SetInput( importFilter->GetOutput() ); writer->SetFileName( "output.png" ); writer->Update(); } the out image is in the same. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419p7586421.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From bill.lorensen at gmail.com Mon Oct 27 11:58:25 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 27 Oct 2014 11:58:25 -0400 Subject: [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: <1414424920694-7586421.post@n2.nabble.com> References: <1414412491137-7586419.post@n2.nabble.com> <1414424920694-7586421.post@n2.nabble.com> Message-ID: What is the layout of the CImg. 1) RGBRGBRGB... 2) RRRRRRRRRRRR...GGGGGGGGGGGGGGGG....BBBBBBBBBBBBBBBBB... On Mon, Oct 27, 2014 at 11:48 AM, assil wrote: > Hi Matt, > > I already did that. my mistake i have plaste the wrong version of the code. > Her is what i have : > > > void Cimg_To_ITK (CImg img) > { > typedef unsigned char PixelType; > typedef itk::RGBPixel< PixelType > RGBPixelType; > typedef itk::Image< RGBPixelType, 2 > RGBImageType; > typedef itk::ImportImageFilter< RGBPixelType, 2 > ImportFilterType; > ImportFilterType::Pointer importFilter = ImportFilterType::New(); > typedef itk::ImageFileWriter< RGBImageType > WriterType; > WriterType::Pointer writer = WriterType::New(); > > > RGBImageType::SizeType imsize; > imsize[0] = img.width(); > imsize[1] = img.height(); > > ImportFilterType::IndexType start; > start.Fill( 0 ); > ImportFilterType::RegionType region; > region.SetIndex( start ); > region.SetSize( imsize ); > importFilter->SetRegion( region ); > > double origin[ 2 ]; > origin[0] = 0.0; // X coordinate > origin[1] = 0.0; // Y coordinate > importFilter->SetOrigin( origin ); > > double spacing[ 2 ]; > spacing[0] = 1.0; // along X direction > spacing[1] = 1.0; // along Y direction > importFilter->SetSpacing( spacing ); > > const unsigned int numberOfPixels = imsize[0] * imsize[1] * 3; > const unsigned int numberOfBytes = numberOfPixels * sizeof( PixelType ); > const bool importImageFilterWillOwnTheBuffer = true; > > unsigned char * localBuffer = new unsigned char[ numberOfPixels ]; > memcpy(localBuffer, img.data(), numberOfBytes); > importFilter->SetImportPointer( localBuffer, > numberOfPixels,importImageFilterWillOwnTheBuffer ); > importFilter->Update(); > writer->SetInput( importFilter->GetOutput() ); > writer->SetFileName( "output.png" ); > writer->Update(); > > } > > > the out image is in the same. > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419p7586421.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -- Unpaid intern in BillsBasement at noware dot com From assil-king at hotmail.fr Mon Oct 27 12:05:34 2014 From: assil-king at hotmail.fr (assil) Date: Mon, 27 Oct 2014 09:05:34 -0700 (PDT) Subject: [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: References: <1414412491137-7586419.post@n2.nabble.com> <1414424920694-7586421.post@n2.nabble.com> Message-ID: <1414425934443-7586423.post@n2.nabble.com> Hi Bill, It's RRRRRRRRRRRR...GGGGGGGGGGGGGGGG....BBBBBBBBBBBBBBBBB... -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419p7586423.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From blowekamp at mail.nih.gov Mon Oct 27 12:14:01 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 27 Oct 2014 12:14:01 -0400 Subject: [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: <1414425934443-7586423.post@n2.nabble.com> References: <1414412491137-7586419.post@n2.nabble.com> <1414424920694-7586421.post@n2.nabble.com> <1414425934443-7586423.post@n2.nabble.com> Message-ID: Hello, I would create separate R, G and B images, with 3 different import filters then use the ComposeImageFilter to make an ITK RGB image. ITK image or RGBPixel, are stored in RGBRGBRGB format. A simular conversion was done here[1], when reading the VisibleHuman data set. You will need to use an ImportImageFilter in stead of the readers used in the example. Brad [1] http://www.itk.org/Doxygen/html/IO_2VisibleHumanStreamReadWrite_8cxx-example.html On Oct 27, 2014, at 12:05 PM, assil wrote: > Hi Bill, > > It's RRRRRRRRRRRR...GGGGGGGGGGGGGGGG....BBBBBBBBBBBBBBBBB... > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419p7586423.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users From rsvpitt at gmail.com Mon Oct 27 13:06:29 2014 From: rsvpitt at gmail.com (Vikas) Date: Mon, 27 Oct 2014 13:06:29 -0400 Subject: [ITK-users] Landmarks in FEM registration Message-ID: Hi, Has anyone used FEM registration with landmarks? I am having trouble specifying landmarks. Is this feature now supported? Thanks Vikas -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhaqx001 at odu.edu Mon Oct 27 13:28:51 2014 From: rhaqx001 at odu.edu (Rabia Haq) Date: Mon, 27 Oct 2014 13:28:51 -0400 Subject: [ITK-users] how to connect components resulting from itkBinaryThinningImageFilter Message-ID: Hello ITK users, I am currently trying to extract the medial axis of a 3D image using itkBinaryThinningImageFilter. The resulting binary image contains a lot of unconnected components. Is there any filter in itk to connect these components and obtain a connected image, from which I can extract a contour? Thank you so much for your time and consideration, regards, Rabia Ph.D. Candidate, Research Assistant Department of Modeling, Simulation and Visualization Engineering, Old Dominion University, Norfolk, VA. -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at insightsoftwareconsortium.org Tue Oct 28 06:30:29 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Tue, 28 Oct 2014 06:30:29 -0400 (EDT) Subject: [ITK-users] New Submission: Validation of real-time intensity based 2D/3D registration for image guided radiotherapy Message-ID: <20141028103029.4B4053D6C67C@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Validation of real-time intensity based 2D/3D registration for image guided radiotherapy Authors: Furtado H., Underwood T., Depuydt T., Stock M., Georg D., Birkfellner W. Abstract: Patient motion during radiotherapy or intra-fractional motion, is one of the major sources of uncertainty in dose application. 2D/3D registration is an intensity based method used successfully to track tumor motion with the potential to reduce uncertainty. Despite promising results, validation remains a problem due to the lack of a gold standard. In this paper, we demonstrate the use of clinical datasets acquired with the VERO LINAC to validate intensity based 2D/3D registration. The patient considered in this study had a gold marker implanted to enable live tumor tracking. We verify our results against the tracked gold marker position. Our results show that it is possible to accurately track the tumor using only intensity based 2D/3D registration. The mean error of our registration is of 1.6 ?? 0.3mm and as low as 1.1 ?? 0.5mm when looking only at the cranial-caudal direction. The results pave the way for a possible clinical application of the method. Download and review this publication at: http://hdl.handle.net/10380/3497 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . From g.lemaitre58 at gmail.com Tue Oct 28 09:33:46 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Tue, 28 Oct 2014 14:33:46 +0100 Subject: [ITK-users] Resample Message-ID: Hi all, I am currently working on resampling. I am using the code available: http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM I was wondering if with the version of ITK-4.7, it is still necessary to shift the data to undo the effect of the rescale intercept by the DICOM reader as coded in the section 4) Thanks, Best regards, -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Oct 28 09:54:17 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 28 Oct 2014 09:54:17 -0400 Subject: [ITK-users] [ITK] Resample In-Reply-To: References: Message-ID: <8CE5D58E-4AFE-4CFE-9E22-2137AA1A243F@mail.nih.gov> Hello, There was a recent Kitware blog post about this issue: http://www.kitware.com/blog/home/post/754 Although after reading it I am still not sure how to answer your question, but it may help. Brad On Oct 28, 2014, at 9:33 AM, Guillaume Lema?tre wrote: > Hi all, > > I am currently working on resampling. I am using the code available: > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > I was wondering if with the version of ITK-4.7, it is still necessary to shift the data to undo the effect of the rescale intercept by the DICOM reader as coded in the section 4) > > Thanks, > Best regards, > -- > LEMA?TRE Guillaume > PhD Candiate > MSc Erasmus Mundus ViBOT (Vision-roBOTic) > MSc Business Innovation and Technology Management > > g.lemaitre58 at gmail.com > > > ViCOROB - Computer Vision and Robotic Team > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > LE2I - Le Creusot > IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Oct 28 10:31:32 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 28 Oct 2014 10:31:32 -0400 Subject: [ITK-users] [ITK] Resample In-Reply-To: <8CE5D58E-4AFE-4CFE-9E22-2137AA1A243F@mail.nih.gov> References: <8CE5D58E-4AFE-4CFE-9E22-2137AA1A243F@mail.nih.gov> Message-ID: The example contains #ifdef's that remove the slope/intercept recalling for ITK 4.6 and above. On Tue, Oct 28, 2014 at 9:54 AM, Bradley Lowekamp wrote: > Hello, > > There was a recent Kitware blog post about this issue: > http://www.kitware.com/blog/home/post/754 > > Although after reading it I am still not sure how to answer your question, > but it may help. > Brad > > On Oct 28, 2014, at 9:33 AM, Guillaume Lema?tre > wrote: > > Hi all, > > I am currently working on resampling. I am using the code available: > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > I was wondering if with the version of ITK-4.7, it is still necessary to > shift the data to undo the effect of the rescale intercept by the DICOM > reader as coded in the section 4) > > Thanks, > Best regards, > -- > > > > > *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT > (Vision-roBOTic)MSc Business Innovation and Technology Management* > g.lemaitre58 at gmail.com > > > *ViCOROB - Computer Vision and Robotic Team* > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > > *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la > Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Unpaid intern in BillsBasement at noware dot com -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Tue Oct 28 11:12:26 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Tue, 28 Oct 2014 16:12:26 +0100 Subject: [ITK-users] Running an ITK program Message-ID: Hi, I'm new to ITK. I have installed ITK, and want to run the example here: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader How can I do that? Should the files be in the same directory of ITK? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From daviddoria at gmail.com Tue Oct 28 11:17:57 2014 From: daviddoria at gmail.com (David Doria) Date: Tue, 28 Oct 2014 11:17:57 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul wrote: > Hi, > > I'm new to ITK. I have installed ITK, and want to run the example here: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > How can I do that? Should the files be in the same directory of ITK? > > Thanks. > Please see this page to get started: http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers Let us know if you have any questions. David -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Oct 28 11:18:22 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 28 Oct 2014 11:18:22 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: Follow the instructions at the bottom of the example page: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#Download_and_Build_ImageFileReader On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul wrote: > Hi, > > I'm new to ITK. I have installed ITK, and want to run the example here: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > How can I do that? Should the files be in the same directory of ITK? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com From abdul.sw84 at gmail.com Tue Oct 28 11:37:49 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Tue, 28 Oct 2014 16:37:49 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: David, Thanks for your reply. I went to the following steps: Windows 1. Open CMake 2. Select your CMakeLists.txt file 3. Select your build system 4. Click "Generate" But, it is not clear. I opened CMake, and selected CMakeLists.txt as the source file, and the directory where my main program is in as the "build" directory, but get the following error: ? On Tue, Oct 28, 2014 at 4:17 PM, David Doria wrote: > On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul > wrote: > >> Hi, >> >> I'm new to ITK. I have installed ITK, and want to run the example here: >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> >> How can I do that? Should the files be in the same directory of ITK? >> >> Thanks. >> > > Please see this page to get started: > > http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers > > Let us know if you have any questions. > > David > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: From abdul.sw84 at gmail.com Tue Oct 28 11:44:51 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Tue, 28 Oct 2014 16:44:51 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: I made a "src" and "bin" directories. When I configure using CMake, this is what I get in "red": CMake Error at CMakeLists.txt:11 (find_package): By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ItkVtkGlue", but CMake did not find one. Could not find a package configuration file provided by "ItkVtkGlue" with any of the following names: ItkVtkGlueConfig.cmake itkvtkglue-config.cmake Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set "ItkVtkGlue_DIR" to a directory containing one of the above files. If "ItkVtkGlue" provides a separate development package or SDK, be sure it has been installed. On Tue, Oct 28, 2014 at 4:37 PM, Abdul Abdul wrote: > David, > > Thanks for your reply. > > I went to the following steps: > Windows > > 1. Open CMake > 2. Select your CMakeLists.txt file > 3. Select your build system > 4. Click "Generate" > > But, it is not clear. I opened CMake, and selected CMakeLists.txt as the > source file, and the directory where my main program is in as the "build" > directory, but get the following error: > > > ? > > > > > On Tue, Oct 28, 2014 at 4:17 PM, David Doria wrote: > >> On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul >> wrote: >> >>> Hi, >>> >>> I'm new to ITK. I have installed ITK, and want to run the example here: >>> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>> >>> How can I do that? Should the files be in the same directory of ITK? >>> >>> Thanks. >>> >> >> Please see this page to get started: >> >> http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers >> >> Let us know if you have any questions. >> >> David >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: From abdul.sw84 at gmail.com Tue Oct 28 11:46:51 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Tue, 28 Oct 2014 16:46:51 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: It seems it is to do with the package. I got the CMakeLists.txt from the link I showed in my question. What would be a suitable CMakeLists.txt to use here? On Tue, Oct 28, 2014 at 4:44 PM, Abdul Abdul wrote: > I made a "src" and "bin" directories. When I configure using CMake, this > is what I get in "red": > > CMake Error at CMakeLists.txt:11 (find_package): > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > has asked CMake to find a package configuration file provided by > "ItkVtkGlue", but CMake did not find one. > > Could not find a package configuration file provided by "ItkVtkGlue" with > any of the following names: > > ItkVtkGlueConfig.cmake > itkvtkglue-config.cmake > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > "ItkVtkGlue" provides a separate development package or SDK, be sure it has > been installed. > > On Tue, Oct 28, 2014 at 4:37 PM, Abdul Abdul wrote: > >> David, >> >> Thanks for your reply. >> >> I went to the following steps: >> Windows >> >> 1. Open CMake >> 2. Select your CMakeLists.txt file >> 3. Select your build system >> 4. Click "Generate" >> >> But, it is not clear. I opened CMake, and selected CMakeLists.txt as the >> source file, and the directory where my main program is in as the "build" >> directory, but get the following error: >> >> >> ? >> >> >> >> >> On Tue, Oct 28, 2014 at 4:17 PM, David Doria >> wrote: >> >>> On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul >>> wrote: >>> >>>> Hi, >>>> >>>> I'm new to ITK. I have installed ITK, and want to run the example here: >>>> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>>> >>>> How can I do that? Should the files be in the same directory of ITK? >>>> >>>> Thanks. >>>> >>> >>> Please see this page to get started: >>> >>> http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers >>> >>> Let us know if you have any questions. >>> >>> David >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: From bill.lorensen at gmail.com Tue Oct 28 12:24:54 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 28 Oct 2014 12:24:54 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: That particular examples requires VTK. Have you built VTK also? On Tue, Oct 28, 2014 at 11:46 AM, Abdul Abdul wrote: > It seems it is to do with the package. I got the CMakeLists.txt from the > link I showed in my question. What would be a suitable CMakeLists.txt to > use here? > > On Tue, Oct 28, 2014 at 4:44 PM, Abdul Abdul wrote: > >> I made a "src" and "bin" directories. When I configure using CMake, this >> is what I get in "red": >> >> CMake Error at CMakeLists.txt:11 (find_package): >> By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project >> has asked CMake to find a package configuration file provided by >> "ItkVtkGlue", but CMake did not find one. >> >> Could not find a package configuration file provided by "ItkVtkGlue" with >> any of the following names: >> >> ItkVtkGlueConfig.cmake >> itkvtkglue-config.cmake >> >> Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set >> "ItkVtkGlue_DIR" to a directory containing one of the above files. If >> "ItkVtkGlue" provides a separate development package or SDK, be sure it >> has >> been installed. >> >> On Tue, Oct 28, 2014 at 4:37 PM, Abdul Abdul >> wrote: >> >>> David, >>> >>> Thanks for your reply. >>> >>> I went to the following steps: >>> Windows >>> >>> 1. Open CMake >>> 2. Select your CMakeLists.txt file >>> 3. Select your build system >>> 4. Click "Generate" >>> >>> But, it is not clear. I opened CMake, and selected CMakeLists.txt as the >>> source file, and the directory where my main program is in as the "build" >>> directory, but get the following error: >>> >>> >>> ? >>> >>> >>> >>> >>> On Tue, Oct 28, 2014 at 4:17 PM, David Doria >>> wrote: >>> >>>> On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> I'm new to ITK. I have installed ITK, and want to run the example >>>>> here: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>>>> >>>>> How can I do that? Should the files be in the same directory of ITK? >>>>> >>>>> Thanks. >>>>> >>>> >>>> Please see this page to get started: >>>> >>>> http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers >>>> >>>> Let us know if you have any questions. >>>> >>>> David >>>> >>> >>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Unpaid intern in BillsBasement at noware dot com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: From matt.mccormick at kitware.com Tue Oct 28 22:22:26 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 28 Oct 2014 22:22:26 -0400 Subject: [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday, 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/carevmgo0kpecsvrontn575i34g On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/c7hsglaqhvn0hdkkbmqki8bs580 For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From fabian.trobles at gmail.com Wed Oct 29 03:27:41 2014 From: fabian.trobles at gmail.com (Fabian Torres) Date: Wed, 29 Oct 2014 15:27:41 +0800 Subject: [ITK-users] Geodesic Active Countours Message-ID: Hi all. I have been trying to use the GeodesicActiveContourLevelSetImageFilter to extract the surface of an object in an image. I have managed to use this in 2D and works fine, my problem comes when I try to use it in 3D images. If I put the propagation, curvature and advection scaling in 0 I have an output from the geodesicActiveContourFilter pretty similar to the input image, but if I change the scaling factors even just a little I get an empty image as an output i.e. all pixels have the same value. typedef itk::GeodesicActiveContourLevelSetImageFilter GeodesicActiveContourFilterType; GeodesicActiveContourFilterType::Pointer geodesicActiveContour = GeodesicActiveContourFilterType::New(); geodesicActiveContour->SetPropagationScaling(0.1); geodesicActiveContour->SetCurvatureScaling(1.0); geodesicActiveContour->SetAdvectionScaling(0.1); geodesicActiveContour->SetIsoSurfaceValue(255); geodesicActiveContour->SetMaximumRMSError(0.02); geodesicActiveContour->SetNumberOfIterations(100); geodesicActiveContour->SetFeatureImage(surfaceFilter->GetOutput()); geodesicActiveContour->SetInput(segFilter->GetOutput()); geodesicActiveContour->Update(); The feature image comes from a surfaceFilter that is some preprocessing with a sobelEdgeDetectionImageFilter, the input data comes from the segFilter that gives an image with an segmentation of the object, where the object pixels have 255 value and the background has 0 value. but as I said if I put the scaling factor as 0 geodesicActiveContour->SetPropagationScaling(0.0); geodesicActiveContour->SetCurvatureScaling(0.0); geodesicActiveContour->SetAdvectionScaling(0.0); The output image does have different values around the object surface. Can any one help me with these? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Wed Oct 29 06:09:21 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 11:09:21 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: I will build VTK. But, the main issue is on the steps to follow to run an ITK program. Does that make sense? For instance, should I create "source" and "build" directories? When I run CMake, what should I do? ....etc Sorry I'm new to this. Thanks. On Tue, Oct 28, 2014 at 5:24 PM, Bill Lorensen wrote: > That particular examples requires VTK. Have you built VTK also? > > > On Tue, Oct 28, 2014 at 11:46 AM, Abdul Abdul > wrote: > >> It seems it is to do with the package. I got the CMakeLists.txt from the >> link I showed in my question. What would be a suitable CMakeLists.txt to >> use here? >> >> On Tue, Oct 28, 2014 at 4:44 PM, Abdul Abdul >> wrote: >> >>> I made a "src" and "bin" directories. When I configure using CMake, this >>> is what I get in "red": >>> >>> CMake Error at CMakeLists.txt:11 (find_package): >>> By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project >>> has asked CMake to find a package configuration file provided by >>> "ItkVtkGlue", but CMake did not find one. >>> >>> Could not find a package configuration file provided by "ItkVtkGlue" with >>> any of the following names: >>> >>> ItkVtkGlueConfig.cmake >>> itkvtkglue-config.cmake >>> >>> Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set >>> "ItkVtkGlue_DIR" to a directory containing one of the above files. If >>> "ItkVtkGlue" provides a separate development package or SDK, be sure it >>> has >>> been installed. >>> >>> On Tue, Oct 28, 2014 at 4:37 PM, Abdul Abdul >>> wrote: >>> >>>> David, >>>> >>>> Thanks for your reply. >>>> >>>> I went to the following steps: >>>> Windows >>>> >>>> 1. Open CMake >>>> 2. Select your CMakeLists.txt file >>>> 3. Select your build system >>>> 4. Click "Generate" >>>> >>>> But, it is not clear. I opened CMake, and selected CMakeLists.txt as >>>> the source file, and the directory where my main program is in as the >>>> "build" directory, but get the following error: >>>> >>>> >>>> ? >>>> >>>> >>>> >>>> >>>> On Tue, Oct 28, 2014 at 4:17 PM, David Doria >>>> wrote: >>>> >>>>> On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I'm new to ITK. I have installed ITK, and want to run the example >>>>>> here: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>>>>> >>>>>> How can I do that? Should the files be in the same directory of ITK? >>>>>> >>>>>> Thanks. >>>>>> >>>>> >>>>> Please see this page to get started: >>>>> >>>>> http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers >>>>> >>>>> Let us know if you have any questions. >>>>> >>>>> David >>>>> >>>> >>>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: From arnaudgelas at gmail.com Wed Oct 29 06:26:31 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 11:26:31 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 Message-ID: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Hi all, I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built with Qt5). Note I use cmake 2.8.12... I get link 1 error: ld library not found for -lQt5::Widgets Any idea how to fix it? Thanks, Arnaud From drescherjm at gmail.com Wed Oct 29 08:03:11 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 08:03:11 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Wed, Oct 29, 2014 at 6:09 AM, Abdul Abdul wrote: > I will build VTK. But, the main issue is on the steps to follow to run an > ITK program. Does that make sense? > > For instance, should I create "source" and "build" directories? > You do not create a source folder. This folder is where your source exists. You do create a build folder. I put the build folder in a completely different tree from the source tree but you can if you want make the build folder a subfolder of the source. > When I run CMake, what should I do? ....etc > Usually in cmake-gui its set the source folder and the build folder. Then Configure. You will be asked what generator to use (Visual Studio 12 2013 Win64 ...) After this you Generate. John -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Wed Oct 29 08:15:15 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 08:15:15 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Arnaud, I build ITK with itkVtkGlue fine on my Mac, but I build against the nightly VTK. I'm not sure if that makes a difference. Bill On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas wrote: > Hi all, > > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built with Qt5). Note I use cmake 2.8.12... > > I get link 1 error: > ld library not found for -lQt5::Widgets > > Any idea how to fix it? > > Thanks, > Arnaud > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -- Unpaid intern in BillsBasement at noware dot com From arnaudgelas at gmail.com Wed Oct 29 08:23:12 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 13:23:12 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, It seems builds fine as long as Qt5 is not involved in the process (?) I just wonder if there is not something missing in vtk's cmake installed files to help finding Qt5::Widgets (?), or if we could only use required libraries from vtk which should not depend on Qt5 (?) Thanks, Arnaud On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen wrote: > Arnaud, > > I build ITK with itkVtkGlue fine on my Mac, but I build against the > nightly VTK. I'm not sure if that makes a difference. > > Bill > > > On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > wrote: > > Hi all, > > > > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built > with Qt5). Note I use cmake 2.8.12... > > > > I get link 1 error: > > ld library not found for -lQt5::Widgets > > > > Any idea how to fix it? > > > > Thanks, > > Arnaud > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Wed Oct 29 08:32:46 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 08:32:46 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: I did not build against an installed VTK. On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas wrote: > Bill, > > It seems builds fine as long as Qt5 is not involved in the process (?) > > I just wonder if there is not something missing in vtk's cmake installed > files to help finding Qt5::Widgets (?), or if we could only use required > libraries from vtk which should not depend on Qt5 (?) > > Thanks, > Arnaud > > On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > wrote: >> >> Arnaud, >> >> I build ITK with itkVtkGlue fine on my Mac, but I build against the >> nightly VTK. I'm not sure if that makes a difference. >> >> Bill >> >> >> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> wrote: >> > Hi all, >> > >> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built >> > with Qt5). Note I use cmake 2.8.12... >> > >> > I get link 1 error: >> > ld library not found for -lQt5::Widgets >> > >> > Any idea how to fix it? >> > >> > Thanks, >> > Arnaud >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com > > -- Unpaid intern in BillsBasement at noware dot com From abdul.sw84 at gmail.com Wed Oct 29 09:56:47 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 14:56:47 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: I got the following error for CMakeLists.txt (attached): CMake Error at CMakeLists.txt:11 (find_package): By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ItkVtkGlue", but CMake did not find one. Could not find a package configuration file provided by "ItkVtkGlue" with any of the following names: ItkVtkGlueConfig.cmake itkvtkglue-config.cmake Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set "ItkVtkGlue_DIR" to a directory containing one of the above files. If "ItkVtkGlue" provides a separate development package or SDK, be sure it has been installed. Do you know why is that? Should I look for "ItkVtkGlue"? Thanks. On Wed, Oct 29, 2014 at 1:03 PM, John Drescher wrote: > > > On Wed, Oct 29, 2014 at 6:09 AM, Abdul Abdul wrote: > >> I will build VTK. But, the main issue is on the steps to follow to run an >> ITK program. Does that make sense? >> >> For instance, should I create "source" and "build" directories? >> > > You do not create a source folder. This folder is where your source > exists. You do create a build folder. I put the build folder in a > completely different tree from the source tree but you can if you want make > the build folder a subfolder of the source. > > >> When I run CMake, what should I do? ....etc >> > > > Usually in cmake-gui its set the source folder and the build folder. Then > Configure. You will be asked what generator to use (Visual Studio 12 2013 > Win64 ...) After this you Generate. > > John > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Wed Oct 29 09:58:23 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 14:58:23 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: Sorry, forgot to attach CMakeLists.txt On Wed, Oct 29, 2014 at 2:56 PM, Abdul Abdul wrote: > I got the following error for CMakeLists.txt (attached): > > CMake Error at CMakeLists.txt:11 (find_package): > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > has asked CMake to find a package configuration file provided by > "ItkVtkGlue", but CMake did not find one. > > Could not find a package configuration file provided by "ItkVtkGlue" with > any of the following names: > > ItkVtkGlueConfig.cmake > itkvtkglue-config.cmake > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > "ItkVtkGlue" provides a separate development package or SDK, be sure it has > been installed. > > Do you know why is that? Should I look for "ItkVtkGlue"? > > Thanks. > > On Wed, Oct 29, 2014 at 1:03 PM, John Drescher > wrote: > >> >> >> On Wed, Oct 29, 2014 at 6:09 AM, Abdul Abdul >> wrote: >> >>> I will build VTK. But, the main issue is on the steps to follow to run >>> an ITK program. Does that make sense? >>> >>> For instance, should I create "source" and "build" directories? >>> >> >> You do not create a source folder. This folder is where your source >> exists. You do create a build folder. I put the build folder in a >> completely different tree from the source tree but you can if you want make >> the build folder a subfolder of the source. >> >> >>> When I run CMake, what should I do? ....etc >>> >> >> >> Usually in cmake-gui its set the source folder and the build folder. Then >> Configure. You will be asked what generator to use (Visual Studio 12 2013 >> Win64 ...) After this you Generate. >> >> John >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- cmake_minimum_required(VERSION 2.8) project(readDisplayImageInfo) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED) find_package(VTK REQUIRED) include(${VTK_USE_FILE}) else() find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue) endif() add_executable(readDisplayImageInfo MACOSX_BUNDLE readDisplayImageInfo.cxx) target_link_libraries(readDisplayImageInfo ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES}) From abdul.sw84 at gmail.com Wed Oct 29 10:03:14 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 15:03:14 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: Sorry I'm really new to that. The example I'm trying to run is here: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader What would a basic CMakeLists.txt for this example be? Thanks. On Wed, Oct 29, 2014 at 3:00 PM, John Drescher wrote: > On Wed, Oct 29, 2014 at 9:56 AM, Abdul Abdul wrote: > > I got the following error for CMakeLists.txt (attached): > > > > CMake Error at CMakeLists.txt:11 (find_package): > > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > > has asked CMake to find a package configuration file provided by > > "ItkVtkGlue", but CMake did not find one. > > > > Could not find a package configuration file provided by "ItkVtkGlue" with > > any of the following names: > > > > ItkVtkGlueConfig.cmake > > itkvtkglue-config.cmake > > > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > > "ItkVtkGlue" provides a separate development package or SDK, be sure it > has > > been installed. > > > > Do you know why is that? Should I look for "ItkVtkGlue"? > > > > This is part of ITK4 (which you have to configure to use ItkVtkGlue) > or a separate package in older versions of ITK. > > John > -------------- next part -------------- An HTML attachment was scrubbed... URL: From drescherjm at gmail.com Wed Oct 29 10:07:38 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 10:07:38 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul wrote: > Sorry I'm really new to that. > > The example I'm trying to run is here: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > What would a basic CMakeLists.txt for this example be? > You have the correct CMakeLists.txt you do not have the correct dependent librarys installed. You need to understand how to build and install software with CMake. John From abdul.sw84 at gmail.com Wed Oct 29 10:10:05 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 15:10:05 +0100 Subject: [ITK-users] Where can I get ItKVtkGlue Message-ID: Hello, I'm trying to run this example: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader But, get the following when I "configure" in CMake: CMake Error at CMakeLists.txt:11 (find_package): By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ItkVtkGlue", but CMake did not find one. Could not find a package configuration file provided by "ItkVtkGlue" with any of the following names: ItkVtkGlueConfig.cmake itkvtkglue-config.cmake Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set "ItkVtkGlue_DIR" to a directory containing one of the above files. If "ItkVtkGlue" provides a separate development package or SDK, be sure it has been installed. It seems I need "ItkVtkGlue"? Where can I download it? And, what should I do to combine it with the program? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Wed Oct 29 10:10:50 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 15:10:50 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: I know how to use CMake already. But, seems something to do with the paths or libraries. On Wed, Oct 29, 2014 at 3:07 PM, John Drescher wrote: > On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul > wrote: > > Sorry I'm really new to that. > > > > The example I'm trying to run is here: > > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > > > What would a basic CMakeLists.txt for this example be? > > > > You have the correct CMakeLists.txt you do not have the correct > dependent librarys installed. You need to understand how to build and > install software with CMake. > > John > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Wed Oct 29 10:11:21 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 15:11:21 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: The question is thus, where to get those libraries? On Wed, Oct 29, 2014 at 3:10 PM, Abdul Abdul wrote: > I know how to use CMake already. But, seems something to do with the paths > or libraries. > > On Wed, Oct 29, 2014 at 3:07 PM, John Drescher > wrote: > >> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >> wrote: >> > Sorry I'm really new to that. >> > >> > The example I'm trying to run is here: >> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> > >> > What would a basic CMakeLists.txt for this example be? >> > >> >> You have the correct CMakeLists.txt you do not have the correct >> dependent librarys installed. You need to understand how to build and >> install software with CMake. >> >> John >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From drescherjm at gmail.com Wed Oct 29 10:17:42 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 10:17:42 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Wed, Oct 29, 2014 at 10:11 AM, Abdul Abdul wrote: > The question is thus, where to get those libraries? You need to build them with CMake. John From drescherjm at gmail.com Wed Oct 29 10:19:53 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 10:19:53 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Wed, Oct 29, 2014 at 10:17 AM, John Drescher wrote: > On Wed, Oct 29, 2014 at 10:11 AM, Abdul Abdul wrote: >> The question is thus, where to get those libraries? > > You need to build them with CMake. What I mean is when you build ITK from source you need to enable the ItkVtkGlue module using cmake. John From cr at neuro.ma.uni-heidelberg.de Wed Oct 29 10:15:17 2014 From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith) Date: Wed, 29 Oct 2014 15:15:17 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Did you build ITK with Module_ITKVtkGlue=ON? (c.f. http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) Christina On 29.10.2014 15:10, Abdul Abdul wrote: > I know how to use CMake already. But, seems something to do with the > paths or libraries. > > On Wed, Oct 29, 2014 at 3:07 PM, John Drescher > wrote: > > On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul > > wrote: > > Sorry I'm really new to that. > > > > The example I'm trying to run is here: > > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > > > What would a basic CMakeLists.txt for this example be? > > > > You have the correct CMakeLists.txt you do not have the correct > dependent librarys installed. You need to understand how to build and > install software with CMake. > > John > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Wed Oct 29 10:37:20 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 10:37:20 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Arnaud, I just tried an ITK build against an installed VTK and it built just fine. Bill On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen wrote: > I did not build against an installed VTK. > > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas wrote: >> Bill, >> >> It seems builds fine as long as Qt5 is not involved in the process (?) >> >> I just wonder if there is not something missing in vtk's cmake installed >> files to help finding Qt5::Widgets (?), or if we could only use required >> libraries from vtk which should not depend on Qt5 (?) >> >> Thanks, >> Arnaud >> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >> wrote: >>> >>> Arnaud, >>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >>> nightly VTK. I'm not sure if that makes a difference. >>> >>> Bill >>> >>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>> wrote: >>> > Hi all, >>> > >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built >>> > with Qt5). Note I use cmake 2.8.12... >>> > >>> > I get link 1 error: >>> > ld library not found for -lQt5::Widgets >>> > >>> > Any idea how to fix it? >>> > >>> > Thanks, >>> > Arnaud >>> > _____________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://www.kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >> >> > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com From arnaudgelas at gmail.com Wed Oct 29 10:48:46 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 15:48:46 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, I can also confirm everything builds fine if VTK is not compiled with Qt5 (which is part of my requirements...) On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen wrote: > Arnaud, > > I just tried an ITK build against an installed VTK and it built just fine. > > Bill > > > On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > wrote: > > I did not build against an installed VTK. > > > > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > wrote: > >> Bill, > >> > >> It seems builds fine as long as Qt5 is not involved in the process (?) > >> > >> I just wonder if there is not something missing in vtk's cmake installed > >> files to help finding Qt5::Widgets (?), or if we could only use required > >> libraries from vtk which should not depend on Qt5 (?) > >> > >> Thanks, > >> Arnaud > >> > >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > > >> wrote: > >>> > >>> Arnaud, > >>> > >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the > >>> nightly VTK. I'm not sure if that makes a difference. > >>> > >>> Bill > >>> > >>> > >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>> wrote: > >>> > Hi all, > >>> > > >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 > (built > >>> > with Qt5). Note I use cmake 2.8.12... > >>> > > >>> > I get link 1 error: > >>> > ld library not found for -lQt5::Widgets > >>> > > >>> > Any idea how to fix it? > >>> > > >>> > Thanks, > >>> > Arnaud > >>> > _____________________________________ > >>> > Powered by www.kitware.com > >>> > > >>> > Visit other Kitware open-source projects at > >>> > http://www.kitware.com/opensource/opensource.html > >>> > > >>> > Kitware offers ITK Training Courses, for more information visit: > >>> > http://www.kitware.com/products/protraining.php > >>> > > >>> > Please keep messages on-topic and check the ITK FAQ at: > >>> > http://www.itk.org/Wiki/ITK_FAQ > >>> > > >>> > Follow this link to subscribe/unsubscribe: > >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>> > >>> > >>> > >>> -- > >>> Unpaid intern in BillsBasement at noware dot com > >> > >> > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmasaunders123 at gmail.com Wed Oct 29 10:56:31 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Wed, 29 Oct 2014 14:56:31 +0000 Subject: [ITK-users] amount of smoothing ITK pyramid scheme Message-ID: Hello all, It is common to smooth images with a Gaussain with particular variance. I have read that the extent of smoothing should depend upon the amount of noise pattern in the images. It's also common to have higher smoothing values with higher shrink values. I am wondering how users first determine the amount of smoothing, do they make any actual measurements which represent the noise pattern in the images? Also is there a mechanism to determine how this level of noise varies dependent upon the shrink factor in a multi pyramid scheme? Thanks for any help Emma -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Wed Oct 29 11:01:57 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 11:01:57 -0400 Subject: [ITK-users] [ITK] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: I have qt enabled for my vtk build, but I am using qt4.7.4. On Wed, Oct 29, 2014 at 10:50 AM, Sam Raby wrote: > I thought Arnaud means that if Qt5 is enabled in VTK, then ITK compilation > with itkVtkGlue-enabled will fail. I had this issue about 3-4 month ago and > I was not able to resolve it. > > -S > > On Wed, Oct 29, 2014 at 9:37 AM, Bill Lorensen > wrote: >> >> Arnaud, >> >> I just tried an ITK build against an installed VTK and it built just fine. >> >> Bill >> >> >> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >> wrote: >> > I did not build against an installed VTK. >> > >> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >> > wrote: >> >> Bill, >> >> >> >> It seems builds fine as long as Qt5 is not involved in the process (?) >> >> >> >> I just wonder if there is not something missing in vtk's cmake >> >> installed >> >> files to help finding Qt5::Widgets (?), or if we could only use >> >> required >> >> libraries from vtk which should not depend on Qt5 (?) >> >> >> >> Thanks, >> >> Arnaud >> >> >> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >> >> >> >> wrote: >> >>> >> >>> Arnaud, >> >>> >> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >> >>> nightly VTK. I'm not sure if that makes a difference. >> >>> >> >>> Bill >> >>> >> >>> >> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> >>> wrote: >> >>> > Hi all, >> >>> > >> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 >> >>> > (built >> >>> > with Qt5). Note I use cmake 2.8.12... >> >>> > >> >>> > I get link 1 error: >> >>> > ld library not found for -lQt5::Widgets >> >>> > >> >>> > Any idea how to fix it? >> >>> > >> >>> > Thanks, >> >>> > Arnaud >> >>> > _____________________________________ >> >>> > Powered by www.kitware.com >> >>> > >> >>> > Visit other Kitware open-source projects at >> >>> > http://www.kitware.com/opensource/opensource.html >> >>> > >> >>> > Kitware offers ITK Training Courses, for more information visit: >> >>> > http://www.kitware.com/products/protraining.php >> >>> > >> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>> > >> >>> > Follow this link to subscribe/unsubscribe: >> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>> >> >>> >> >>> >> >>> -- >> >>> Unpaid intern in BillsBasement at noware dot com >> >> >> >> >> > >> > >> > >> > -- >> > Unpaid intern in BillsBasement at noware dot com >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community > > -- Unpaid intern in BillsBasement at noware dot com From chinander at gmail.com Wed Oct 29 11:03:26 2014 From: chinander at gmail.com (Mike Chinander) Date: Wed, 29 Oct 2014 10:03:26 -0500 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Can you share your CMakeLists.txt file? Are you using something like the following commands: ADD_EXECUTABLE(myexe ${MYSRCS}) TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} ${VTK_LIBRARIES}) On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas wrote: > Bill, > > I can also confirm everything builds fine if VTK is not compiled with Qt5 > (which is part of my requirements...) > > > > On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > wrote: > >> Arnaud, >> >> I just tried an ITK build against an installed VTK and it built just fine. >> >> Bill >> >> >> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >> wrote: >> > I did not build against an installed VTK. >> > >> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >> wrote: >> >> Bill, >> >> >> >> It seems builds fine as long as Qt5 is not involved in the process (?) >> >> >> >> I just wonder if there is not something missing in vtk's cmake >> installed >> >> files to help finding Qt5::Widgets (?), or if we could only use >> required >> >> libraries from vtk which should not depend on Qt5 (?) >> >> >> >> Thanks, >> >> Arnaud >> >> >> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen < >> bill.lorensen at gmail.com> >> >> wrote: >> >>> >> >>> Arnaud, >> >>> >> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >> >>> nightly VTK. I'm not sure if that makes a difference. >> >>> >> >>> Bill >> >>> >> >>> >> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> >>> wrote: >> >>> > Hi all, >> >>> > >> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 >> (built >> >>> > with Qt5). Note I use cmake 2.8.12... >> >>> > >> >>> > I get link 1 error: >> >>> > ld library not found for -lQt5::Widgets >> >>> > >> >>> > Any idea how to fix it? >> >>> > >> >>> > Thanks, >> >>> > Arnaud >> >>> > _____________________________________ >> >>> > Powered by www.kitware.com >> >>> > >> >>> > Visit other Kitware open-source projects at >> >>> > http://www.kitware.com/opensource/opensource.html >> >>> > >> >>> > Kitware offers ITK Training Courses, for more information visit: >> >>> > http://www.kitware.com/products/protraining.php >> >>> > >> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>> > >> >>> > Follow this link to subscribe/unsubscribe: >> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>> >> >>> >> >>> >> >>> -- >> >>> Unpaid intern in BillsBasement at noware dot com >> >> >> >> >> > >> > >> > >> > -- >> > Unpaid intern in BillsBasement at noware dot com >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Wed Oct 29 11:06:52 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 16:06:52 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: <5450F675.5010404@neuro.ma.uni-heidelberg.de> References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Message-ID: Yes, I now downloaded ItkVtkGlue, and configured and generated it using CMake. Now, when I try to configure the program mentioned, I get the following: CMake Error at CMakeLists.txt:12 (include): include could not find load file: C:/Users/Abdul/Desktop/itk I'm using the same CMakeLists.txt as in the example (attached). Do you know why I'm getting this error? Thanks. On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith < cr at neuro.ma.uni-heidelberg.de> wrote: > Did you build ITK with Module_ITKVtkGlue=ON? (c.f. > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) > > Christina > > > > On 29.10.2014 15:10, Abdul Abdul wrote: > > I know how to use CMake already. But, seems something to do with the paths > or libraries. > > On Wed, Oct 29, 2014 at 3:07 PM, John Drescher > wrote: > >> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >> wrote: >> > Sorry I'm really new to that. >> > >> > The example I'm trying to run is here: >> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> > >> > What would a basic CMakeLists.txt for this example be? >> > >> >> You have the correct CMakeLists.txt you do not have the correct >> dependent librarys installed. You need to understand how to build and >> install software with CMake. >> >> John >> > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at:http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe:http://public.kitware.com/mailman/listinfo/insight-users > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- cmake_minimum_required(VERSION 2.8) project(ImageFileReader) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED) find_package(VTK REQUIRED) include(${VTK_USE_FILE}) else() find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue) endif() add_executable(ImageFileReader MACOSX_BUNDLE ImageFileReader.cxx) target_link_libraries(ImageFileReader ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES}) From arnaudgelas at gmail.com Wed Oct 29 11:09:21 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 16:09:21 +0100 Subject: [ITK-users] [ITK] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, Until now, I have been using Qt4; and I can confirm it was working fine! It seems that Qt5 paths are not propagated in exported vtk cmake folder!? I see 2 ways of fixing it: * fixing exported cmake files in VTK to write proper information. Although I am not sure what needs to be exported? * reduce the libraries contained in VTK_LIBRARIES to the minimum set for ITKVtkGlue and hope there is no propagated link to Qt5 (actually I don't see why there should be) ? What do you think? Thanks, Arnaud On Wed, Oct 29, 2014 at 4:01 PM, Bill Lorensen wrote: > I have qt enabled for my vtk build, but I am using qt4.7.4. > > > On Wed, Oct 29, 2014 at 10:50 AM, Sam Raby wrote: > > I thought Arnaud means that if Qt5 is enabled in VTK, then ITK > compilation > > with itkVtkGlue-enabled will fail. I had this issue about 3-4 month ago > and > > I was not able to resolve it. > > > > -S > > > > On Wed, Oct 29, 2014 at 9:37 AM, Bill Lorensen > > wrote: > >> > >> Arnaud, > >> > >> I just tried an ITK build against an installed VTK and it built just > fine. > >> > >> Bill > >> > >> > >> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > > >> wrote: > >> > I did not build against an installed VTK. > >> > > >> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >> > wrote: > >> >> Bill, > >> >> > >> >> It seems builds fine as long as Qt5 is not involved in the process > (?) > >> >> > >> >> I just wonder if there is not something missing in vtk's cmake > >> >> installed > >> >> files to help finding Qt5::Widgets (?), or if we could only use > >> >> required > >> >> libraries from vtk which should not depend on Qt5 (?) > >> >> > >> >> Thanks, > >> >> Arnaud > >> >> > >> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >> >> > >> >> wrote: > >> >>> > >> >>> Arnaud, > >> >>> > >> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the > >> >>> nightly VTK. I'm not sure if that makes a difference. > >> >>> > >> >>> Bill > >> >>> > >> >>> > >> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >> >>> wrote: > >> >>> > Hi all, > >> >>> > > >> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 > >> >>> > (built > >> >>> > with Qt5). Note I use cmake 2.8.12... > >> >>> > > >> >>> > I get link 1 error: > >> >>> > ld library not found for -lQt5::Widgets > >> >>> > > >> >>> > Any idea how to fix it? > >> >>> > > >> >>> > Thanks, > >> >>> > Arnaud > >> >>> > _____________________________________ > >> >>> > Powered by www.kitware.com > >> >>> > > >> >>> > Visit other Kitware open-source projects at > >> >>> > http://www.kitware.com/opensource/opensource.html > >> >>> > > >> >>> > Kitware offers ITK Training Courses, for more information visit: > >> >>> > http://www.kitware.com/products/protraining.php > >> >>> > > >> >>> > Please keep messages on-topic and check the ITK FAQ at: > >> >>> > http://www.itk.org/Wiki/ITK_FAQ > >> >>> > > >> >>> > Follow this link to subscribe/unsubscribe: > >> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >> >>> > >> >>> > >> >>> > >> >>> -- > >> >>> Unpaid intern in BillsBasement at noware dot com > >> >> > >> >> > >> > > >> > > >> > > >> > -- > >> > Unpaid intern in BillsBasement at noware dot com > >> > >> > >> > >> -- > >> Unpaid intern in BillsBasement at noware dot com > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-users > >> _______________________________________________ > >> Community mailing list > >> Community at itk.org > >> http://public.kitware.com/mailman/listinfo/community > > > > > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Wed Oct 29 11:10:35 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 16:10:35 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Message-ID: Those are the settings I'm having: ? On Wed, Oct 29, 2014 at 4:06 PM, Abdul Abdul wrote: > Yes, I now downloaded ItkVtkGlue, and configured and generated it using > CMake. > > Now, when I try to configure the program mentioned, I get the following: > > CMake Error at CMakeLists.txt:12 (include): > include could not find load file: > > C:/Users/Abdul/Desktop/itk > > I'm using the same CMakeLists.txt as in the example (attached). > > Do you know why I'm getting this error? > > Thanks. > > On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith < > cr at neuro.ma.uni-heidelberg.de> wrote: > >> Did you build ITK with Module_ITKVtkGlue=ON? (c.f. >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) >> >> Christina >> >> >> >> On 29.10.2014 15:10, Abdul Abdul wrote: >> >> I know how to use CMake already. But, seems something to do with the >> paths or libraries. >> >> On Wed, Oct 29, 2014 at 3:07 PM, John Drescher >> wrote: >> >>> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >>> wrote: >>> > Sorry I'm really new to that. >>> > >>> > The example I'm trying to run is here: >>> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>> > >>> > What would a basic CMakeLists.txt for this example be? >>> > >>> >>> You have the correct CMakeLists.txt you do not have the correct >>> dependent librarys installed. You need to understand how to build and >>> install software with CMake. >>> >>> John >>> >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at:http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe:http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 21131 bytes Desc: not available URL: From arnaudgelas at gmail.com Wed Oct 29 11:11:58 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 16:11:58 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Mike, It is difficult to refer to one single CMakeLists.txt, since it is tied up to ITK's modularization. But here are the files to look at: https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake Best Arnaud On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander wrote: > Can you share your CMakeLists.txt file? Are you using something like the > following commands: > > ADD_EXECUTABLE(myexe ${MYSRCS}) > TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} ${VTK_LIBRARIES}) > > On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas > wrote: > >> Bill, >> >> I can also confirm everything builds fine if VTK is not compiled with Qt5 >> (which is part of my requirements...) >> >> >> >> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >> wrote: >> >>> Arnaud, >>> >>> I just tried an ITK build against an installed VTK and it built just >>> fine. >>> >>> Bill >>> >>> >>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>> wrote: >>> > I did not build against an installed VTK. >>> > >>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>> wrote: >>> >> Bill, >>> >> >>> >> It seems builds fine as long as Qt5 is not involved in the process (?) >>> >> >>> >> I just wonder if there is not something missing in vtk's cmake >>> installed >>> >> files to help finding Qt5::Widgets (?), or if we could only use >>> required >>> >> libraries from vtk which should not depend on Qt5 (?) >>> >> >>> >> Thanks, >>> >> Arnaud >>> >> >>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen < >>> bill.lorensen at gmail.com> >>> >> wrote: >>> >>> >>> >>> Arnaud, >>> >>> >>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >>> >>> nightly VTK. I'm not sure if that makes a difference. >>> >>> >>> >>> Bill >>> >>> >>> >>> >>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> > >>> >>> wrote: >>> >>> > Hi all, >>> >>> > >>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 >>> (built >>> >>> > with Qt5). Note I use cmake 2.8.12... >>> >>> > >>> >>> > I get link 1 error: >>> >>> > ld library not found for -lQt5::Widgets >>> >>> > >>> >>> > Any idea how to fix it? >>> >>> > >>> >>> > Thanks, >>> >>> > Arnaud >>> >>> > _____________________________________ >>> >>> > Powered by www.kitware.com >>> >>> > >>> >>> > Visit other Kitware open-source projects at >>> >>> > http://www.kitware.com/opensource/opensource.html >>> >>> > >>> >>> > Kitware offers ITK Training Courses, for more information visit: >>> >>> > http://www.kitware.com/products/protraining.php >>> >>> > >>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>> >>> > >>> >>> > Follow this link to subscribe/unsubscribe: >>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> Unpaid intern in BillsBasement at noware dot com >>> >> >>> >> >>> > >>> > >>> > >>> > -- >>> > Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Wed Oct 29 11:12:25 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 11:12:25 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Message-ID: Try building your ITK with Module_ITKVtkGlue=ON It has been a while since I checked building against a separately downloaded ItkVtkGlue. It is possible that it no longer works. Bill On Wed, Oct 29, 2014 at 11:06 AM, Abdul Abdul wrote: > Yes, I now downloaded ItkVtkGlue, and configured and generated it using > CMake. > > Now, when I try to configure the program mentioned, I get the following: > > CMake Error at CMakeLists.txt:12 (include): > include could not find load file: > > C:/Users/Abdul/Desktop/itk > > I'm using the same CMakeLists.txt as in the example (attached). > > Do you know why I'm getting this error? > > Thanks. > > On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith > wrote: >> >> Did you build ITK with Module_ITKVtkGlue=ON? (c.f. >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) >> >> Christina >> >> >> >> On 29.10.2014 15:10, Abdul Abdul wrote: >> >> I know how to use CMake already. But, seems something to do with the paths >> or libraries. >> >> On Wed, Oct 29, 2014 at 3:07 PM, John Drescher >> wrote: >>> >>> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >>> wrote: >>> > Sorry I'm really new to that. >>> > >>> > The example I'm trying to run is here: >>> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>> > >>> > What would a basic CMakeLists.txt for this example be? >>> > >>> >>> You have the correct CMakeLists.txt you do not have the correct >>> dependent librarys installed. You need to understand how to build and >>> install software with CMake. >>> >>> John >> >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com From cr at neuro.ma.uni-heidelberg.de Wed Oct 29 11:13:47 2014 From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith) Date: Wed, 29 Oct 2014 16:13:47 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Message-ID: <5451042B.9060102@neuro.ma.uni-heidelberg.de> On 29.10.2014 16:10, Abdul Abdul wrote: > Those are the settings I'm having: > > Probably I need new glasses but I can't read anything. Toggle to advanced settings and look for Module_ITKVtkGlue and make sure it is set to On - no need to download additional software - it is all there already. Christina > ? > > On Wed, Oct 29, 2014 at 4:06 PM, Abdul Abdul > wrote: > > Yes, I now downloaded ItkVtkGlue, and configured and generated it > using CMake. > > Now, when I try to configure the program mentioned, I get the > following: > > CMake Error at CMakeLists.txt:12 (include): > include could not find load file: > > C:/Users/Abdul/Desktop/itk > > I'm using the same CMakeLists.txt as in the example (attached). > > Do you know why I'm getting this error? > > Thanks. > > On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith > > wrote: > > Did you build ITK with Module_ITKVtkGlue=ON? (c.f. > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) > > Christina > > > > On 29.10.2014 15:10, Abdul Abdul wrote: >> I know how to use CMake already. But, seems something to do >> with the paths or libraries. >> >> On Wed, Oct 29, 2014 at 3:07 PM, John Drescher >> > wrote: >> >> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >> > wrote: >> > Sorry I'm really new to that. >> > >> > The example I'm trying to run is here: >> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> > >> > What would a basic CMakeLists.txt for this example be? >> > >> >> You have the correct CMakeLists.txt you do not have the >> correct >> dependent librarys installed. You need to understand how >> to build and >> install software with CMake. >> >> John >> >> >> >> >> _____________________________________ >> Powered bywww.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 21131 bytes Desc: not available URL: From abdul.sw84 at gmail.com Wed Oct 29 11:26:52 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 16:26:52 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: <5451042B.9060102@neuro.ma.uni-heidelberg.de> References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: Sorry for the small image. I attach it here. For the "advanced settings", I couldn't find such option in CMake. Should I be looking for that somewhere else? Thanks. On Wed, Oct 29, 2014 at 4:13 PM, Chr. Rossmanith < cr at neuro.ma.uni-heidelberg.de> wrote: > On 29.10.2014 16:10, Abdul Abdul wrote: > > Those are the settings I'm having: > > > Probably I need new glasses but I can't read anything. > > Toggle to advanced settings and look for Module_ITKVtkGlue and make sure > it is set to On - no need to download additional software - it is all there > already. > > Christina > > ? > > On Wed, Oct 29, 2014 at 4:06 PM, Abdul Abdul wrote: > >> Yes, I now downloaded ItkVtkGlue, and configured and generated it using >> CMake. >> >> Now, when I try to configure the program mentioned, I get the following: >> >> CMake Error at CMakeLists.txt:12 (include): >> include could not find load file: >> >> C:/Users/Abdul/Desktop/itk >> >> I'm using the same CMakeLists.txt as in the example (attached). >> >> Do you know why I'm getting this error? >> >> Thanks. >> >> On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith < >> cr at neuro.ma.uni-heidelberg.de> wrote: >> >>> Did you build ITK with Module_ITKVtkGlue=ON? (c.f. >>> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) >>> >>> Christina >>> >>> >>> >>> On 29.10.2014 15:10, Abdul Abdul wrote: >>> >>> I know how to use CMake already. But, seems something to do with the >>> paths or libraries. >>> >>> On Wed, Oct 29, 2014 at 3:07 PM, John Drescher >>> wrote: >>> >>>> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >>>> wrote: >>>> > Sorry I'm really new to that. >>>> > >>>> > The example I'm trying to run is here: >>>> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>>> > >>>> > What would a basic CMakeLists.txt for this example be? >>>> > >>>> >>>> You have the correct CMakeLists.txt you do not have the correct >>>> dependent librarys installed. You need to understand how to build and >>>> install software with CMake. >>>> >>>> John >>>> >>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at:http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe:http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 21131 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 21131 bytes Desc: not available URL: From drescherjm at gmail.com Wed Oct 29 11:29:21 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 11:29:21 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Wed, Oct 29, 2014 at 11:26 AM, Abdul Abdul wrote: > Sorry for the small image. I attach it here. > > For the "advanced settings", I couldn't find such option in CMake. Should > I be looking for that somewhere else? > > Thanks. > > Is this a picture of you configuring ITK or the example. We are all telling you to configure and build ITK before you move on to the example. John -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Oct 29 11:29:44 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Oct 2014 11:29:44 -0400 Subject: [ITK-users] Where can I get ItKVtkGlue In-Reply-To: References: Message-ID: Hi Abdul, ITKVtkGlue used to be a separate project, but it is now integrated into ITK as the module ITKVtkGlue. You can enable in your ITK CMake configuration by setting Module_ITKVtkGlue to ON. It requires a build of VTK. Hope this helps, Matt On Wed, Oct 29, 2014 at 10:10 AM, Abdul Abdul wrote: > Hello, > > I'm trying to run this example: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > But, get the following when I "configure" in CMake: > > CMake Error at CMakeLists.txt:11 (find_package): > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > has asked CMake to find a package configuration file provided by > "ItkVtkGlue", but CMake did not find one. > > Could not find a package configuration file provided by "ItkVtkGlue" with > any of the following names: > > ItkVtkGlueConfig.cmake > itkvtkglue-config.cmake > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > "ItkVtkGlue" provides a separate development package or SDK, be sure it has > been installed. > > It seems I need "ItkVtkGlue"? Where can I download it? And, what should I do > to combine it with the program? > > Thanks. > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From bill.lorensen at gmail.com Wed Oct 29 11:31:42 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 11:31:42 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Arnaud, Can you try to build one of the ITK wiki examples against your installed VTK? This might help narrow down the problem. Whether it is a VTK of ITK issue. http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow Bill On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas wrote: > Mike, > > It is difficult to refer to one single CMakeLists.txt, since it is tied up > to ITK's modularization. > > But here are the files to look at: > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > > Best > Arnaud > > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander wrote: >> >> Can you share your CMakeLists.txt file? Are you using something like the >> following commands: >> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >> ${VTK_LIBRARIES}) >> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >> wrote: >>> >>> Bill, >>> >>> I can also confirm everything builds fine if VTK is not compiled with Qt5 >>> (which is part of my requirements...) >>> >>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>> wrote: >>>> >>>> Arnaud, >>>> >>>> I just tried an ITK build against an installed VTK and it built just >>>> fine. >>>> >>>> Bill >>>> >>>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>>> wrote: >>>> > I did not build against an installed VTK. >>>> > >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>>> > wrote: >>>> >> Bill, >>>> >> >>>> >> It seems builds fine as long as Qt5 is not involved in the process >>>> >> (?) >>>> >> >>>> >> I just wonder if there is not something missing in vtk's cmake >>>> >> installed >>>> >> files to help finding Qt5::Widgets (?), or if we could only use >>>> >> required >>>> >> libraries from vtk which should not depend on Qt5 (?) >>>> >> >>>> >> Thanks, >>>> >> Arnaud >>>> >> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>>> >> >>>> >> wrote: >>>> >>> >>>> >>> Arnaud, >>>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>>> >>> >>>> >>> Bill >>>> >>> >>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>>> >>> >>>> >>> wrote: >>>> >>> > Hi all, >>>> >>> > >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 >>>> >>> > (built >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>>> >>> > >>>> >>> > I get link 1 error: >>>> >>> > ld library not found for -lQt5::Widgets >>>> >>> > >>>> >>> > Any idea how to fix it? >>>> >>> > >>>> >>> > Thanks, >>>> >>> > Arnaud >>>> >>> > _____________________________________ >>>> >>> > Powered by www.kitware.com >>>> >>> > >>>> >>> > Visit other Kitware open-source projects at >>>> >>> > http://www.kitware.com/opensource/opensource.html >>>> >>> > >>>> >>> > Kitware offers ITK Training Courses, for more information visit: >>>> >>> > http://www.kitware.com/products/protraining.php >>>> >>> > >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>>> >>> > >>>> >>> > Follow this link to subscribe/unsubscribe: >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> Unpaid intern in BillsBasement at noware dot com >>>> >> >>>> >> >>>> > >>>> > >>>> > >>>> > -- >>>> > Unpaid intern in BillsBasement at noware dot com >>>> >>>> >>>> >>>> -- >>>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com From abdul.sw84 at gmail.com Wed Oct 29 11:31:45 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 16:31:45 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: ITK is already being built. The picture is for the example. On Wed, Oct 29, 2014 at 4:29 PM, John Drescher wrote: > > > On Wed, Oct 29, 2014 at 11:26 AM, Abdul Abdul > wrote: > >> Sorry for the small image. I attach it here. >> >> For the "advanced settings", I couldn't find such option in CMake. Should >> I be looking for that somewhere else? >> >> Thanks. >> >> > Is this a picture of you configuring ITK or the example. We are all > telling you to configure and build ITK before you move on to the example. > > John > -------------- next part -------------- An HTML attachment was scrubbed... URL: From drescherjm at gmail.com Wed Oct 29 11:33:51 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 11:33:51 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Wed, Oct 29, 2014 at 11:31 AM, Abdul Abdul wrote: > ITK is already being built. The picture is for the example. Then go back and build ITK. While you configure ITK4 make sure you enable the itkvtkglue module. You do not get this by default or in a binary download. This also requires that you have or build VTK. if this is on windows I highly recommend that you build all of these from source. John From arnaudgelas at gmail.com Wed Oct 29 11:46:13 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 16:46:13 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, Same link error with this example... On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen wrote: > Arnaud, > > Can you try to build one of the ITK wiki examples against your > installed VTK? This might help narrow down the problem. Whether it is > a VTK of ITK issue. > http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > > Bill > > On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > wrote: > > Mike, > > > > It is difficult to refer to one single CMakeLists.txt, since it is tied > up > > to ITK's modularization. > > > > But here are the files to look at: > > > > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > > > > Best > > Arnaud > > > > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > wrote: > >> > >> Can you share your CMakeLists.txt file? Are you using something like the > >> following commands: > >> > >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >> ${VTK_LIBRARIES}) > >> > >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas > >> wrote: > >>> > >>> Bill, > >>> > >>> I can also confirm everything builds fine if VTK is not compiled with > Qt5 > >>> (which is part of my requirements...) > >>> > >>> > >>> > >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen < > bill.lorensen at gmail.com> > >>> wrote: > >>>> > >>>> Arnaud, > >>>> > >>>> I just tried an ITK build against an installed VTK and it built just > >>>> fine. > >>>> > >>>> Bill > >>>> > >>>> > >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen < > bill.lorensen at gmail.com> > >>>> wrote: > >>>> > I did not build against an installed VTK. > >>>> > > >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >>>> > wrote: > >>>> >> Bill, > >>>> >> > >>>> >> It seems builds fine as long as Qt5 is not involved in the process > >>>> >> (?) > >>>> >> > >>>> >> I just wonder if there is not something missing in vtk's cmake > >>>> >> installed > >>>> >> files to help finding Qt5::Widgets (?), or if we could only use > >>>> >> required > >>>> >> libraries from vtk which should not depend on Qt5 (?) > >>>> >> > >>>> >> Thanks, > >>>> >> Arnaud > >>>> >> > >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >>>> >> > >>>> >> wrote: > >>>> >>> > >>>> >>> Arnaud, > >>>> >>> > >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against > the > >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >>>> >>> > >>>> >>> Bill > >>>> >>> > >>>> >>> > >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>>> >>> > >>>> >>> wrote: > >>>> >>> > Hi all, > >>>> >>> > > >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 > >>>> >>> > (built > >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >>>> >>> > > >>>> >>> > I get link 1 error: > >>>> >>> > ld library not found for -lQt5::Widgets > >>>> >>> > > >>>> >>> > Any idea how to fix it? > >>>> >>> > > >>>> >>> > Thanks, > >>>> >>> > Arnaud > >>>> >>> > _____________________________________ > >>>> >>> > Powered by www.kitware.com > >>>> >>> > > >>>> >>> > Visit other Kitware open-source projects at > >>>> >>> > http://www.kitware.com/opensource/opensource.html > >>>> >>> > > >>>> >>> > Kitware offers ITK Training Courses, for more information visit: > >>>> >>> > http://www.kitware.com/products/protraining.php > >>>> >>> > > >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: > >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >>>> >>> > > >>>> >>> > Follow this link to subscribe/unsubscribe: > >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>>> >>> > >>>> >>> > >>>> >>> > >>>> >>> -- > >>>> >>> Unpaid intern in BillsBasement at noware dot com > >>>> >> > >>>> >> > >>>> > > >>>> > > >>>> > > >>>> > -- > >>>> > Unpaid intern in BillsBasement at noware dot com > >>>> > >>>> > >>>> > >>>> -- > >>>> Unpaid intern in BillsBasement at noware dot com > >>> > >>> > >>> > >>> _____________________________________ > >>> Powered by www.kitware.com > >>> > >>> Visit other Kitware open-source projects at > >>> http://www.kitware.com/opensource/opensource.html > >>> > >>> Kitware offers ITK Training Courses, for more information visit: > >>> http://www.kitware.com/products/protraining.php > >>> > >>> Please keep messages on-topic and check the ITK FAQ at: > >>> http://www.itk.org/Wiki/ITK_FAQ > >>> > >>> Follow this link to subscribe/unsubscribe: > >>> http://public.kitware.com/mailman/listinfo/insight-users > >>> > >> > >> > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-users > >> > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Wed Oct 29 11:50:25 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 11:50:25 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Great. That means it is a VTK issue. I'm downloading qt5 on my fedora system. I'll see if I can reproduce there. On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas wrote: > Bill, > > Same link error with this example... > > > On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > wrote: >> >> Arnaud, >> >> Can you try to build one of the ITK wiki examples against your >> installed VTK? This might help narrow down the problem. Whether it is >> a VTK of ITK issue. >> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >> >> Bill >> >> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >> wrote: >> > Mike, >> > >> > It is difficult to refer to one single CMakeLists.txt, since it is tied >> > up >> > to ITK's modularization. >> > >> > But here are the files to look at: >> > >> > >> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >> > >> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >> > >> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >> > >> > Best >> > Arnaud >> > >> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >> > wrote: >> >> >> >> Can you share your CMakeLists.txt file? Are you using something like >> >> the >> >> following commands: >> >> >> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >> >> ${VTK_LIBRARIES}) >> >> >> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >> >> wrote: >> >>> >> >>> Bill, >> >>> >> >>> I can also confirm everything builds fine if VTK is not compiled with >> >>> Qt5 >> >>> (which is part of my requirements...) >> >>> >> >>> >> >>> >> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >> >>> >> >>> wrote: >> >>>> >> >>>> Arnaud, >> >>>> >> >>>> I just tried an ITK build against an installed VTK and it built just >> >>>> fine. >> >>>> >> >>>> Bill >> >>>> >> >>>> >> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >> >>>> >> >>>> wrote: >> >>>> > I did not build against an installed VTK. >> >>>> > >> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >> >>>> > >> >>>> > wrote: >> >>>> >> Bill, >> >>>> >> >> >>>> >> It seems builds fine as long as Qt5 is not involved in the process >> >>>> >> (?) >> >>>> >> >> >>>> >> I just wonder if there is not something missing in vtk's cmake >> >>>> >> installed >> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use >> >>>> >> required >> >>>> >> libraries from vtk which should not depend on Qt5 (?) >> >>>> >> >> >>>> >> Thanks, >> >>>> >> Arnaud >> >>>> >> >> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >> >>>> >> >> >>>> >> wrote: >> >>>> >>> >> >>>> >>> Arnaud, >> >>>> >>> >> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against >> >>>> >>> the >> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >> >>>> >>> >> >>>> >>> Bill >> >>>> >>> >> >>>> >>> >> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> >>>> >>> >> >>>> >>> wrote: >> >>>> >>> > Hi all, >> >>>> >>> > >> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >> >>>> >>> > 6.1.0 >> >>>> >>> > (built >> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >> >>>> >>> > >> >>>> >>> > I get link 1 error: >> >>>> >>> > ld library not found for -lQt5::Widgets >> >>>> >>> > >> >>>> >>> > Any idea how to fix it? >> >>>> >>> > >> >>>> >>> > Thanks, >> >>>> >>> > Arnaud >> >>>> >>> > _____________________________________ >> >>>> >>> > Powered by www.kitware.com >> >>>> >>> > >> >>>> >>> > Visit other Kitware open-source projects at >> >>>> >>> > http://www.kitware.com/opensource/opensource.html >> >>>> >>> > >> >>>> >>> > Kitware offers ITK Training Courses, for more information >> >>>> >>> > visit: >> >>>> >>> > http://www.kitware.com/products/protraining.php >> >>>> >>> > >> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>>> >>> > >> >>>> >>> > Follow this link to subscribe/unsubscribe: >> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>>> >>> >> >>>> >>> >> >>>> >>> >> >>>> >>> -- >> >>>> >>> Unpaid intern in BillsBasement at noware dot com >> >>>> >> >> >>>> >> >> >>>> > >> >>>> > >> >>>> > >> >>>> > -- >> >>>> > Unpaid intern in BillsBasement at noware dot com >> >>>> >> >>>> >> >>>> >> >>>> -- >> >>>> Unpaid intern in BillsBasement at noware dot com >> >>> >> >>> >> >>> >> >>> _____________________________________ >> >>> Powered by www.kitware.com >> >>> >> >>> Visit other Kitware open-source projects at >> >>> http://www.kitware.com/opensource/opensource.html >> >>> >> >>> Kitware offers ITK Training Courses, for more information visit: >> >>> http://www.kitware.com/products/protraining.php >> >>> >> >>> Please keep messages on-topic and check the ITK FAQ at: >> >>> http://www.itk.org/Wiki/ITK_FAQ >> >>> >> >>> Follow this link to subscribe/unsubscribe: >> >>> http://public.kitware.com/mailman/listinfo/insight-users >> >>> >> >> >> >> >> >> _____________________________________ >> >> Powered by www.kitware.com >> >> >> >> Visit other Kitware open-source projects at >> >> http://www.kitware.com/opensource/opensource.html >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >> http://www.kitware.com/products/protraining.php >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >> http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> Follow this link to subscribe/unsubscribe: >> >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> > >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com > > -- Unpaid intern in BillsBasement at noware dot com From bill.lorensen at gmail.com Wed Oct 29 12:13:34 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 12:13:34 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Built the arrow example against an installed ITK with Qt5 on fedora. Arnaud, Can you provide the link.txt file in the Arrow bin tree? Bill On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen wrote: > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora > system. I'll see if I can reproduce there. > > > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas wrote: >> Bill, >> >> Same link error with this example... >> >> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen >> wrote: >>> >>> Arnaud, >>> >>> Can you try to build one of the ITK wiki examples against your >>> installed VTK? This might help narrow down the problem. Whether it is >>> a VTK of ITK issue. >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >>> >>> Bill >>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >>> wrote: >>> > Mike, >>> > >>> > It is difficult to refer to one single CMakeLists.txt, since it is tied >>> > up >>> > to ITK's modularization. >>> > >>> > But here are the files to look at: >>> > >>> > >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >>> > >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >>> > >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >>> > >>> > Best >>> > Arnaud >>> > >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >>> > wrote: >>> >> >>> >> Can you share your CMakeLists.txt file? Are you using something like >>> >> the >>> >> following commands: >>> >> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >>> >> ${VTK_LIBRARIES}) >>> >> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >>> >> wrote: >>> >>> >>> >>> Bill, >>> >>> >>> >>> I can also confirm everything builds fine if VTK is not compiled with >>> >>> Qt5 >>> >>> (which is part of my requirements...) >>> >>> >>> >>> >>> >>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>> >>> >>> >>> wrote: >>> >>>> >>> >>>> Arnaud, >>> >>>> >>> >>>> I just tried an ITK build against an installed VTK and it built just >>> >>>> fine. >>> >>>> >>> >>>> Bill >>> >>>> >>> >>>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>> >>>> >>> >>>> wrote: >>> >>>> > I did not build against an installed VTK. >>> >>>> > >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>> >>>> > >>> >>>> > wrote: >>> >>>> >> Bill, >>> >>>> >> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the process >>> >>>> >> (?) >>> >>>> >> >>> >>>> >> I just wonder if there is not something missing in vtk's cmake >>> >>>> >> installed >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use >>> >>>> >> required >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >>> >>>> >> >>> >>>> >> Thanks, >>> >>>> >> Arnaud >>> >>>> >> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>> >>>> >> >>> >>>> >> wrote: >>> >>>> >>> >>> >>>> >>> Arnaud, >>> >>>> >>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against >>> >>>> >>> the >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>> >>>> >>> >>> >>>> >>> Bill >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>> >>>> >>> >>> >>>> >>> wrote: >>> >>>> >>> > Hi all, >>> >>>> >>> > >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >>> >>>> >>> > 6.1.0 >>> >>>> >>> > (built >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>> >>>> >>> > >>> >>>> >>> > I get link 1 error: >>> >>>> >>> > ld library not found for -lQt5::Widgets >>> >>>> >>> > >>> >>>> >>> > Any idea how to fix it? >>> >>>> >>> > >>> >>>> >>> > Thanks, >>> >>>> >>> > Arnaud >>> >>>> >>> > _____________________________________ >>> >>>> >>> > Powered by www.kitware.com >>> >>>> >>> > >>> >>>> >>> > Visit other Kitware open-source projects at >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >>> >>>> >>> > >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >>> >>>> >>> > visit: >>> >>>> >>> > http://www.kitware.com/products/protraining.php >>> >>>> >>> > >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>> >>>> >>> > >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> -- >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >>> >>>> >> >>> >>>> >> >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> > -- >>> >>>> > Unpaid intern in BillsBasement at noware dot com >>> >>>> >>> >>>> >>> >>>> >>> >>>> -- >>> >>>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> >>> >>> >>> >>> _____________________________________ >>> >>> Powered by www.kitware.com >>> >>> >>> >>> Visit other Kitware open-source projects at >>> >>> http://www.kitware.com/opensource/opensource.html >>> >>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> >>> http://www.kitware.com/products/protraining.php >>> >>> >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> >>> >>> Follow this link to subscribe/unsubscribe: >>> >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >> >>> >> >>> >> _____________________________________ >>> >> Powered by www.kitware.com >>> >> >>> >> Visit other Kitware open-source projects at >>> >> http://www.kitware.com/opensource/opensource.html >>> >> >>> >> Kitware offers ITK Training Courses, for more information visit: >>> >> http://www.kitware.com/products/protraining.php >>> >> >>> >> Please keep messages on-topic and check the ITK FAQ at: >>> >> http://www.itk.org/Wiki/ITK_FAQ >>> >> >>> >> Follow this link to subscribe/unsubscribe: >>> >> http://public.kitware.com/mailman/listinfo/insight-users >>> >> >>> > >>> > >>> > _____________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://www.kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> > >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >> >> > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com From arnaudgelas at gmail.com Wed Oct 29 12:18:00 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 17:18:00 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Thank you very much for looking into it! I am also digging on my side. It seems to me that the problems come from ${vtk-module}_EXPORT_CODE_INSTALL which is not exported into corresponding installed ${vtk-module} cmake file. Normally this cmake variable should contain "find_package( Qt5Widgets QUIET)" given the path corresponding dir. But it seems it is not present in the install tree for all module dependent on Qt5... On Wed, Oct 29, 2014 at 4:50 PM, Bill Lorensen wrote: > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora > system. I'll see if I can reproduce there. > > > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas > wrote: > > Bill, > > > > Same link error with this example... > > > > > > On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > > wrote: > >> > >> Arnaud, > >> > >> Can you try to build one of the ITK wiki examples against your > >> installed VTK? This might help narrow down the problem. Whether it is > >> a VTK of ITK issue. > >> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > >> > >> Bill > >> > >> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > >> wrote: > >> > Mike, > >> > > >> > It is difficult to refer to one single CMakeLists.txt, since it is > tied > >> > up > >> > to ITK's modularization. > >> > > >> > But here are the files to look at: > >> > > >> > > >> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > >> > > >> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > >> > > >> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > >> > > >> > Best > >> > Arnaud > >> > > >> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > >> > wrote: > >> >> > >> >> Can you share your CMakeLists.txt file? Are you using something like > >> >> the > >> >> following commands: > >> >> > >> >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >> >> ${VTK_LIBRARIES}) > >> >> > >> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas > > >> >> wrote: > >> >>> > >> >>> Bill, > >> >>> > >> >>> I can also confirm everything builds fine if VTK is not compiled > with > >> >>> Qt5 > >> >>> (which is part of my requirements...) > >> >>> > >> >>> > >> >>> > >> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > >> >>> > >> >>> wrote: > >> >>>> > >> >>>> Arnaud, > >> >>>> > >> >>>> I just tried an ITK build against an installed VTK and it built > just > >> >>>> fine. > >> >>>> > >> >>>> Bill > >> >>>> > >> >>>> > >> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > >> >>>> > >> >>>> wrote: > >> >>>> > I did not build against an installed VTK. > >> >>>> > > >> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >> >>>> > > >> >>>> > wrote: > >> >>>> >> Bill, > >> >>>> >> > >> >>>> >> It seems builds fine as long as Qt5 is not involved in the > process > >> >>>> >> (?) > >> >>>> >> > >> >>>> >> I just wonder if there is not something missing in vtk's cmake > >> >>>> >> installed > >> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use > >> >>>> >> required > >> >>>> >> libraries from vtk which should not depend on Qt5 (?) > >> >>>> >> > >> >>>> >> Thanks, > >> >>>> >> Arnaud > >> >>>> >> > >> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >> >>>> >> > >> >>>> >> wrote: > >> >>>> >>> > >> >>>> >>> Arnaud, > >> >>>> >>> > >> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against > >> >>>> >>> the > >> >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >> >>>> >>> > >> >>>> >>> Bill > >> >>>> >>> > >> >>>> >>> > >> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >> >>>> >>> > >> >>>> >>> wrote: > >> >>>> >>> > Hi all, > >> >>>> >>> > > >> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk > >> >>>> >>> > 6.1.0 > >> >>>> >>> > (built > >> >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >> >>>> >>> > > >> >>>> >>> > I get link 1 error: > >> >>>> >>> > ld library not found for -lQt5::Widgets > >> >>>> >>> > > >> >>>> >>> > Any idea how to fix it? > >> >>>> >>> > > >> >>>> >>> > Thanks, > >> >>>> >>> > Arnaud > >> >>>> >>> > _____________________________________ > >> >>>> >>> > Powered by www.kitware.com > >> >>>> >>> > > >> >>>> >>> > Visit other Kitware open-source projects at > >> >>>> >>> > http://www.kitware.com/opensource/opensource.html > >> >>>> >>> > > >> >>>> >>> > Kitware offers ITK Training Courses, for more information > >> >>>> >>> > visit: > >> >>>> >>> > http://www.kitware.com/products/protraining.php > >> >>>> >>> > > >> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: > >> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >> >>>> >>> > > >> >>>> >>> > Follow this link to subscribe/unsubscribe: > >> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >> >>>> >>> > >> >>>> >>> > >> >>>> >>> > >> >>>> >>> -- > >> >>>> >>> Unpaid intern in BillsBasement at noware dot com > >> >>>> >> > >> >>>> >> > >> >>>> > > >> >>>> > > >> >>>> > > >> >>>> > -- > >> >>>> > Unpaid intern in BillsBasement at noware dot com > >> >>>> > >> >>>> > >> >>>> > >> >>>> -- > >> >>>> Unpaid intern in BillsBasement at noware dot com > >> >>> > >> >>> > >> >>> > >> >>> _____________________________________ > >> >>> Powered by www.kitware.com > >> >>> > >> >>> Visit other Kitware open-source projects at > >> >>> http://www.kitware.com/opensource/opensource.html > >> >>> > >> >>> Kitware offers ITK Training Courses, for more information visit: > >> >>> http://www.kitware.com/products/protraining.php > >> >>> > >> >>> Please keep messages on-topic and check the ITK FAQ at: > >> >>> http://www.itk.org/Wiki/ITK_FAQ > >> >>> > >> >>> Follow this link to subscribe/unsubscribe: > >> >>> http://public.kitware.com/mailman/listinfo/insight-users > >> >>> > >> >> > >> >> > >> >> _____________________________________ > >> >> Powered by www.kitware.com > >> >> > >> >> Visit other Kitware open-source projects at > >> >> http://www.kitware.com/opensource/opensource.html > >> >> > >> >> Kitware offers ITK Training Courses, for more information visit: > >> >> http://www.kitware.com/products/protraining.php > >> >> > >> >> Please keep messages on-topic and check the ITK FAQ at: > >> >> http://www.itk.org/Wiki/ITK_FAQ > >> >> > >> >> Follow this link to subscribe/unsubscribe: > >> >> http://public.kitware.com/mailman/listinfo/insight-users > >> >> > >> > > >> > > >> > _____________________________________ > >> > Powered by www.kitware.com > >> > > >> > Visit other Kitware open-source projects at > >> > http://www.kitware.com/opensource/opensource.html > >> > > >> > Kitware offers ITK Training Courses, for more information visit: > >> > http://www.kitware.com/products/protraining.php > >> > > >> > Please keep messages on-topic and check the ITK FAQ at: > >> > http://www.itk.org/Wiki/ITK_FAQ > >> > > >> > Follow this link to subscribe/unsubscribe: > >> > http://public.kitware.com/mailman/listinfo/insight-users > >> > > >> > >> > >> > >> -- > >> Unpaid intern in BillsBasement at noware dot com > > > > > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Wed Oct 29 12:19:35 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 17:19:35 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, Not sure what you mean by link.txt? Do you mean my CMakeCache.txt? --- Note that if I had find_package( Qt5Widgets QUIET ) into example's cmakelists, then it works fine... I think it is really related to the cmake var ${vtk-module}_EXPORT_CODE_INSTALL in vtkModuleMacros.cmake On Wed, Oct 29, 2014 at 5:13 PM, Bill Lorensen wrote: > Built the arrow example against an installed ITK with Qt5 on fedora. > > Arnaud, > > Can you provide the link.txt file in the Arrow bin tree? > > Bill > > On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen > wrote: > > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora > > system. I'll see if I can reproduce there. > > > > > > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas > wrote: > >> Bill, > >> > >> Same link error with this example... > >> > >> > >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > > >> wrote: > >>> > >>> Arnaud, > >>> > >>> Can you try to build one of the ITK wiki examples against your > >>> installed VTK? This might help narrow down the problem. Whether it is > >>> a VTK of ITK issue. > >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > >>> > >>> Bill > >>> > >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > >>> wrote: > >>> > Mike, > >>> > > >>> > It is difficult to refer to one single CMakeLists.txt, since it is > tied > >>> > up > >>> > to ITK's modularization. > >>> > > >>> > But here are the files to look at: > >>> > > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > >>> > > >>> > Best > >>> > Arnaud > >>> > > >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > > >>> > wrote: > >>> >> > >>> >> Can you share your CMakeLists.txt file? Are you using something like > >>> >> the > >>> >> following commands: > >>> >> > >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >>> >> ${VTK_LIBRARIES}) > >>> >> > >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >>> >> wrote: > >>> >>> > >>> >>> Bill, > >>> >>> > >>> >>> I can also confirm everything builds fine if VTK is not compiled > with > >>> >>> Qt5 > >>> >>> (which is part of my requirements...) > >>> >>> > >>> >>> > >>> >>> > >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > >>> >>> > >>> >>> wrote: > >>> >>>> > >>> >>>> Arnaud, > >>> >>>> > >>> >>>> I just tried an ITK build against an installed VTK and it built > just > >>> >>>> fine. > >>> >>>> > >>> >>>> Bill > >>> >>>> > >>> >>>> > >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > >>> >>>> > >>> >>>> wrote: > >>> >>>> > I did not build against an installed VTK. > >>> >>>> > > >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >>> >>>> > > >>> >>>> > wrote: > >>> >>>> >> Bill, > >>> >>>> >> > >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the > process > >>> >>>> >> (?) > >>> >>>> >> > >>> >>>> >> I just wonder if there is not something missing in vtk's cmake > >>> >>>> >> installed > >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use > >>> >>>> >> required > >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) > >>> >>>> >> > >>> >>>> >> Thanks, > >>> >>>> >> Arnaud > >>> >>>> >> > >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >>> >>>> >> > >>> >>>> >> wrote: > >>> >>>> >>> > >>> >>>> >>> Arnaud, > >>> >>>> >>> > >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build > against > >>> >>>> >>> the > >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >>> >>>> >>> > >>> >>>> >>> Bill > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>> >>>> >>> > >>> >>>> >>> wrote: > >>> >>>> >>> > Hi all, > >>> >>>> >>> > > >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk > >>> >>>> >>> > 6.1.0 > >>> >>>> >>> > (built > >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >>> >>>> >>> > > >>> >>>> >>> > I get link 1 error: > >>> >>>> >>> > ld library not found for -lQt5::Widgets > >>> >>>> >>> > > >>> >>>> >>> > Any idea how to fix it? > >>> >>>> >>> > > >>> >>>> >>> > Thanks, > >>> >>>> >>> > Arnaud > >>> >>>> >>> > _____________________________________ > >>> >>>> >>> > Powered by www.kitware.com > >>> >>>> >>> > > >>> >>>> >>> > Visit other Kitware open-source projects at > >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html > >>> >>>> >>> > > >>> >>>> >>> > Kitware offers ITK Training Courses, for more information > >>> >>>> >>> > visit: > >>> >>>> >>> > http://www.kitware.com/products/protraining.php > >>> >>>> >>> > > >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: > >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >>> >>>> >>> > > >>> >>>> >>> > Follow this link to subscribe/unsubscribe: > >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> -- > >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com > >>> >>>> >> > >>> >>>> >> > >>> >>>> > > >>> >>>> > > >>> >>>> > > >>> >>>> > -- > >>> >>>> > Unpaid intern in BillsBasement at noware dot com > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> -- > >>> >>>> Unpaid intern in BillsBasement at noware dot com > >>> >>> > >>> >>> > >>> >>> > >>> >>> _____________________________________ > >>> >>> Powered by www.kitware.com > >>> >>> > >>> >>> Visit other Kitware open-source projects at > >>> >>> http://www.kitware.com/opensource/opensource.html > >>> >>> > >>> >>> Kitware offers ITK Training Courses, for more information visit: > >>> >>> http://www.kitware.com/products/protraining.php > >>> >>> > >>> >>> Please keep messages on-topic and check the ITK FAQ at: > >>> >>> http://www.itk.org/Wiki/ITK_FAQ > >>> >>> > >>> >>> Follow this link to subscribe/unsubscribe: > >>> >>> http://public.kitware.com/mailman/listinfo/insight-users > >>> >>> > >>> >> > >>> >> > >>> >> _____________________________________ > >>> >> Powered by www.kitware.com > >>> >> > >>> >> Visit other Kitware open-source projects at > >>> >> http://www.kitware.com/opensource/opensource.html > >>> >> > >>> >> Kitware offers ITK Training Courses, for more information visit: > >>> >> http://www.kitware.com/products/protraining.php > >>> >> > >>> >> Please keep messages on-topic and check the ITK FAQ at: > >>> >> http://www.itk.org/Wiki/ITK_FAQ > >>> >> > >>> >> Follow this link to subscribe/unsubscribe: > >>> >> http://public.kitware.com/mailman/listinfo/insight-users > >>> >> > >>> > > >>> > > >>> > _____________________________________ > >>> > Powered by www.kitware.com > >>> > > >>> > Visit other Kitware open-source projects at > >>> > http://www.kitware.com/opensource/opensource.html > >>> > > >>> > Kitware offers ITK Training Courses, for more information visit: > >>> > http://www.kitware.com/products/protraining.php > >>> > > >>> > Please keep messages on-topic and check the ITK FAQ at: > >>> > http://www.itk.org/Wiki/ITK_FAQ > >>> > > >>> > Follow this link to subscribe/unsubscribe: > >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>> > > >>> > >>> > >>> > >>> -- > >>> Unpaid intern in BillsBasement at noware dot com > >> > >> > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arnaudgelas at gmail.com Wed Oct 29 12:23:01 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 17:23:01 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: David, Thanks for the input! I will give a try to the master branch of VTK. I have been trying: * VTK 6.1 (which is the last stable release, corresponding to the latest hash on the release branch) * cmake 2.8.12 Not that if that has been fixed onto master, it would be great to backport the corresponding patches onto the release branch??? Thank you very much!! I'll report tomorrow morning if it works with the master branch. I gotta go now... Best, Arnaud On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: > Are you all using the same VTK here? I think older VTK trees have problems > with Qt5, but recent 'master' should work fine... Also, same version of > CMake? Or are you using older CMake? > > I think this is largely fixed already if you use the latest 'master' > versions of CMake, VTK and Qt5. > > (But I could be wrong.... I've not used Qt5 personally yet. Just recalling > things I've read on the lists recently....) > > HTH, > D > > > On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen > wrote: > >> Built the arrow example against an installed ITK with Qt5 on fedora. >> >> Arnaud, >> >> Can you provide the link.txt file in the Arrow bin tree? >> >> Bill >> >> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen >> wrote: >> > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora >> > system. I'll see if I can reproduce there. >> > >> > >> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas >> wrote: >> >> Bill, >> >> >> >> Same link error with this example... >> >> >> >> >> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen < >> bill.lorensen at gmail.com> >> >> wrote: >> >>> >> >>> Arnaud, >> >>> >> >>> Can you try to build one of the ITK wiki examples against your >> >>> installed VTK? This might help narrow down the problem. Whether it is >> >>> a VTK of ITK issue. >> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >> >>> >> >>> Bill >> >>> >> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > > >> >>> wrote: >> >>> > Mike, >> >>> > >> >>> > It is difficult to refer to one single CMakeLists.txt, since it is >> tied >> >>> > up >> >>> > to ITK's modularization. >> >>> > >> >>> > But here are the files to look at: >> >>> > >> >>> > >> >>> > >> https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >> >>> > >> >>> > >> https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >> >>> > >> >>> > >> https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >> >>> > >> >>> > Best >> >>> > Arnaud >> >>> > >> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander < >> chinander at gmail.com> >> >>> > wrote: >> >>> >> >> >>> >> Can you share your CMakeLists.txt file? Are you using something >> like >> >>> >> the >> >>> >> following commands: >> >>> >> >> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >> >>> >> ${VTK_LIBRARIES}) >> >>> >> >> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas < >> arnaudgelas at gmail.com> >> >>> >> wrote: >> >>> >>> >> >>> >>> Bill, >> >>> >>> >> >>> >>> I can also confirm everything builds fine if VTK is not compiled >> with >> >>> >>> Qt5 >> >>> >>> (which is part of my requirements...) >> >>> >>> >> >>> >>> >> >>> >>> >> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >> >>> >>> >> >>> >>> wrote: >> >>> >>>> >> >>> >>>> Arnaud, >> >>> >>>> >> >>> >>>> I just tried an ITK build against an installed VTK and it built >> just >> >>> >>>> fine. >> >>> >>>> >> >>> >>>> Bill >> >>> >>>> >> >>> >>>> >> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >> >>> >>>> >> >>> >>>> wrote: >> >>> >>>> > I did not build against an installed VTK. >> >>> >>>> > >> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >> >>> >>>> > >> >>> >>>> > wrote: >> >>> >>>> >> Bill, >> >>> >>>> >> >> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the >> process >> >>> >>>> >> (?) >> >>> >>>> >> >> >>> >>>> >> I just wonder if there is not something missing in vtk's cmake >> >>> >>>> >> installed >> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only >> use >> >>> >>>> >> required >> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >> >>> >>>> >> >> >>> >>>> >> Thanks, >> >>> >>>> >> Arnaud >> >>> >>>> >> >> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >> >>> >>>> >> >> >>> >>>> >> wrote: >> >>> >>>> >>> >> >>> >>>> >>> Arnaud, >> >>> >>>> >>> >> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build >> against >> >>> >>>> >>> the >> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >> >>> >>>> >>> >> >>> >>>> >>> Bill >> >>> >>>> >>> >> >>> >>>> >>> >> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> >>> >>>> >>> >> >>> >>>> >>> wrote: >> >>> >>>> >>> > Hi all, >> >>> >>>> >>> > >> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >> >>> >>>> >>> > 6.1.0 >> >>> >>>> >>> > (built >> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >> >>> >>>> >>> > >> >>> >>>> >>> > I get link 1 error: >> >>> >>>> >>> > ld library not found for -lQt5::Widgets >> >>> >>>> >>> > >> >>> >>>> >>> > Any idea how to fix it? >> >>> >>>> >>> > >> >>> >>>> >>> > Thanks, >> >>> >>>> >>> > Arnaud >> >>> >>>> >>> > _____________________________________ >> >>> >>>> >>> > Powered by www.kitware.com >> >>> >>>> >>> > >> >>> >>>> >>> > Visit other Kitware open-source projects at >> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >> >>> >>>> >>> > >> >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >> >>> >>>> >>> > visit: >> >>> >>>> >>> > http://www.kitware.com/products/protraining.php >> >>> >>>> >>> > >> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>> >>>> >>> > >> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >> >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>> >>>> >>> >> >>> >>>> >>> >> >>> >>>> >>> >> >>> >>>> >>> -- >> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >> >>> >>>> >> >> >>> >>>> >> >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > -- >> >>> >>>> > Unpaid intern in BillsBasement at noware dot com >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> -- >> >>> >>>> Unpaid intern in BillsBasement at noware dot com >> >>> >>> >> >>> >>> >> >>> >>> >> >>> >>> _____________________________________ >> >>> >>> Powered by www.kitware.com >> >>> >>> >> >>> >>> Visit other Kitware open-source projects at >> >>> >>> http://www.kitware.com/opensource/opensource.html >> >>> >>> >> >>> >>> Kitware offers ITK Training Courses, for more information visit: >> >>> >>> http://www.kitware.com/products/protraining.php >> >>> >>> >> >>> >>> Please keep messages on-topic and check the ITK FAQ at: >> >>> >>> http://www.itk.org/Wiki/ITK_FAQ >> >>> >>> >> >>> >>> Follow this link to subscribe/unsubscribe: >> >>> >>> http://public.kitware.com/mailman/listinfo/insight-users >> >>> >>> >> >>> >> >> >>> >> >> >>> >> _____________________________________ >> >>> >> Powered by www.kitware.com >> >>> >> >> >>> >> Visit other Kitware open-source projects at >> >>> >> http://www.kitware.com/opensource/opensource.html >> >>> >> >> >>> >> Kitware offers ITK Training Courses, for more information visit: >> >>> >> http://www.kitware.com/products/protraining.php >> >>> >> >> >>> >> Please keep messages on-topic and check the ITK FAQ at: >> >>> >> http://www.itk.org/Wiki/ITK_FAQ >> >>> >> >> >>> >> Follow this link to subscribe/unsubscribe: >> >>> >> http://public.kitware.com/mailman/listinfo/insight-users >> >>> >> >> >>> > >> >>> > >> >>> > _____________________________________ >> >>> > Powered by www.kitware.com >> >>> > >> >>> > Visit other Kitware open-source projects at >> >>> > http://www.kitware.com/opensource/opensource.html >> >>> > >> >>> > Kitware offers ITK Training Courses, for more information visit: >> >>> > http://www.kitware.com/products/protraining.php >> >>> > >> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>> > >> >>> > Follow this link to subscribe/unsubscribe: >> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>> > >> >>> >> >>> >> >>> >> >>> -- >> >>> Unpaid intern in BillsBasement at noware dot com >> >> >> >> >> > >> > >> > >> > -- >> > Unpaid intern in BillsBasement at noware dot com >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From DLRdave at aol.com Wed Oct 29 12:19:52 2014 From: DLRdave at aol.com (David Cole) Date: Wed, 29 Oct 2014 12:19:52 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Are you all using the same VTK here? I think older VTK trees have problems with Qt5, but recent 'master' should work fine... Also, same version of CMake? Or are you using older CMake? I think this is largely fixed already if you use the latest 'master' versions of CMake, VTK and Qt5. (But I could be wrong.... I've not used Qt5 personally yet. Just recalling things I've read on the lists recently....) HTH, D On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen wrote: > Built the arrow example against an installed ITK with Qt5 on fedora. > > Arnaud, > > Can you provide the link.txt file in the Arrow bin tree? > > Bill > > On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen > wrote: > > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora > > system. I'll see if I can reproduce there. > > > > > > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas > wrote: > >> Bill, > >> > >> Same link error with this example... > >> > >> > >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > > >> wrote: > >>> > >>> Arnaud, > >>> > >>> Can you try to build one of the ITK wiki examples against your > >>> installed VTK? This might help narrow down the problem. Whether it is > >>> a VTK of ITK issue. > >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > >>> > >>> Bill > >>> > >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > >>> wrote: > >>> > Mike, > >>> > > >>> > It is difficult to refer to one single CMakeLists.txt, since it is > tied > >>> > up > >>> > to ITK's modularization. > >>> > > >>> > But here are the files to look at: > >>> > > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > >>> > > >>> > Best > >>> > Arnaud > >>> > > >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > > >>> > wrote: > >>> >> > >>> >> Can you share your CMakeLists.txt file? Are you using something like > >>> >> the > >>> >> following commands: > >>> >> > >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >>> >> ${VTK_LIBRARIES}) > >>> >> > >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >>> >> wrote: > >>> >>> > >>> >>> Bill, > >>> >>> > >>> >>> I can also confirm everything builds fine if VTK is not compiled > with > >>> >>> Qt5 > >>> >>> (which is part of my requirements...) > >>> >>> > >>> >>> > >>> >>> > >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > >>> >>> > >>> >>> wrote: > >>> >>>> > >>> >>>> Arnaud, > >>> >>>> > >>> >>>> I just tried an ITK build against an installed VTK and it built > just > >>> >>>> fine. > >>> >>>> > >>> >>>> Bill > >>> >>>> > >>> >>>> > >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > >>> >>>> > >>> >>>> wrote: > >>> >>>> > I did not build against an installed VTK. > >>> >>>> > > >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >>> >>>> > > >>> >>>> > wrote: > >>> >>>> >> Bill, > >>> >>>> >> > >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the > process > >>> >>>> >> (?) > >>> >>>> >> > >>> >>>> >> I just wonder if there is not something missing in vtk's cmake > >>> >>>> >> installed > >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use > >>> >>>> >> required > >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) > >>> >>>> >> > >>> >>>> >> Thanks, > >>> >>>> >> Arnaud > >>> >>>> >> > >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >>> >>>> >> > >>> >>>> >> wrote: > >>> >>>> >>> > >>> >>>> >>> Arnaud, > >>> >>>> >>> > >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build > against > >>> >>>> >>> the > >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >>> >>>> >>> > >>> >>>> >>> Bill > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>> >>>> >>> > >>> >>>> >>> wrote: > >>> >>>> >>> > Hi all, > >>> >>>> >>> > > >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk > >>> >>>> >>> > 6.1.0 > >>> >>>> >>> > (built > >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >>> >>>> >>> > > >>> >>>> >>> > I get link 1 error: > >>> >>>> >>> > ld library not found for -lQt5::Widgets > >>> >>>> >>> > > >>> >>>> >>> > Any idea how to fix it? > >>> >>>> >>> > > >>> >>>> >>> > Thanks, > >>> >>>> >>> > Arnaud > >>> >>>> >>> > _____________________________________ > >>> >>>> >>> > Powered by www.kitware.com > >>> >>>> >>> > > >>> >>>> >>> > Visit other Kitware open-source projects at > >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html > >>> >>>> >>> > > >>> >>>> >>> > Kitware offers ITK Training Courses, for more information > >>> >>>> >>> > visit: > >>> >>>> >>> > http://www.kitware.com/products/protraining.php > >>> >>>> >>> > > >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: > >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >>> >>>> >>> > > >>> >>>> >>> > Follow this link to subscribe/unsubscribe: > >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> -- > >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com > >>> >>>> >> > >>> >>>> >> > >>> >>>> > > >>> >>>> > > >>> >>>> > > >>> >>>> > -- > >>> >>>> > Unpaid intern in BillsBasement at noware dot com > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> -- > >>> >>>> Unpaid intern in BillsBasement at noware dot com > >>> >>> > >>> >>> > >>> >>> > >>> >>> _____________________________________ > >>> >>> Powered by www.kitware.com > >>> >>> > >>> >>> Visit other Kitware open-source projects at > >>> >>> http://www.kitware.com/opensource/opensource.html > >>> >>> > >>> >>> Kitware offers ITK Training Courses, for more information visit: > >>> >>> http://www.kitware.com/products/protraining.php > >>> >>> > >>> >>> Please keep messages on-topic and check the ITK FAQ at: > >>> >>> http://www.itk.org/Wiki/ITK_FAQ > >>> >>> > >>> >>> Follow this link to subscribe/unsubscribe: > >>> >>> http://public.kitware.com/mailman/listinfo/insight-users > >>> >>> > >>> >> > >>> >> > >>> >> _____________________________________ > >>> >> Powered by www.kitware.com > >>> >> > >>> >> Visit other Kitware open-source projects at > >>> >> http://www.kitware.com/opensource/opensource.html > >>> >> > >>> >> Kitware offers ITK Training Courses, for more information visit: > >>> >> http://www.kitware.com/products/protraining.php > >>> >> > >>> >> Please keep messages on-topic and check the ITK FAQ at: > >>> >> http://www.itk.org/Wiki/ITK_FAQ > >>> >> > >>> >> Follow this link to subscribe/unsubscribe: > >>> >> http://public.kitware.com/mailman/listinfo/insight-users > >>> >> > >>> > > >>> > > >>> > _____________________________________ > >>> > Powered by www.kitware.com > >>> > > >>> > Visit other Kitware open-source projects at > >>> > http://www.kitware.com/opensource/opensource.html > >>> > > >>> > Kitware offers ITK Training Courses, for more information visit: > >>> > http://www.kitware.com/products/protraining.php > >>> > > >>> > Please keep messages on-topic and check the ITK FAQ at: > >>> > http://www.itk.org/Wiki/ITK_FAQ > >>> > > >>> > Follow this link to subscribe/unsubscribe: > >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>> > > >>> > >>> > >>> > >>> -- > >>> Unpaid intern in BillsBasement at noware dot com > >> > >> > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot com > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Wed Oct 29 13:21:39 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 18:21:39 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: I downloaded the latest version of ITK again, and when configuring, I couldn't find the ItkVtkGlue option. I attached what I have in CMake. On Wed, Oct 29, 2014 at 4:33 PM, John Drescher wrote: > On Wed, Oct 29, 2014 at 11:31 AM, Abdul Abdul > wrote: > > ITK is already being built. The picture is for the example. > > Then go back and build ITK. While you configure ITK4 make sure you > enable the itkvtkglue module. You do not get this by default or in a > binary download. This also requires that you have or build VTK. if > this is on windows I highly recommend that you build all of these from > source. > > John > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 85410 bytes Desc: not available URL: From abdul.sw84 at gmail.com Wed Oct 29 13:24:14 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 18:24:14 +0100 Subject: [ITK-users] Where can I get ItKVtkGlue In-Reply-To: References: Message-ID: Hi Matt, Hi Matt, Thanks for your kind reply. I downloaded the latest version of ITK, and when I tried to make a "configuration", I couldn't find the ItkVtkGlue option. I hereby attach what I get in CMake. Thanks. On Wed, Oct 29, 2014 at 4:29 PM, Matt McCormick wrote: > Hi Abdul, > > ITKVtkGlue used to be a separate project, but it is now integrated > into ITK as the module ITKVtkGlue. You can enable in your ITK CMake > configuration by setting > > Module_ITKVtkGlue > > to ON. > > It requires a build of VTK. > > Hope this helps, > Matt > > On Wed, Oct 29, 2014 at 10:10 AM, Abdul Abdul > wrote: > > Hello, > > > > I'm trying to run this example: > > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > > > But, get the following when I "configure" in CMake: > > > > CMake Error at CMakeLists.txt:11 (find_package): > > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > > has asked CMake to find a package configuration file provided by > > "ItkVtkGlue", but CMake did not find one. > > > > Could not find a package configuration file provided by "ItkVtkGlue" with > > any of the following names: > > > > ItkVtkGlueConfig.cmake > > itkvtkglue-config.cmake > > > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > > "ItkVtkGlue" provides a separate development package or SDK, be sure it > has > > been installed. > > > > It seems I need "ItkVtkGlue"? Where can I download it? And, what should > I do > > to combine it with the program? > > > > Thanks. > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 85410 bytes Desc: not available URL: From drescherjm at gmail.com Wed Oct 29 13:30:00 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 13:30:00 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Wed, Oct 29, 2014 at 1:21 PM, Abdul Abdul wrote: > I downloaded the latest version of ITK again, and when configuring, I > couldn't find the ItkVtkGlue option. I attached what I have in CMake. You need to click the Advanced checkbox. I would also click the Grouped box as well. John From bill.lorensen at gmail.com Wed Oct 29 13:34:45 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 13:34:45 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: I just verified that I see the failure with VTK 6.1, but not VTK master. On Wed, Oct 29, 2014 at 12:23 PM, Arnaud Gelas wrote: > David, > > Thanks for the input! I will give a try to the master branch of VTK. > > I have been trying: > * VTK 6.1 (which is the last stable release, corresponding to the latest > hash on the release branch) > * cmake 2.8.12 > > Not that if that has been fixed onto master, it would be great to backport > the corresponding patches onto the release branch??? > > Thank you very much!! > > I'll report tomorrow morning if it works with the master branch. I gotta go > now... > > Best, > Arnaud > > On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: >> >> Are you all using the same VTK here? I think older VTK trees have problems >> with Qt5, but recent 'master' should work fine... Also, same version of >> CMake? Or are you using older CMake? >> >> I think this is largely fixed already if you use the latest 'master' >> versions of CMake, VTK and Qt5. >> >> (But I could be wrong.... I've not used Qt5 personally yet. Just recalling >> things I've read on the lists recently....) >> >> HTH, >> D >> >> >> On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen >> wrote: >>> >>> Built the arrow example against an installed ITK with Qt5 on fedora. >>> >>> Arnaud, >>> >>> Can you provide the link.txt file in the Arrow bin tree? >>> >>> Bill >>> >>> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen >>> wrote: >>> > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora >>> > system. I'll see if I can reproduce there. >>> > >>> > >>> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas >>> > wrote: >>> >> Bill, >>> >> >>> >> Same link error with this example... >>> >> >>> >> >>> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen >>> >> >>> >> wrote: >>> >>> >>> >>> Arnaud, >>> >>> >>> >>> Can you try to build one of the ITK wiki examples against your >>> >>> installed VTK? This might help narrow down the problem. Whether it is >>> >>> a VTK of ITK issue. >>> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >>> >>> >>> >>> Bill >>> >>> >>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >>> >>> >>> >>> wrote: >>> >>> > Mike, >>> >>> > >>> >>> > It is difficult to refer to one single CMakeLists.txt, since it is >>> >>> > tied >>> >>> > up >>> >>> > to ITK's modularization. >>> >>> > >>> >>> > But here are the files to look at: >>> >>> > >>> >>> > >>> >>> > >>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >>> >>> > >>> >>> > >>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >>> >>> > >>> >>> > >>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >>> >>> > >>> >>> > Best >>> >>> > Arnaud >>> >>> > >>> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >>> >>> > >>> >>> > wrote: >>> >>> >> >>> >>> >> Can you share your CMakeLists.txt file? Are you using something >>> >>> >> like >>> >>> >> the >>> >>> >> following commands: >>> >>> >> >>> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >>> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >>> >>> >> ${VTK_LIBRARIES}) >>> >>> >> >>> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >>> >>> >> >>> >>> >> wrote: >>> >>> >>> >>> >>> >>> Bill, >>> >>> >>> >>> >>> >>> I can also confirm everything builds fine if VTK is not compiled >>> >>> >>> with >>> >>> >>> Qt5 >>> >>> >>> (which is part of my requirements...) >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>> >>> >>> >>> >>> >>> wrote: >>> >>> >>>> >>> >>> >>>> Arnaud, >>> >>> >>>> >>> >>> >>>> I just tried an ITK build against an installed VTK and it built >>> >>> >>>> just >>> >>> >>>> fine. >>> >>> >>>> >>> >>> >>>> Bill >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>> >>> >>>> >>> >>> >>>> wrote: >>> >>> >>>> > I did not build against an installed VTK. >>> >>> >>>> > >>> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>> >>> >>>> > >>> >>> >>>> > wrote: >>> >>> >>>> >> Bill, >>> >>> >>>> >> >>> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the >>> >>> >>>> >> process >>> >>> >>>> >> (?) >>> >>> >>>> >> >>> >>> >>>> >> I just wonder if there is not something missing in vtk's >>> >>> >>>> >> cmake >>> >>> >>>> >> installed >>> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only >>> >>> >>>> >> use >>> >>> >>>> >> required >>> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >>> >>> >>>> >> >>> >>> >>>> >> Thanks, >>> >>> >>>> >> Arnaud >>> >>> >>>> >> >>> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>> >>> >>>> >> >>> >>> >>>> >> wrote: >>> >>> >>>> >>> >>> >>> >>>> >>> Arnaud, >>> >>> >>>> >>> >>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build >>> >>> >>>> >>> against >>> >>> >>>> >>> the >>> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>> >>> >>>> >>> >>> >>> >>>> >>> Bill >>> >>> >>>> >>> >>> >>> >>>> >>> >>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>> >>> >>>> >>> >>> >>> >>>> >>> wrote: >>> >>> >>>> >>> > Hi all, >>> >>> >>>> >>> > >>> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >>> >>> >>>> >>> > 6.1.0 >>> >>> >>>> >>> > (built >>> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>> >>> >>>> >>> > >>> >>> >>>> >>> > I get link 1 error: >>> >>> >>>> >>> > ld library not found for -lQt5::Widgets >>> >>> >>>> >>> > >>> >>> >>>> >>> > Any idea how to fix it? >>> >>> >>>> >>> > >>> >>> >>>> >>> > Thanks, >>> >>> >>>> >>> > Arnaud >>> >>> >>>> >>> > _____________________________________ >>> >>> >>>> >>> > Powered by www.kitware.com >>> >>> >>>> >>> > >>> >>> >>>> >>> > Visit other Kitware open-source projects at >>> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >>> >>> >>>> >>> > >>> >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >>> >>> >>>> >>> > visit: >>> >>> >>>> >>> > http://www.kitware.com/products/protraining.php >>> >>> >>>> >>> > >>> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>> >>> >>>> >>> > >>> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >>> >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>>> >>> >>> >>> >>>> >>> >>> >>> >>>> >>> >>> >>> >>>> >>> -- >>> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>>> >> >>> >>> >>>> >> >>> >>> >>>> > >>> >>> >>>> > >>> >>> >>>> > >>> >>> >>>> > -- >>> >>> >>>> > Unpaid intern in BillsBasement at noware dot com >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> -- >>> >>> >>>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _____________________________________ >>> >>> >>> Powered by www.kitware.com >>> >>> >>> >>> >>> >>> Visit other Kitware open-source projects at >>> >>> >>> http://www.kitware.com/opensource/opensource.html >>> >>> >>> >>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> >>> >>> http://www.kitware.com/products/protraining.php >>> >>> >>> >>> >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> >>> >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> >>> >>> >>> >>> Follow this link to subscribe/unsubscribe: >>> >>> >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> >>> >> >>> >>> >> >>> >>> >> _____________________________________ >>> >>> >> Powered by www.kitware.com >>> >>> >> >>> >>> >> Visit other Kitware open-source projects at >>> >>> >> http://www.kitware.com/opensource/opensource.html >>> >>> >> >>> >>> >> Kitware offers ITK Training Courses, for more information visit: >>> >>> >> http://www.kitware.com/products/protraining.php >>> >>> >> >>> >>> >> Please keep messages on-topic and check the ITK FAQ at: >>> >>> >> http://www.itk.org/Wiki/ITK_FAQ >>> >>> >> >>> >>> >> Follow this link to subscribe/unsubscribe: >>> >>> >> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >>> >>> > >>> >>> > >>> >>> > _____________________________________ >>> >>> > Powered by www.kitware.com >>> >>> > >>> >>> > Visit other Kitware open-source projects at >>> >>> > http://www.kitware.com/opensource/opensource.html >>> >>> > >>> >>> > Kitware offers ITK Training Courses, for more information visit: >>> >>> > http://www.kitware.com/products/protraining.php >>> >>> > >>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>> >>> > >>> >>> > Follow this link to subscribe/unsubscribe: >>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>> > >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> Unpaid intern in BillsBasement at noware dot com >>> >> >>> >> >>> > >>> > >>> > >>> > -- >>> > Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -- Unpaid intern in BillsBasement at noware dot com From bill.lorensen at gmail.com Wed Oct 29 16:16:56 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 16:16:56 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Arnaud, This is the gerrit patch that fixed the issue: http://review.source.kitware.com/#/c/15423/ If you cherry pick onto your VTK source and verify that it fixes your link error, I'll try to get it applied to VTK6.1. Bill On Wed, Oct 29, 2014 at 1:34 PM, Bill Lorensen wrote: > I just verified that I see the failure with VTK 6.1, but not VTK master. > > > On Wed, Oct 29, 2014 at 12:23 PM, Arnaud Gelas wrote: >> David, >> >> Thanks for the input! I will give a try to the master branch of VTK. >> >> I have been trying: >> * VTK 6.1 (which is the last stable release, corresponding to the latest >> hash on the release branch) >> * cmake 2.8.12 >> >> Not that if that has been fixed onto master, it would be great to backport >> the corresponding patches onto the release branch??? >> >> Thank you very much!! >> >> I'll report tomorrow morning if it works with the master branch. I gotta go >> now... >> >> Best, >> Arnaud >> >> On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: >>> >>> Are you all using the same VTK here? I think older VTK trees have problems >>> with Qt5, but recent 'master' should work fine... Also, same version of >>> CMake? Or are you using older CMake? >>> >>> I think this is largely fixed already if you use the latest 'master' >>> versions of CMake, VTK and Qt5. >>> >>> (But I could be wrong.... I've not used Qt5 personally yet. Just recalling >>> things I've read on the lists recently....) >>> >>> HTH, >>> D >>> >>> >>> On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen >>> wrote: >>>> >>>> Built the arrow example against an installed ITK with Qt5 on fedora. >>>> >>>> Arnaud, >>>> >>>> Can you provide the link.txt file in the Arrow bin tree? >>>> >>>> Bill >>>> >>>> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen >>>> wrote: >>>> > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora >>>> > system. I'll see if I can reproduce there. >>>> > >>>> > >>>> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas >>>> > wrote: >>>> >> Bill, >>>> >> >>>> >> Same link error with this example... >>>> >> >>>> >> >>>> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen >>>> >> >>>> >> wrote: >>>> >>> >>>> >>> Arnaud, >>>> >>> >>>> >>> Can you try to build one of the ITK wiki examples against your >>>> >>> installed VTK? This might help narrow down the problem. Whether it is >>>> >>> a VTK of ITK issue. >>>> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >>>> >>> >>>> >>> Bill >>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >>>> >>> >>>> >>> wrote: >>>> >>> > Mike, >>>> >>> > >>>> >>> > It is difficult to refer to one single CMakeLists.txt, since it is >>>> >>> > tied >>>> >>> > up >>>> >>> > to ITK's modularization. >>>> >>> > >>>> >>> > But here are the files to look at: >>>> >>> > >>>> >>> > >>>> >>> > >>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >>>> >>> > >>>> >>> > >>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >>>> >>> > >>>> >>> > >>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >>>> >>> > >>>> >>> > Best >>>> >>> > Arnaud >>>> >>> > >>>> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >>>> >>> > >>>> >>> > wrote: >>>> >>> >> >>>> >>> >> Can you share your CMakeLists.txt file? Are you using something >>>> >>> >> like >>>> >>> >> the >>>> >>> >> following commands: >>>> >>> >> >>>> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >>>> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >>>> >>> >> ${VTK_LIBRARIES}) >>>> >>> >> >>>> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >>>> >>> >> >>>> >>> >> wrote: >>>> >>> >>> >>>> >>> >>> Bill, >>>> >>> >>> >>>> >>> >>> I can also confirm everything builds fine if VTK is not compiled >>>> >>> >>> with >>>> >>> >>> Qt5 >>>> >>> >>> (which is part of my requirements...) >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>>> >>> >>> >>>> >>> >>> wrote: >>>> >>> >>>> >>>> >>> >>>> Arnaud, >>>> >>> >>>> >>>> >>> >>>> I just tried an ITK build against an installed VTK and it built >>>> >>> >>>> just >>>> >>> >>>> fine. >>>> >>> >>>> >>>> >>> >>>> Bill >>>> >>> >>>> >>>> >>> >>>> >>>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>>> >>> >>>> >>>> >>> >>>> wrote: >>>> >>> >>>> > I did not build against an installed VTK. >>>> >>> >>>> > >>>> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>>> >>> >>>> > >>>> >>> >>>> > wrote: >>>> >>> >>>> >> Bill, >>>> >>> >>>> >> >>>> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the >>>> >>> >>>> >> process >>>> >>> >>>> >> (?) >>>> >>> >>>> >> >>>> >>> >>>> >> I just wonder if there is not something missing in vtk's >>>> >>> >>>> >> cmake >>>> >>> >>>> >> installed >>>> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only >>>> >>> >>>> >> use >>>> >>> >>>> >> required >>>> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >>>> >>> >>>> >> >>>> >>> >>>> >> Thanks, >>>> >>> >>>> >> Arnaud >>>> >>> >>>> >> >>>> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>>> >>> >>>> >> >>>> >>> >>>> >> wrote: >>>> >>> >>>> >>> >>>> >>> >>>> >>> Arnaud, >>>> >>> >>>> >>> >>>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build >>>> >>> >>>> >>> against >>>> >>> >>>> >>> the >>>> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>>> >>> >>>> >>> >>>> >>> >>>> >>> Bill >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>>> >>> >>>> >>> >>>> >>> >>>> >>> wrote: >>>> >>> >>>> >>> > Hi all, >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >>>> >>> >>>> >>> > 6.1.0 >>>> >>> >>>> >>> > (built >>>> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > I get link 1 error: >>>> >>> >>>> >>> > ld library not found for -lQt5::Widgets >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Any idea how to fix it? >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Thanks, >>>> >>> >>>> >>> > Arnaud >>>> >>> >>>> >>> > _____________________________________ >>>> >>> >>>> >>> > Powered by www.kitware.com >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Visit other Kitware open-source projects at >>>> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >>>> >>> >>>> >>> > visit: >>>> >>> >>>> >>> > http://www.kitware.com/products/protraining.php >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>>> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >>>> >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >>>> >>> >>>> >> >>>> >>> >>>> >> >>>> >>> >>>> > >>>> >>> >>>> > >>>> >>> >>>> > >>>> >>> >>>> > -- >>>> >>> >>>> > Unpaid intern in BillsBasement at noware dot com >>>> >>> >>>> >>>> >>> >>>> >>>> >>> >>>> >>>> >>> >>>> -- >>>> >>> >>>> Unpaid intern in BillsBasement at noware dot com >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> _____________________________________ >>>> >>> >>> Powered by www.kitware.com >>>> >>> >>> >>>> >>> >>> Visit other Kitware open-source projects at >>>> >>> >>> http://www.kitware.com/opensource/opensource.html >>>> >>> >>> >>>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>>> >>> >>> http://www.kitware.com/products/protraining.php >>>> >>> >>> >>>> >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>>> >>> >>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>> >>> >>>> >>> >>> Follow this link to subscribe/unsubscribe: >>>> >>> >>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> >>>> >>> >> >>>> >>> >> >>>> >>> >> _____________________________________ >>>> >>> >> Powered by www.kitware.com >>>> >>> >> >>>> >>> >> Visit other Kitware open-source projects at >>>> >>> >> http://www.kitware.com/opensource/opensource.html >>>> >>> >> >>>> >>> >> Kitware offers ITK Training Courses, for more information visit: >>>> >>> >> http://www.kitware.com/products/protraining.php >>>> >>> >> >>>> >>> >> Please keep messages on-topic and check the ITK FAQ at: >>>> >>> >> http://www.itk.org/Wiki/ITK_FAQ >>>> >>> >> >>>> >>> >> Follow this link to subscribe/unsubscribe: >>>> >>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >> >>>> >>> > >>>> >>> > >>>> >>> > _____________________________________ >>>> >>> > Powered by www.kitware.com >>>> >>> > >>>> >>> > Visit other Kitware open-source projects at >>>> >>> > http://www.kitware.com/opensource/opensource.html >>>> >>> > >>>> >>> > Kitware offers ITK Training Courses, for more information visit: >>>> >>> > http://www.kitware.com/products/protraining.php >>>> >>> > >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>>> >>> > >>>> >>> > Follow this link to subscribe/unsubscribe: >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> > >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> Unpaid intern in BillsBasement at noware dot com >>>> >> >>>> >> >>>> > >>>> > >>>> > >>>> > -- >>>> > Unpaid intern in BillsBasement at noware dot com >>>> >>>> >>>> >>>> -- >>>> Unpaid intern in BillsBasement at noware dot com >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com From bill.lorensen at gmail.com Wed Oct 29 16:22:31 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 16:22:31 -0400 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Actually, I get a conflict when I cherry pick. A git expert will need to comment on how to update vtk6.1 On Wed, Oct 29, 2014 at 4:16 PM, Bill Lorensen wrote: > Arnaud, > > This is the gerrit patch that fixed the issue: > http://review.source.kitware.com/#/c/15423/ > > If you cherry pick onto your VTK source and verify that it fixes your > link error, I'll try to get it applied to VTK6.1. > > Bill > > > On Wed, Oct 29, 2014 at 1:34 PM, Bill Lorensen wrote: >> I just verified that I see the failure with VTK 6.1, but not VTK master. >> >> >> On Wed, Oct 29, 2014 at 12:23 PM, Arnaud Gelas wrote: >>> David, >>> >>> Thanks for the input! I will give a try to the master branch of VTK. >>> >>> I have been trying: >>> * VTK 6.1 (which is the last stable release, corresponding to the latest >>> hash on the release branch) >>> * cmake 2.8.12 >>> >>> Not that if that has been fixed onto master, it would be great to backport >>> the corresponding patches onto the release branch??? >>> >>> Thank you very much!! >>> >>> I'll report tomorrow morning if it works with the master branch. I gotta go >>> now... >>> >>> Best, >>> Arnaud >>> >>> On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: >>>> >>>> Are you all using the same VTK here? I think older VTK trees have problems >>>> with Qt5, but recent 'master' should work fine... Also, same version of >>>> CMake? Or are you using older CMake? >>>> >>>> I think this is largely fixed already if you use the latest 'master' >>>> versions of CMake, VTK and Qt5. >>>> >>>> (But I could be wrong.... I've not used Qt5 personally yet. Just recalling >>>> things I've read on the lists recently....) >>>> >>>> HTH, >>>> D >>>> >>>> >>>> On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen >>>> wrote: >>>>> >>>>> Built the arrow example against an installed ITK with Qt5 on fedora. >>>>> >>>>> Arnaud, >>>>> >>>>> Can you provide the link.txt file in the Arrow bin tree? >>>>> >>>>> Bill >>>>> >>>>> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen >>>>> wrote: >>>>> > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora >>>>> > system. I'll see if I can reproduce there. >>>>> > >>>>> > >>>>> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas >>>>> > wrote: >>>>> >> Bill, >>>>> >> >>>>> >> Same link error with this example... >>>>> >> >>>>> >> >>>>> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen >>>>> >> >>>>> >> wrote: >>>>> >>> >>>>> >>> Arnaud, >>>>> >>> >>>>> >>> Can you try to build one of the ITK wiki examples against your >>>>> >>> installed VTK? This might help narrow down the problem. Whether it is >>>>> >>> a VTK of ITK issue. >>>>> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >>>>> >>> >>>>> >>> Bill >>>>> >>> >>>>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >>>>> >>> >>>>> >>> wrote: >>>>> >>> > Mike, >>>>> >>> > >>>>> >>> > It is difficult to refer to one single CMakeLists.txt, since it is >>>>> >>> > tied >>>>> >>> > up >>>>> >>> > to ITK's modularization. >>>>> >>> > >>>>> >>> > But here are the files to look at: >>>>> >>> > >>>>> >>> > >>>>> >>> > >>>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >>>>> >>> > >>>>> >>> > >>>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >>>>> >>> > >>>>> >>> > >>>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >>>>> >>> > >>>>> >>> > Best >>>>> >>> > Arnaud >>>>> >>> > >>>>> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >>>>> >>> > >>>>> >>> > wrote: >>>>> >>> >> >>>>> >>> >> Can you share your CMakeLists.txt file? Are you using something >>>>> >>> >> like >>>>> >>> >> the >>>>> >>> >> following commands: >>>>> >>> >> >>>>> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >>>>> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >>>>> >>> >> ${VTK_LIBRARIES}) >>>>> >>> >> >>>>> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >>>>> >>> >> >>>>> >>> >> wrote: >>>>> >>> >>> >>>>> >>> >>> Bill, >>>>> >>> >>> >>>>> >>> >>> I can also confirm everything builds fine if VTK is not compiled >>>>> >>> >>> with >>>>> >>> >>> Qt5 >>>>> >>> >>> (which is part of my requirements...) >>>>> >>> >>> >>>>> >>> >>> >>>>> >>> >>> >>>>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>>>> >>> >>> >>>>> >>> >>> wrote: >>>>> >>> >>>> >>>>> >>> >>>> Arnaud, >>>>> >>> >>>> >>>>> >>> >>>> I just tried an ITK build against an installed VTK and it built >>>>> >>> >>>> just >>>>> >>> >>>> fine. >>>>> >>> >>>> >>>>> >>> >>>> Bill >>>>> >>> >>>> >>>>> >>> >>>> >>>>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>>>> >>> >>>> >>>>> >>> >>>> wrote: >>>>> >>> >>>> > I did not build against an installed VTK. >>>>> >>> >>>> > >>>>> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>>>> >>> >>>> > >>>>> >>> >>>> > wrote: >>>>> >>> >>>> >> Bill, >>>>> >>> >>>> >> >>>>> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the >>>>> >>> >>>> >> process >>>>> >>> >>>> >> (?) >>>>> >>> >>>> >> >>>>> >>> >>>> >> I just wonder if there is not something missing in vtk's >>>>> >>> >>>> >> cmake >>>>> >>> >>>> >> installed >>>>> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only >>>>> >>> >>>> >> use >>>>> >>> >>>> >> required >>>>> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >>>>> >>> >>>> >> >>>>> >>> >>>> >> Thanks, >>>>> >>> >>>> >> Arnaud >>>>> >>> >>>> >> >>>>> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>>>> >>> >>>> >> >>>>> >>> >>>> >> wrote: >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> Arnaud, >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build >>>>> >>> >>>> >>> against >>>>> >>> >>>> >>> the >>>>> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> Bill >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> wrote: >>>>> >>> >>>> >>> > Hi all, >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >>>>> >>> >>>> >>> > 6.1.0 >>>>> >>> >>>> >>> > (built >>>>> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > I get link 1 error: >>>>> >>> >>>> >>> > ld library not found for -lQt5::Widgets >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Any idea how to fix it? >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Thanks, >>>>> >>> >>>> >>> > Arnaud >>>>> >>> >>>> >>> > _____________________________________ >>>>> >>> >>>> >>> > Powered by www.kitware.com >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Visit other Kitware open-source projects at >>>>> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >>>>> >>> >>>> >>> > visit: >>>>> >>> >>>> >>> > http://www.kitware.com/products/protraining.php >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>>>> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >>>>> >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> -- >>>>> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >>>>> >>> >>>> >> >>>>> >>> >>>> >> >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> > -- >>>>> >>> >>>> > Unpaid intern in BillsBasement at noware dot com >>>>> >>> >>>> >>>>> >>> >>>> >>>>> >>> >>>> >>>>> >>> >>>> -- >>>>> >>> >>>> Unpaid intern in BillsBasement at noware dot com >>>>> >>> >>> >>>>> >>> >>> >>>>> >>> >>> >>>>> >>> >>> _____________________________________ >>>>> >>> >>> Powered by www.kitware.com >>>>> >>> >>> >>>>> >>> >>> Visit other Kitware open-source projects at >>>>> >>> >>> http://www.kitware.com/opensource/opensource.html >>>>> >>> >>> >>>>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>>>> >>> >>> http://www.kitware.com/products/protraining.php >>>>> >>> >>> >>>>> >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>>>> >>> >>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>> >>> >>>>> >>> >>> Follow this link to subscribe/unsubscribe: >>>>> >>> >>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>> >>> >>>>> >>> >> >>>>> >>> >> >>>>> >>> >> _____________________________________ >>>>> >>> >> Powered by www.kitware.com >>>>> >>> >> >>>>> >>> >> Visit other Kitware open-source projects at >>>>> >>> >> http://www.kitware.com/opensource/opensource.html >>>>> >>> >> >>>>> >>> >> Kitware offers ITK Training Courses, for more information visit: >>>>> >>> >> http://www.kitware.com/products/protraining.php >>>>> >>> >> >>>>> >>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>> >>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>> >> >>>>> >>> >> Follow this link to subscribe/unsubscribe: >>>>> >>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>> >> >>>>> >>> > >>>>> >>> > >>>>> >>> > _____________________________________ >>>>> >>> > Powered by www.kitware.com >>>>> >>> > >>>>> >>> > Visit other Kitware open-source projects at >>>>> >>> > http://www.kitware.com/opensource/opensource.html >>>>> >>> > >>>>> >>> > Kitware offers ITK Training Courses, for more information visit: >>>>> >>> > http://www.kitware.com/products/protraining.php >>>>> >>> > >>>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>>>> >>> > >>>>> >>> > Follow this link to subscribe/unsubscribe: >>>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>> > >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> Unpaid intern in BillsBasement at noware dot com >>>>> >> >>>>> >> >>>>> > >>>>> > >>>>> > >>>>> > -- >>>>> > Unpaid intern in BillsBasement at noware dot com >>>>> >>>>> >>>>> >>>>> -- >>>>> Unpaid intern in BillsBasement at noware dot com >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com From matt.mccormick at kitware.com Wed Oct 29 17:16:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Oct 2014 17:16:24 -0400 Subject: [ITK-users] Where can I get ItKVtkGlue In-Reply-To: References: Message-ID: Hi Abdul, You must click the "Advanced" checkbox to see this variable. HTH, Matt On Wed, Oct 29, 2014 at 1:24 PM, Abdul Abdul wrote: > Hi Matt, > > Hi Matt, > > Thanks for your kind reply. I downloaded the latest version of ITK, and when > I tried to make a "configuration", I couldn't find the ItkVtkGlue option. > > I hereby attach what I get in CMake. > > Thanks. > > On Wed, Oct 29, 2014 at 4:29 PM, Matt McCormick > wrote: >> >> Hi Abdul, >> >> ITKVtkGlue used to be a separate project, but it is now integrated >> into ITK as the module ITKVtkGlue. You can enable in your ITK CMake >> configuration by setting >> >> Module_ITKVtkGlue >> >> to ON. >> >> It requires a build of VTK. >> >> Hope this helps, >> Matt >> >> On Wed, Oct 29, 2014 at 10:10 AM, Abdul Abdul >> wrote: >> > Hello, >> > >> > I'm trying to run this example: >> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> > >> > But, get the following when I "configure" in CMake: >> > >> > CMake Error at CMakeLists.txt:11 (find_package): >> > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this >> > project >> > has asked CMake to find a package configuration file provided by >> > "ItkVtkGlue", but CMake did not find one. >> > >> > Could not find a package configuration file provided by "ItkVtkGlue" >> > with >> > any of the following names: >> > >> > ItkVtkGlueConfig.cmake >> > itkvtkglue-config.cmake >> > >> > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set >> > "ItkVtkGlue_DIR" to a directory containing one of the above files. If >> > "ItkVtkGlue" provides a separate development package or SDK, be sure it >> > has >> > been installed. >> > >> > It seems I need "ItkVtkGlue"? Where can I download it? And, what should >> > I do >> > to combine it with the program? >> > >> > Thanks. >> > >> > >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > > > From llliu at umich.edu Wed Oct 29 21:14:07 2014 From: llliu at umich.edu (Lianli Liu) Date: Wed, 29 Oct 2014 21:14:07 -0400 Subject: [ITK-users] difference between warpimagefilter and displacmentfield transform Message-ID: Hi all, Can anyone kindly explain the difference between the two? It seems to me that the both apply a displacment to each pixel in the image. Thanks! Best, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Oct 29 22:39:46 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Oct 2014 22:39:46 -0400 Subject: [ITK-users] difference between warpimagefilter and displacmentfield transform In-Reply-To: References: Message-ID: Hi Lianli, Yes, either one can be used. Thanks, Matt On Wed, Oct 29, 2014 at 9:14 PM, Lianli Liu wrote: > Hi all, > > Can anyone kindly explain the difference between the two? It seems to me > that the both apply a displacment to each pixel in the image. Thanks! > > Best, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > From arnaudgelas at gmail.com Thu Oct 30 03:39:10 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 30 Oct 2014 08:39:10 +0100 Subject: [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Hi Bill, Thanks for link to the corresponding patch on gerrit! >From the release branch, if you cherry-pick this commit, then it fixes the issue. $ git checkout release $ git cherry-pick 23fbbebc3cfc63ebf13b7321e9c198a5ad000e5c It would be really great if this patch could be applied onto the release branch!!! Thank you very much!!! Cheers, Arnaud On Wed, Oct 29, 2014 at 9:22 PM, Bill Lorensen wrote: > Actually, I get a conflict when I cherry pick. A git expert will need > to comment on how to update vtk6.1 > > > On Wed, Oct 29, 2014 at 4:16 PM, Bill Lorensen > wrote: > > Arnaud, > > > > This is the gerrit patch that fixed the issue: > > http://review.source.kitware.com/#/c/15423/ > > > > If you cherry pick onto your VTK source and verify that it fixes your > > link error, I'll try to get it applied to VTK6.1. > > > > Bill > > > > > > On Wed, Oct 29, 2014 at 1:34 PM, Bill Lorensen > wrote: > >> I just verified that I see the failure with VTK 6.1, but not VTK master. > >> > >> > >> On Wed, Oct 29, 2014 at 12:23 PM, Arnaud Gelas > wrote: > >>> David, > >>> > >>> Thanks for the input! I will give a try to the master branch of VTK. > >>> > >>> I have been trying: > >>> * VTK 6.1 (which is the last stable release, corresponding to the > latest > >>> hash on the release branch) > >>> * cmake 2.8.12 > >>> > >>> Not that if that has been fixed onto master, it would be great to > backport > >>> the corresponding patches onto the release branch??? > >>> > >>> Thank you very much!! > >>> > >>> I'll report tomorrow morning if it works with the master branch. I > gotta go > >>> now... > >>> > >>> Best, > >>> Arnaud > >>> > >>> On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: > >>>> > >>>> Are you all using the same VTK here? I think older VTK trees have > problems > >>>> with Qt5, but recent 'master' should work fine... Also, same version > of > >>>> CMake? Or are you using older CMake? > >>>> > >>>> I think this is largely fixed already if you use the latest 'master' > >>>> versions of CMake, VTK and Qt5. > >>>> > >>>> (But I could be wrong.... I've not used Qt5 personally yet. Just > recalling > >>>> things I've read on the lists recently....) > >>>> > >>>> HTH, > >>>> D > >>>> > >>>> > >>>> On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen < > bill.lorensen at gmail.com> > >>>> wrote: > >>>>> > >>>>> Built the arrow example against an installed ITK with Qt5 on fedora. > >>>>> > >>>>> Arnaud, > >>>>> > >>>>> Can you provide the link.txt file in the Arrow bin tree? > >>>>> > >>>>> Bill > >>>>> > >>>>> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen < > bill.lorensen at gmail.com> > >>>>> wrote: > >>>>> > Great. That means it is a VTK issue. I'm downloading qt5 on my > fedora > >>>>> > system. I'll see if I can reproduce there. > >>>>> > > >>>>> > > >>>>> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >>>>> > wrote: > >>>>> >> Bill, > >>>>> >> > >>>>> >> Same link error with this example... > >>>>> >> > >>>>> >> > >>>>> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > >>>>> >> > >>>>> >> wrote: > >>>>> >>> > >>>>> >>> Arnaud, > >>>>> >>> > >>>>> >>> Can you try to build one of the ITK wiki examples against your > >>>>> >>> installed VTK? This might help narrow down the problem. Whether > it is > >>>>> >>> a VTK of ITK issue. > >>>>> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > >>>>> >>> > >>>>> >>> Bill > >>>>> >>> > >>>>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > >>>>> >>> > >>>>> >>> wrote: > >>>>> >>> > Mike, > >>>>> >>> > > >>>>> >>> > It is difficult to refer to one single CMakeLists.txt, since > it is > >>>>> >>> > tied > >>>>> >>> > up > >>>>> >>> > to ITK's modularization. > >>>>> >>> > > >>>>> >>> > But here are the files to look at: > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > >>>>> >>> > > >>>>> >>> > Best > >>>>> >>> > Arnaud > >>>>> >>> > > >>>>> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > >>>>> >>> > > >>>>> >>> > wrote: > >>>>> >>> >> > >>>>> >>> >> Can you share your CMakeLists.txt file? Are you using > something > >>>>> >>> >> like > >>>>> >>> >> the > >>>>> >>> >> following commands: > >>>>> >>> >> > >>>>> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >>>>> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >>>>> >>> >> ${VTK_LIBRARIES}) > >>>>> >>> >> > >>>>> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas > >>>>> >>> >> > >>>>> >>> >> wrote: > >>>>> >>> >>> > >>>>> >>> >>> Bill, > >>>>> >>> >>> > >>>>> >>> >>> I can also confirm everything builds fine if VTK is not > compiled > >>>>> >>> >>> with > >>>>> >>> >>> Qt5 > >>>>> >>> >>> (which is part of my requirements...) > >>>>> >>> >>> > >>>>> >>> >>> > >>>>> >>> >>> > >>>>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > >>>>> >>> >>> > >>>>> >>> >>> wrote: > >>>>> >>> >>>> > >>>>> >>> >>>> Arnaud, > >>>>> >>> >>>> > >>>>> >>> >>>> I just tried an ITK build against an installed VTK and it > built > >>>>> >>> >>>> just > >>>>> >>> >>>> fine. > >>>>> >>> >>>> > >>>>> >>> >>>> Bill > >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > >>>>> >>> >>>> > >>>>> >>> >>>> wrote: > >>>>> >>> >>>> > I did not build against an installed VTK. > >>>>> >>> >>>> > > >>>>> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >>>>> >>> >>>> > > >>>>> >>> >>>> > wrote: > >>>>> >>> >>>> >> Bill, > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in > the > >>>>> >>> >>>> >> process > >>>>> >>> >>>> >> (?) > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> I just wonder if there is not something missing in vtk's > >>>>> >>> >>>> >> cmake > >>>>> >>> >>>> >> installed > >>>>> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could > only > >>>>> >>> >>>> >> use > >>>>> >>> >>>> >> required > >>>>> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> Thanks, > >>>>> >>> >>>> >> Arnaud > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> wrote: > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> Arnaud, > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build > >>>>> >>> >>>> >>> against > >>>>> >>> >>>> >>> the > >>>>> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> Bill > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> wrote: > >>>>> >>> >>>> >>> > Hi all, > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue > with vtk > >>>>> >>> >>>> >>> > 6.1.0 > >>>>> >>> >>>> >>> > (built > >>>>> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > I get link 1 error: > >>>>> >>> >>>> >>> > ld library not found for -lQt5::Widgets > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Any idea how to fix it? > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Thanks, > >>>>> >>> >>>> >>> > Arnaud > >>>>> >>> >>>> >>> > _____________________________________ > >>>>> >>> >>>> >>> > Powered by www.kitware.com > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Visit other Kitware open-source projects at > >>>>> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Kitware offers ITK Training Courses, for more > information > >>>>> >>> >>>> >>> > visit: > >>>>> >>> >>>> >>> > http://www.kitware.com/products/protraining.php > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ > at: > >>>>> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: > >>>>> >>> >>>> >>> > > http://public.kitware.com/mailman/listinfo/insight-users > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> -- > >>>>> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> > >>>>> >>> >>>> > > >>>>> >>> >>>> > > >>>>> >>> >>>> > > >>>>> >>> >>>> > -- > >>>>> >>> >>>> > Unpaid intern in BillsBasement at noware dot com > >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> -- > >>>>> >>> >>>> Unpaid intern in BillsBasement at noware dot com > >>>>> >>> >>> > >>>>> >>> >>> > >>>>> >>> >>> > >>>>> >>> >>> _____________________________________ > >>>>> >>> >>> Powered by www.kitware.com > >>>>> >>> >>> > >>>>> >>> >>> Visit other Kitware open-source projects at > >>>>> >>> >>> http://www.kitware.com/opensource/opensource.html > >>>>> >>> >>> > >>>>> >>> >>> Kitware offers ITK Training Courses, for more information > visit: > >>>>> >>> >>> http://www.kitware.com/products/protraining.php > >>>>> >>> >>> > >>>>> >>> >>> Please keep messages on-topic and check the ITK FAQ at: > >>>>> >>> >>> http://www.itk.org/Wiki/ITK_FAQ > >>>>> >>> >>> > >>>>> >>> >>> Follow this link to subscribe/unsubscribe: > >>>>> >>> >>> http://public.kitware.com/mailman/listinfo/insight-users > >>>>> >>> >>> > >>>>> >>> >> > >>>>> >>> >> > >>>>> >>> >> _____________________________________ > >>>>> >>> >> Powered by www.kitware.com > >>>>> >>> >> > >>>>> >>> >> Visit other Kitware open-source projects at > >>>>> >>> >> http://www.kitware.com/opensource/opensource.html > >>>>> >>> >> > >>>>> >>> >> Kitware offers ITK Training Courses, for more information > visit: > >>>>> >>> >> http://www.kitware.com/products/protraining.php > >>>>> >>> >> > >>>>> >>> >> Please keep messages on-topic and check the ITK FAQ at: > >>>>> >>> >> http://www.itk.org/Wiki/ITK_FAQ > >>>>> >>> >> > >>>>> >>> >> Follow this link to subscribe/unsubscribe: > >>>>> >>> >> http://public.kitware.com/mailman/listinfo/insight-users > >>>>> >>> >> > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > _____________________________________ > >>>>> >>> > Powered by www.kitware.com > >>>>> >>> > > >>>>> >>> > Visit other Kitware open-source projects at > >>>>> >>> > http://www.kitware.com/opensource/opensource.html > >>>>> >>> > > >>>>> >>> > Kitware offers ITK Training Courses, for more information > visit: > >>>>> >>> > http://www.kitware.com/products/protraining.php > >>>>> >>> > > >>>>> >>> > Please keep messages on-topic and check the ITK FAQ at: > >>>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >>>>> >>> > > >>>>> >>> > Follow this link to subscribe/unsubscribe: > >>>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>>>> >>> > > >>>>> >>> > >>>>> >>> > >>>>> >>> > >>>>> >>> -- > >>>>> >>> Unpaid intern in BillsBasement at noware dot com > >>>>> >> > >>>>> >> > >>>>> > > >>>>> > > >>>>> > > >>>>> > -- > >>>>> > Unpaid intern in BillsBasement at noware dot com > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Unpaid intern in BillsBasement at noware dot com > >>>>> _____________________________________ > >>>>> Powered by www.kitware.com > >>>>> > >>>>> Visit other Kitware open-source projects at > >>>>> http://www.kitware.com/opensource/opensource.html > >>>>> > >>>>> Kitware offers ITK Training Courses, for more information visit: > >>>>> http://www.kitware.com/products/protraining.php > >>>>> > >>>>> Please keep messages on-topic and check the ITK FAQ at: > >>>>> http://www.itk.org/Wiki/ITK_FAQ > >>>>> > >>>>> Follow this link to subscribe/unsubscribe: > >>>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>> > >>>> > >>> > >> > >> > >> > >> -- > >> Unpaid intern in BillsBasement at noware dot com > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Thu Oct 30 17:37:35 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:37:35 +0100 Subject: [ITK-users] Where can I get ItKVtkGlue In-Reply-To: References: Message-ID: Hi Matt, You are right. Got it. Thanks a lot. On Wed, Oct 29, 2014 at 4:29 PM, Matt McCormick wrote: > Hi Abdul, > > ITKVtkGlue used to be a separate project, but it is now integrated > into ITK as the module ITKVtkGlue. You can enable in your ITK CMake > configuration by setting > > Module_ITKVtkGlue > > to ON. > > It requires a build of VTK. > > Hope this helps, > Matt > > On Wed, Oct 29, 2014 at 10:10 AM, Abdul Abdul > wrote: > > Hello, > > > > I'm trying to run this example: > > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > > > But, get the following when I "configure" in CMake: > > > > CMake Error at CMakeLists.txt:11 (find_package): > > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > > has asked CMake to find a package configuration file provided by > > "ItkVtkGlue", but CMake did not find one. > > > > Could not find a package configuration file provided by "ItkVtkGlue" with > > any of the following names: > > > > ItkVtkGlueConfig.cmake > > itkvtkglue-config.cmake > > > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > > "ItkVtkGlue" provides a separate development package or SDK, be sure it > has > > been installed. > > > > It seems I need "ItkVtkGlue"? Where can I download it? And, what should > I do > > to combine it with the program? > > > > Thanks. > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Thu Oct 30 17:38:04 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:38:04 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: Yes, you are right John. Thanks a lot. On Wed, Oct 29, 2014 at 6:30 PM, John Drescher wrote: > On Wed, Oct 29, 2014 at 1:21 PM, Abdul Abdul wrote: > > I downloaded the latest version of ITK again, and when configuring, I > > couldn't find the ItkVtkGlue option. I attached what I have in CMake. > > You need to click the Advanced checkbox. I would also click the > Grouped box as well. > > John > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Thu Oct 30 17:47:20 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:47:20 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: I was able to do the configuration and generation successfully. I'm using Visual Studio to run the program. I got the following when trying to do so: LINK : fatal error LNK1181: cannot open input file 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 ---- Do you know why is that? I know that I can run that from the command line and pass an image, but, I don't have the release of the program. Thanks. On Thu, Oct 30, 2014 at 10:38 PM, Abdul Abdul wrote: > Yes, you are right John. Thanks a lot. > > On Wed, Oct 29, 2014 at 6:30 PM, John Drescher > wrote: > >> On Wed, Oct 29, 2014 at 1:21 PM, Abdul Abdul >> wrote: >> > I downloaded the latest version of ITK again, and when configuring, I >> > couldn't find the ItkVtkGlue option. I attached what I have in CMake. >> >> You need to click the Advanced checkbox. I would also click the >> Grouped box as well. >> >> John >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Thu Oct 30 17:48:50 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:48:50 +0100 Subject: [ITK-users] LINK : fatal error LNK1181 Message-ID: Hello, I'm trying to run this program: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue But, get the following in Visual Studio: LINK : fatal error LNK1181: cannot open input file 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 ---- Do you know why is that? I know that I can run that from the command line and pass an image, but, I don't have the release of the program. Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From drescherjm at gmail.com Thu Oct 30 17:51:19 2014 From: drescherjm at gmail.com (John Drescher) Date: Thu, 30 Oct 2014 17:51:19 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Thu, Oct 30, 2014 at 5:47 PM, Abdul Abdul wrote: > I was able to do the configuration and generation successfully. > > I'm using Visual Studio to run the program. > > I got the following when trying to do so: > > LINK : fatal error LNK1181: cannot open input file > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 > ---- > > Do you know why is that? I know that I can run that from the command line > and pass an image, but, I don't have the release of the program. I am not so familiar with vtk-6.1 specifics so someone else may have to help. Which project are you building when you get this error? Did you verify that there were no errors on the vtk build? John From cory.quammen at kitware.com Thu Oct 30 17:52:23 2014 From: cory.quammen at kitware.com (Cory Quammen) Date: Thu, 30 Oct 2014 17:52:23 -0400 Subject: [ITK-users] LINK : fatal error LNK1181 In-Reply-To: References: Message-ID: I suspect you built only the Debug version of VTK, but you are trying to build your example in Release mode. Build your example in Debug mode instead. On Thu, Oct 30, 2014 at 5:48 PM, Abdul Abdul wrote: > Hello, > > I'm trying to run this program: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue > > But, get the following in Visual Studio: > > LINK : fatal error LNK1181: cannot open input file > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 > ---- > > Do you know why is that? I know that I can run that from the command line > and pass an image, but, I don't have the release of the program. > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Thu Oct 30 17:52:41 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:52:41 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: This is the project I'm trying to run: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader On Thu, Oct 30, 2014 at 10:51 PM, John Drescher wrote: > On Thu, Oct 30, 2014 at 5:47 PM, Abdul Abdul wrote: > > I was able to do the configuration and generation successfully. > > > > I'm using Visual Studio to run the program. > > > > I got the following when trying to do so: > > > > LINK : fatal error LNK1181: cannot open input file > > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' > > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 > > ---- > > > > Do you know why is that? I know that I can run that from the command line > > and pass an image, but, I don't have the release of the program. > > I am not so familiar with vtk-6.1 specifics so someone else may have > to help. Which project are you building when you get this error? Did > you verify that there were no errors on the vtk build? > > John > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Thu Oct 30 17:54:30 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:54:30 +0100 Subject: [ITK-users] LINK : fatal error LNK1181 In-Reply-To: References: Message-ID: I got the following when in Debug mode for the example: 2>LINK : fatal error LNK1104: cannot open file 'C:\ITK\build\lib\Debug\itkdouble-conversion-4.6.lib' 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Debug Win32 ------ 3>Project not selected to build for this solution configuration ========== Build: 1 succeeded, 1 failed, 0 up-to-date, 1 skipped ========== I'll try to build ITK and VTK in release or debug mode once again and see what happens. Thanks. On Thu, Oct 30, 2014 at 10:52 PM, Cory Quammen wrote: > I suspect you built only the Debug version of VTK, but you are trying to > build your example in Release mode. Build your example in Debug mode > instead. > > On Thu, Oct 30, 2014 at 5:48 PM, Abdul Abdul wrote: > >> Hello, >> >> I'm trying to run this program: >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue >> >> But, get the following in Visual Studio: >> >> LINK : fatal error LNK1181: cannot open input file >> 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' >> 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 >> ---- >> >> Do you know why is that? I know that I can run that from the command line >> and pass an image, but, I don't have the release of the program. >> >> Thanks. >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From drescherjm at gmail.com Thu Oct 30 17:54:24 2014 From: drescherjm at gmail.com (John Drescher) Date: Thu, 30 Oct 2014 17:54:24 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Thu, Oct 30, 2014 at 5:52 PM, Abdul Abdul wrote: > This is the project I'm trying to run: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader I thought you had the error building ITK again.. Anyways I would try Cory's answer.. John From cory.quammen at kitware.com Thu Oct 30 17:55:35 2014 From: cory.quammen at kitware.com (Cory Quammen) Date: Thu, 30 Oct 2014 17:55:35 -0400 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: Abdul, Please try to ask your questions in only one email thread. That will make it easier for others to follow along now and in the future if they search the archives. I just answered a question you posted in this thread that you duplicated in a new thread. Thanks, Cory On Thu, Oct 30, 2014 at 5:52 PM, Abdul Abdul wrote: > This is the project I'm trying to run: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > On Thu, Oct 30, 2014 at 10:51 PM, John Drescher > wrote: > >> On Thu, Oct 30, 2014 at 5:47 PM, Abdul Abdul >> wrote: >> > I was able to do the configuration and generation successfully. >> > >> > I'm using Visual Studio to run the program. >> > >> > I got the following when trying to do so: >> > >> > LINK : fatal error LNK1181: cannot open input file >> > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' >> > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 >> > ---- >> > >> > Do you know why is that? I know that I can run that from the command >> line >> > and pass an image, but, I don't have the release of the program. >> >> I am not so familiar with vtk-6.1 specifics so someone else may have >> to help. Which project are you building when you get this error? Did >> you verify that there were no errors on the vtk build? >> >> John >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Fri Oct 31 03:11:07 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 31 Oct 2014 08:11:07 +0100 Subject: [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: Yes, got what you mean Cory. Thanks all for your kind replies. I have built ITK with the itkVtkGlue module checked, and have build VTK, both on release mode. I could then configure and generate the program successfully. Thanks. On Thu, Oct 30, 2014 at 10:55 PM, Cory Quammen wrote: > Abdul, > > Please try to ask your questions in only one email thread. That will make > it easier for others to follow along now and in the future if they search > the archives. I just answered a question you posted in this thread that you > duplicated in a new thread. > > Thanks, > Cory > > On Thu, Oct 30, 2014 at 5:52 PM, Abdul Abdul wrote: > >> This is the project I'm trying to run: >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> >> On Thu, Oct 30, 2014 at 10:51 PM, John Drescher >> wrote: >> >>> On Thu, Oct 30, 2014 at 5:47 PM, Abdul Abdul >>> wrote: >>> > I was able to do the configuration and generation successfully. >>> > >>> > I'm using Visual Studio to run the program. >>> > >>> > I got the following when trying to do so: >>> > >>> > LINK : fatal error LNK1181: cannot open input file >>> > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' >>> > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release >>> Win32 >>> > ---- >>> > >>> > Do you know why is that? I know that I can run that from the command >>> line >>> > and pass an image, but, I don't have the release of the program. >>> >>> I am not so familiar with vtk-6.1 specifics so someone else may have >>> to help. Which project are you building when you get this error? Did >>> you verify that there were no errors on the vtk build? >>> >>> John >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Fri Oct 31 03:22:07 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 31 Oct 2014 08:22:07 +0100 Subject: [ITK-users] Message when trying to run an ITK program Message-ID: Hello, I'm trying to run this program through Visual Studio 2013: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader When I do that, I get the following message: *unable to start program 'C:\itk-example\build\Release\ALL_BUILD'.* *The system cannot find the file specified.* How can I solve this issue? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Fri Oct 31 03:28:06 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Fri, 31 Oct 2014 07:28:06 +0000 Subject: [ITK-users] Message when trying to run an ITK program In-Reply-To: References: Message-ID: In Solution Explorer, right-click on the program you are building and then Set as Startup Project. By default VS treats ALL_BUILD as the startup project, which is what it tries to execute when you do Debug > Start Without Debugging. Gib ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Abdul Abdul [abdul.sw84 at gmail.com] Sent: Friday, 31 October 2014 8:22 p.m. To: ITK Subject: [ITK-users] Message when trying to run an ITK program Hello, I'm trying to run this program through Visual Studio 2013: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader When I do that, I get the following message: unable to start program 'C:\itk-example\build\Release\ALL_BUILD'. The system cannot find the file specified. How can I solve this issue? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tanghui.seu at gmail.com Fri Oct 31 04:53:53 2014 From: tanghui.seu at gmail.com (Hui Tang) Date: Fri, 31 Oct 2014 16:53:53 +0800 Subject: [ITK-users] BinaryDilateImageFilter has an issue? Message-ID: Dear all, I can not get dilation or erosion from BinaryDilateImageFilter or BinaryErodeImageFilter I mostly copied from the example and thought it should work without any problems. Here is my code. Anyone knows what is wrong here? Thanks a lot in advance ! unsigned int radius = 7; typedef itk::BinaryBallStructuringElement StructuringElementType; StructuringElementType structuringElement; structuringElement.SetRadius(radius); structuringElement.CreateStructuringElement(); typedef itk::BinaryDilateImageFilter BinaryDilateImageFilterType; BinaryDilateImageFilterType::Pointer dilateFilter = BinaryDilateImageFilterType::New(); dilateFilter->SetInput(readerint->GetOutput()); dilateFilter->SetKernel(structuringElement); dilateFilter->Update(); Best, Hui -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Fri Oct 31 06:44:32 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Fri, 31 Oct 2014 10:44:32 +0000 Subject: [ITK-users] BinaryDilateImageFilter has an issue? In-Reply-To: References: Message-ID: Hi Hui, Could you describe what exactly the problem is? Also, couId you also paste the earlier part of your code (where Image3DIntType and readerint are defined)? On Fri, Oct 31, 2014 at 8:53 AM, Hui Tang wrote: > Dear all, > > I can not get dilation or erosion from BinaryDilateImageFilter or > BinaryErodeImageFilter > > I mostly copied from the example and thought it should work without any > problems. > > Here is my code. > Anyone knows what is wrong here? Thanks a lot in advance ! > > > unsigned int radius = 7; > > typedef itk::BinaryBallStructuringElement StructuringElementType; > > StructuringElementType structuringElement; > > structuringElement.SetRadius(radius); > > structuringElement.CreateStructuringElement(); > > > > typedef itk::BinaryDilateImageFilter StructuringElementType> BinaryDilateImageFilterType; > > BinaryDilateImageFilterType::Pointer dilateFilter = > BinaryDilateImageFilterType::New(); > > dilateFilter->SetInput(readerint->GetOutput()); > > dilateFilter->SetKernel(structuringElement); > > dilateFilter->Update(); > > > > Best, > > > > Hui > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From indianzeppelin at gmail.com Fri Oct 31 12:56:26 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Fri, 31 Oct 2014 16:56:26 +0000 Subject: [ITK-users] BinaryDilateImageFilter has an issue? In-Reply-To: References: Message-ID: Hi Hui, Here's an explanation (someone more knowledgeable can correct me or explain it in a better way). See [1]. The dilate (as well as the erode) filter considers as foreground those pixels which have a "DilateValue". If this value is not set, it defaults to the maximum possible value of the *PixelType *which in your case is the maximum value of the *signed int* type. So, if you know the foreground value of your binary image, you might want to try setting this "DilateValue", by using *dilateFilter->SetDilateValue(). *You can also use the MinimumMaximumImageCalculator to find the maximum value (see [2]). As an aside, wouldn't it be better to use *unsigned char* instead of *int *in this case, since the image is binary? [1] http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html [2] http://www.itk.org/Doxygen/html/classitk_1_1MinimumMaximumImageCalculator.html#a39a9bfc33090e47df71d5b9cd6665ccb On Fri, Oct 31, 2014 at 10:58 AM, tanghui.seu wrote: > Hi Grish > > Thanks a lot for your reply! > The dilate Filter outputs the same as the input image. > > Image3DIntType is itk?:image > I correctly read in a binary image. > > Sorry that i can not provide the code now..... it is in my workstation. > Thanks a lot again! > > > ???????? > > > Girish Mallya Udupi wrote: > > Hi Hui, > > Could you describe what exactly the problem is? Also, couId you also paste > the earlier part of your code (where Image3DIntType and readerint are > defined)? > > > On Fri, Oct 31, 2014 at 8:53 AM, Hui Tang wrote: > >> Dear all, >> >> I can not get dilation or erosion from BinaryDilateImageFilter or >> BinaryErodeImageFilter >> >> I mostly copied from the example and thought it should work without any >> problems. >> >> Here is my code. >> Anyone knows what is wrong here? Thanks a lot in advance ! >> >> >> unsigned int radius = 7; >> >> typedef itk::BinaryBallStructuringElement StructuringElementType; >> >> StructuringElementType structuringElement; >> >> structuringElement.SetRadius(radius); >> >> structuringElement.CreateStructuringElement(); >> >> >> >> typedef itk::BinaryDilateImageFilter > StructuringElementType> BinaryDilateImageFilterType; >> >> BinaryDilateImageFilterType::Pointer dilateFilter = >> BinaryDilateImageFilterType::New(); >> >> dilateFilter->SetInput(readerint->GetOutput()); >> >> dilateFilter->SetKernel(structuringElement); >> >> dilateFilter->Update(); >> >> >> >> Best, >> >> >> >> Hui >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Regards, > Girish > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogerbramon at gmail.com Fri Oct 31 13:55:24 2014 From: rogerbramon at gmail.com (Roger Bramon Feixas) Date: Fri, 31 Oct 2014 18:55:24 +0100 Subject: [ITK-users] [ITK] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> <544A073B.4080905@imnc.in2p3.fr> Message-ID: Hi, I also have this link problem trying to build using msvc2013_opengl + ITK 4.6.1 + VTK 6.1 + GDCM 2.4.4 + Qt 5.3.2. We are using qmake as well. Any suggestion will be appreciated. Many thanks, Roger On Fri, Oct 24, 2014 at 4:57 PM, Matt McCormick wrote: > Hi Fran?oise, > > > CMake is recommended -- it will avoid this problem and others. It > works well with Qt. > > Thanks, > Matt > > On Fri, Oct 24, 2014 at 4:00 AM, Fran?oise Lefebvre > wrote: > > > > No, I'm not. I have always used a .pro file and qmake. > > > > Le 23/10/2014 23:37, Matt McCormick a ?crit : > > > >> Hi, > >> > >> Are you using CMake to configure your project? > >> > >> Matt > >> > >> On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre > >> wrote: > >>> > >>> Hi, > >>> > >>> I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the > >>> same > >>> link error. > >>> > >>> FL > >>> > >>> > >>> Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : > >>> > >>>> Yes I did. > >>>> > >>>> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : > >>>>> > >>>>> Did you try the latest 4.6.1 release? > >>>>> > >>>>> Brad > >>>>> > >>>>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre > >>>>> > >>>>> wrote: > >>>>> > >>>>>> Hi, > >>>>>> > >>>>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default > >>>>>> parameters and the Module_ITKReview on. > >>>>>> > >>>>>> I am now trying to compile a program developed in C++ using Qt5.1.1 > >>>>>> and > >>>>>> Microsoft Visual C++ express 2010 on Windows 7. > >>>>>> > >>>>>> I get the following link error : > >>>>>> > >>>>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe > non > >>>>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction > "public: > >>>>>> static class itksys::Encoding::CommandLineArguments __cdecl > >>>>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const > >>>>>> *)" > >>>>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) > >>>>>> > >>>>>> I didn't get this error when compiling with itk4.3 . > >>>>>> > >>>>>> Any hint ? > >>>>>> > >>>>>> Thank you for your help, > >>>>>> > >>>>>> F. Lefebvre > >>>>>> > >>>>>> _____________________________________ > >>>>>> Powered by www.kitware.com > >>>>>> > >>>>>> Visit other Kitware open-source projects at > >>>>>> http://www.kitware.com/opensource/opensource.html > >>>>>> > >>>>>> Kitware offers ITK Training Courses, for more information visit: > >>>>>> http://www.kitware.com/products/protraining.php > >>>>>> > >>>>>> Please keep messages on-topic and check the ITK FAQ at: > >>>>>> http://www.itk.org/Wiki/ITK_FAQ > >>>>>> > >>>>>> Follow this link to subscribe/unsubscribe: > >>>>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>>>> _______________________________________________ > >>>>>> Community mailing list > >>>>>> Community at itk.org > >>>>>> http://public.kitware.com/mailman/listinfo/community > >>>> > >>>> > >>> _____________________________________ > >>> Powered by www.kitware.com > >>> > >>> Visit other Kitware open-source projects at > >>> http://www.kitware.com/opensource/opensource.html > >>> > >>> Kitware offers ITK Training Courses, for more information visit: > >>> http://www.kitware.com/products/protraining.php > >>> > >>> Please keep messages on-topic and check the ITK FAQ at: > >>> http://www.itk.org/Wiki/ITK_FAQ > >>> > >>> Follow this link to subscribe/unsubscribe: > >>> http://public.kitware.com/mailman/listinfo/insight-users > > > > > > -- > > Fran?oise LEFEBVRE > > IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) > > Campus d'Orsay - B?t 440 > > 91405 ORSAY Cedex > > 01 69 15 51 87 > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.lemaitre58 at gmail.com Fri Oct 31 19:03:36 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Sat, 1 Nov 2014 00:03:36 +0100 Subject: [ITK-users] SimpleITK - Reading different DICOM serie Message-ID: Hi all, I am currently using SimpleITK with python to read directly some DICOM data. My dataset is corresponding to an MRI modality composed of 40 series. Each serie is a 3D volume. I would like to read the serie one-by-one. As a minimal example, I can post the following code: reader = sitk.ImageSeriesReader() # For each serie found for serie in reader.GetGDCMSeriesIDs(path_to_data): # Get the dicom filename corresponding to the current serie dicom_names = reader.GetGDCMSeriesFileNames(path_to_data, serie) reader.SetFileNames(dicom_names) image = reader.Execute() I got the following error: WARNING: In /home/lemaitre/anaconda/conda-bld/work/build/ITK/Modules/IO/GDCM/src/itkGDCMSeriesFileNames.cxx, line 138 GDCMSeriesFileNames (0x3078840): No Series were found However, the output of reader.GetGDCMSeriesIDs(path_to_data) seems ok: ('1.2.826.0.1.3680043.2.1125.1.12083572272639445972057901411530444', ............................ 40 lines ........................... '1.2.826.0.1.3680043.2.1125.1.98804240625293208256969403455867278') So my question is the following. What is the right way to passing the serieID to the GetGDCMSeriesFileNames() function. Thanks in advance, Best regards, -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: