From will.schroeder at kitware.com Fri Jun 8 11:06:30 2018 From: will.schroeder at kitware.com (Will Schroeder) Date: Fri, 8 Jun 2018 11:06:30 -0400 Subject: [ITK-users] Letters of Support for VTK proposal Message-ID: *Dear VTK Community-Kitware is submitting a VTK development grant proposal to the NIH in early July, and we?d like you to send us a letter of support for that proposal. This four year proposal aims to make significant improvements to VTK including rendering enhancements (VR and AR), better support for the web (such as VTK.js), improved data integration (supporting deep learning systems and federated, distributed databases, for example), and updated mechanisms for community support (improving the software and contribution process, documentation).We are very excited about the proposal since it will make a very positive impact on VTK, its community, and the many applications that use VTK. Several years ago we received a similar award and were able to revamp our rendering support (OpenGL), improve our software processes, and lay the foundation for VTK.js (among other achievements). Now, we can really use your help with our follow-on proposal. Part of the strategy of our proposal is to demonstrate to the reviewers that VTK plays a critical part in medical innovation. Along this line, we want to hear from the developers and users of VTK, so that they can indicate their support for VTK and our proposal.If you?d like to help, we have included three example letters. Please modify one of them to fit your circumstances, copy it to your letterhead, sign it, and then send it (a scanned pdf is fine) directly to me by June 30. These letters in no way obligate you or your employer, they simply state ?VTK is great and important to my work.? Also, don?t worry if you are not doing biomedical research, we want to hear from everybody. Note that this information (i.e., the names of endorsers) is considered private, only the writers of the VTK proposal and the NIH review team will see this information.If you have any questions or concerns, please feel free to contact me directly. Thanks and we hope to hear from you (by June 30). Feel free to forward this to friends and family.Sincerely,Will SchroederStephen AylwardKen MartinExample support letters follow:Example 1=========Dr. Ken MartinKitware, Inc.28 Corporate DriveClifton Park, NY 12065, USADear Dr. Martin,I am writing to indicate my support for your NIH proposal for the continued development of VTK. The VTK standards and software are absolutely critical to my lab, the ___ Lab at ___ University, and to my collaborators around the world. Even as we speak, I am working on a project involving complex visualizations using 3D Slicer, Osirix, ParaView, and ITKSnap (which are largely built on VTK). Several of my students also use VTK software libraries to write customized user interfaces and visualizations for my scientific and clinical collaborators. Our most recent application was for a physiologist who wanted to explore very specialized data related to the movement of the tongue in speech after glossectomy surgery.There are many worthy software projects under development around the world, but very few who can claim to be foundational. VTK can claim this, and I'm certain it can claim to be at the core of hundreds of software products that will be used by many biomedical researchers and thousands more that will be developed and used in-house. The complexity of visualization tasks has continued to grow with the volume of data and its connections across scales and from anatomy to function and from individuals to populations. VTK is keeping up with the demand?leading the rest, in fact?and should be a high priority for continued funding.Example 2=========Dr. William J. SchroederKitware, Inc.28 Corporate DriveClifton Park, NY 12065, USADear Dr. Schroeder,I enthusiastically endorse your proposed effort to support and improve VTK. We use this open source software in our work and have found it extremely helpful as we create new technological solutions. We have developed a software application that is currently being used by around the world for scientific data visualization to gain new insights. Your Visualization Toolkit has provided the software tools needed to develop that application that has satisfied the needs of a very diverse customer base. We definitely would be interested in your proposed VR/AR enhancements and improved integration with web services. VTK fills a vital role in the international community?s scientific computing infrastructure; additional developments along the lines that you propose will certainly accelerate innovation.Example 3=========Dr. Stephen R. AylwardKitware, Inc.101 East Weaver St, Ste G4Carrboro, NC 27510, USADear Dr. Aylward,I am writing in ardent support of your NIH proposal to continue the development, enhancement, and dissemination of the Visualization Toolkit (VTK). Not only do I use it in several projects myself, but I have found that it fosters the dissemination and extension of research by allowing the community to efficiently reproduce research, to easily combine contributions in unexpected ways, and to transfer research into production. Developing and maintaining a project as large and complex as VTK while fostering such an active community is a breathtaking achievement, and I hope Kitware obtains the funding it needs to keep this work up. * -- William J. Schroeder, PhD Kitware, Inc. - Building the World's Technical Computing Software 28 Corporate Drive Clifton Park, NY 12065 will.schroeder at kitware.com http://www.kitware.com (518) 881-4902 -------------- next part -------------- An HTML attachment was scrubbed... URL: From richard.brown at ucl.ac.uk Mon Jun 11 10:17:59 2018 From: richard.brown at ucl.ac.uk (mbcx9rb9) Date: Mon, 11 Jun 2018 07:17:59 -0700 (MST) Subject: [ITK-users] OrientImageFilter flipping VectorImage Message-ID: <1528726679658-0.post@n7.nabble.com> I have a multicomponent nifti image. It's a 3D volume and each voxel contains 3 values. I can then either save this to disk as a multicomponent nifti image or as 3 single component images. Using fslhd, I verify that all the headers of the single- and multi-component files are identical, except for the obvious fact that one is single component and the other is multi (e.g., dim0=3 vs. dim0=5). One thing that is particularly important is that they both are in RAS, as shown in this snippet: qform_xorient Right-to-Left qform_yorient Anterior-to-Posterior qform_zorient Superior-to-Inferior I read and reorient the images with a templated method: typedef itk::ImageFileReader ReaderType; ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(filename); reader->Update(); ITKImageType::Pointer itk_image_orig = reader->GetOutput(); typename itk::OrientImageFilter::Pointer orienter = itk::OrientImageFilter::New(); orienter->UseImageDirectionOn(); orienter->SetInput(itk_image_orig); orienter->SetDesiredCoordinateOrientation( itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAS); orienter->Update(); ITKImageType::Pointer itk_image = orienter->GetOutput(); std::cout << "\nflip axis:\n" << orienter->GetFlipAxes() << "\n"; Where the template is: - itk::Image for the single component images or - itk::VectorImage for the multi component images ======== The problem ======== The images are given in RAS and the desired output is RAS, so no changes should take place. output for single component images: "flip axis: [0, 0, 0]" output for multi component images: "flip axis: [0, 0, 1]" This is causing problems as the origin moves accordingly for multicomponent images. Is there any obvious reason as to why this is happening? Have I made a mistake somewhere? Is this a bug? Thanks -- Sent from: http://itk-users.7.n7.nabble.com/ From richard.brown at ucl.ac.uk Mon Jun 11 10:12:07 2018 From: richard.brown at ucl.ac.uk (mbcx9rb9) Date: Mon, 11 Jun 2018 07:12:07 -0700 (MST) Subject: [ITK-users] OrientImageFilter flipping VectorImage Message-ID: <1528726327408-0.post@n7.nabble.com> I have a multicomponent nifti image. It's a 3D volume and each voxel contains 3 values. I can then either save this to disk as a multicomponent nifti image or as 3 single component images. Using fslhd, I verify that all the headers of the single- and multi-component files are identical, except for the obvious fact that one is single component and the other is multi (e.g., dim0=3 vs. dim0=5). One thing that is particularly important is that they both are in RAS, as shown in this snippet: qform_xorient Right-to-Left qform_yorient Anterior-to-Posterior qform_zorient Superior-to-Inferior I read and reorient the images with a templated method: typedef itk::ImageFileReader ReaderType; ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName(filename); reader->Update(); ITKImageType::Pointer itk_image_orig = reader->GetOutput(); typename itk::OrientImageFilter::Pointer orienter = itk::OrientImageFilter::New(); orienter->UseImageDirectionOn(); orienter->SetInput(itk_image_orig); orienter->SetDesiredCoordinateOrientation( itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAS); orienter->Update(); ITKImageType::Pointer itk_image = orienter->GetOutput(); std::cout << "\nflip axis:\n" << orienter->GetFlipAxes() << "\n"; Where the template is: - itk::Image for the single component images or - itk::VectorImage for the multi component images ======== The problem ======== The images are given in RAS and the desired output is RAS, so no changes should take place. output for single component images: "flip axis: [0, 0, 0]" output for multi component images: "flip axis: [0, 0, 1]" This is causing problems as the origin moves accordingly for multicomponent images. Is there any obvious reason as to why this is happening? Have I made a mistake somewhere? Is this a bug? Thanks -- Sent from: http://itk-users.7.n7.nabble.com/ From richard.brown at ucl.ac.uk Mon Jun 11 12:04:09 2018 From: richard.brown at ucl.ac.uk (mbcx9rb9) Date: Mon, 11 Jun 2018 09:04:09 -0700 (MST) Subject: [ITK-users] OrientImageFilter flipping VectorImage In-Reply-To: <1528726327408-0.post@n7.nabble.com> References: <1528726327408-0.post@n7.nabble.com> Message-ID: <1528733049253-0.post@n7.nabble.com> After further investigation, the problem starts when the image is read. std::cout << itk_image_orig->GetDirection(); for itk::Image gives: 1 0 0 0 1 0 0 0 -1 but for itk::VectorImage gives: 1 0 0 0 1 0 0 0 1 As I said, the headers are identical (the bits I can see, at least): sizeof_hdr 348 data_type FLOAT32 dim0 5 dim1 285 dim2 285 dim3 127 dim4 1 dim5 3 dim6 1 dim7 1 vox_units mm time_units Unknown datatype 16 nbyper 4 bitpix 32 pixdim0 0.000000 pixdim1 2.086260 pixdim2 2.086260 pixdim3 2.031250 pixdim4 1.000000 pixdim5 1.000000 pixdim6 1.000000 pixdim7 1.000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 -2.086260 0.000000 -0.000000 296.248932 qto_xyz:2 0.000000 -2.086260 -0.000000 296.248932 qto_xyz:3 0.000000 0.000000 -2.031250 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Anterior-to-Posterior qform_zorient Superior-to-Inferior sform_name Unknown sform_code 0 sto_xyz:1 0.000000 0.000000 0.000000 0.000000 sto_xyz:2 0.000000 0.000000 0.000000 0.000000 sto_xyz:3 0.000000 0.000000 0.000000 0.000000 sto_xyz:4 0.000000 0.000000 0.000000 0.000000 sform_xorient Unknown sform_yorient Unknown sform_zorient Unknown file_type NIFTI-1+ file_code 1 descrip aux_file -- Sent from: http://itk-users.7.n7.nabble.com/ From llliu at umich.edu Mon Jun 11 16:47:06 2018 From: llliu at umich.edu (Lianli Liu) Date: Mon, 11 Jun 2018 16:47:06 -0400 Subject: [ITK-users] Error compile LandmarkBasedTransformInitializer.cxx Message-ID: Hi all, I am trying to compile LandmarkBasedTransformInitializer.cxx, but receive a lot of errors such as ?CreateFixedImage? declared void void CreateFixedImage(ImageType::Pointer image) Is it because that I need VTK for those Wiki examples, or there are other problems? I am using ITK 4.13.0. Thanks! Best, Lianli -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Jun 12 01:17:12 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 12 Jun 2018 07:17:12 +0200 Subject: [ITK-users] Error compile LandmarkBasedTransformInitializer.cxx In-Reply-To: References: Message-ID: Hi Lianli, can you repost the question on the forum , and provide a link to the example you are trying to compile? Regards, D?enan On Mon, Jun 11, 2018 at 10:47 PM Lianli Liu wrote: > Hi all, > > I am trying to compile LandmarkBasedTransformInitializer.cxx, but receive > a lot of errors such as ?CreateFixedImage? declared void > void CreateFixedImage(ImageType::Pointer image) > > Is it because that I need VTK for those Wiki examples, or there are other > problems? I am using ITK 4.13.0. > > Thanks! > > Best, > Lianli > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > 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: > https://itk.org/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From coyarzunlaura at googlemail.com Tue Jun 19 08:36:25 2018 From: coyarzunlaura at googlemail.com (Cristina Oyarzun) Date: Tue, 19 Jun 2018 14:36:25 +0200 Subject: [ITK-users] Deadline extended!! MICCAI CLIP 2018 Workshop on Clinical Image-based Procedures: Translational Research in Medical Imaging Message-ID: CALL FOR PAPERS MICCAI 2018 Workshop on Clinical Image-based Procedures: Translational Research in Medical Imaging September 16, 2018 Granada, Spain Website:http://miccai-clip.org/ ============================== ========================================== SCOPE The outstanding proliferation of medical image applications has created a need for greater study and scrutiny of the clinical application and validation of such methods. New strategies are essential to ensure a smooth and effective translation of computational image-based techniques into the clinic. For these reasons CLIP 2018?s major focus is on translational research filling the gaps between basic science and clinical applications. A highlight of the workshop is the subject of strategies for personalized medicine to enhance diagnosis, treatment and interventions. Authors are encouraged to submit work centered on specific clinical applications, including techniques and procedures based on comprehensive clinical image data. Submissions related to applications already in use and evaluated by clinical users are particularly encouraged. The event will bring together world-class specialists to present ways to strengthen links between computer scientists and engineers, and clinicians. TOPICS *Strategies for patient-specific and anatomical modeling to support planning and interventions *Clinical studies employing advanced image-guided methods *Clinical translation and validation of image-guided systems *Current challenges and emerging techniques in image-based procedures *Identification of parameters and error analysis in image-based procedures *Multimodal image integration for modeling, planning and guidance *Clinical applications in open and minimally invasive procedures PAPER SUBMISSION Papers will be limited to ten pages following the MICCAI submission guidelines. Prospective authors should refer to the Paper Submission section on the workshop website for details on how to submit papers to be presented at the workshop. All submissions will be peer-reviewed by at least 2 members of the program committee. The selection of the papers will be based on the significance of results, novelty, technical merit, relevance and clarity of presentation. Papers will be presented in a day long single track workshop starting with plenary sessions. Accepted papers will be published as a proceedings volume in the Springer Lecture Notes in Computer Science (LNCS) series after the workshop. WORKSHOP FORMAT Accepted papers will be presented in a day long single track workshop. The final program will consist of invited speakers and original papers with time allocated for discussions. Electronic proceedings will be arranged for all of the papers presented at the workshop. IMPORTANT DATES * June 25, 2018: Paper submission due date * tbd: Notification of acceptance * tbd: Final camera-ready paper submission deadline CONTACT Inquires about the workshop should be sent to the Information Desk ( info at miccai-clip.org). ORGANIZERS (in alphabetical order) Klaus Drechsler (Fraunhofer IGD, Germany) Marius Erdt (Fraunhofer IDM at NTU, Singapore) Miguel Gonz?lez Ballester (ICREA - Universitat Pompeu Fabra, Spain) Marius George Linguraru (Children's National Medical Center, USA) Cristina Oyarzun Laura (Fraunhofer IGD, Germany) Raj Shekhar (Children's National Medical Center, USA) Stefan Wesarg (Fraunhofer IGD, Germany) ======================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From chyumm at yahoo.com Tue Jun 19 08:30:21 2018 From: chyumm at yahoo.com (Jay Li) Date: Tue, 19 Jun 2018 08:30:21 -0400 Subject: [ITK-users] (no subject) Message-ID: <1529411427.VFmDfA6xzE7euVFmFfEvAP@mf-smf-ucb033c1> http://amazing.saintclarensrecords.com Jay Li -------------- next part -------------- An HTML attachment was scrubbed... URL: From elli.pfaehler at gmail.com Thu Jun 21 06:02:58 2018 From: elli.pfaehler at gmail.com (Elisabeth Pfaehler) Date: Thu, 21 Jun 2018 12:02:58 +0200 Subject: [ITK-users] Interpolation grid Message-ID: Dear all, I have one question: I have an image and a corresponding mask with a label marking a tumor region. I interpolate now both images using tri-linear interpolation. For aligning mask and image, I set in both cases the output origin to the origin of the original image. So far, everything is very fine. But now, I have the task to align the interpolated image grid of both image and mask so that the grid centers correspond for image and mask. I do not know if I was very clear with what I want to do, but is there any way to align interpolated image grids to the grid center and not the origin using ITK? Thanks a lot for your help, Elli -------------- next part -------------- An HTML attachment was scrubbed... URL: From zjinger at hotmail.com Sun Jun 24 23:27:37 2018 From: zjinger at hotmail.com (Zou Jing) Date: Mon, 25 Jun 2018 03:27:37 +0000 Subject: [ITK-users] ScalarImageToTextureFeaturesFilter Message-ID: Dear all, I am new to ITK and I want to calculate texture features of NIFTI images. But the result of different images are all the same, the result are 1 0 1 0 0 0 I?d appreciate it if you could help me . Many thanks. Here attached the code : #include "itkImage.h" #include "itkScalarImageToTextureFeaturesFilter.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkNiftiImageIO.h" typedef itk::Image ImageType; int main() { typedef itk::ImageFileReaderReaderType; ReaderType::Pointer reader = ReaderType::New(); ReaderType::Pointer reader1 = ReaderType::New(); reader->SetFileName("C:/Users/studentx/Downloads/lung_data/NormalLung2/F63y/F63_2013.nii"); reader->Update(); reader1->SetFileName("C:/Users/studentx/Downloads/lung_data/NormalLung2/F63y/F63_2013_mask.nii"); reader1->Update(); typedef itk::Statistics::ScalarImageToTextureFeaturesFilter TextureFilterType; TextureFilterType::Pointer textureFilter = TextureFilterType::New(); textureFilter->SetInput(reader->GetOutput()); textureFilter->SetMaskImage(reader1->GetOutput()); textureFilter->Update(); const TextureFilterType::FeatureValueVector* output = textureFilter->GetFeatureMeans(); for (unsigned int i = 0; i < output->size(); ++i) { std::cout << (*output)[i] << std::endl; } return EXIT_SUCCESS; } -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.radoux at uclouvain.be Tue Jun 26 03:11:05 2018 From: julien.radoux at uclouvain.be (radouxju) Date: Tue, 26 Jun 2018 00:11:05 -0700 (MST) Subject: [ITK-users] blind deconvolution : how to declare "parametric kernel" Message-ID: <1529997065177-0.post@n2.nabble.com> Dear list, I am trying to compile an application using the itk::ParametricBlindLeastSquaresDeconvolutionImageFilter . My problem is that I don't understand what I should use as type for the TKernelSource in the template of the filter. Basically I would like to use a 2D Gaussian kernel and, if I understand correctly, the filter will update its parameters, but how do I define the size and type of this kernel in my cxx ? -- Sent from: http://itk-insight-users.2283740.n2.nabble.com/ From will.schroeder at kitware.com Tue Jun 26 05:57:04 2018 From: will.schroeder at kitware.com (Will Schroeder) Date: Tue, 26 Jun 2018 05:57:04 -0400 Subject: [ITK-users] Letters of Support for VTK proposal In-Reply-To: References: Message-ID: We really can use more letters of support, they mean a lot in the review process. Please consider sending us one. And thanks to those of you that already have. Best, Will On Fri, Jun 8, 2018 at 11:06 AM Will Schroeder wrote: > > > > > > > > > > > > > > > > > > > > > > *Dear VTK Community-Kitware is submitting a VTK development grant proposal > to the NIH in early July, and we?d like you to send us a letter of support > for that proposal. This four year proposal aims to make significant > improvements to VTK including rendering enhancements (VR and AR), better > support for the web (such as VTK.js), improved data integration (supporting > deep learning systems and federated, distributed databases, for example), > and updated mechanisms for community support (improving the software and > contribution process, documentation).We are very excited about the proposal > since it will make a very positive impact on VTK, its community, and the > many applications that use VTK. Several years ago we received a similar > award and were able to revamp our rendering support (OpenGL), improve our > software processes, and lay the foundation for VTK.js (among other > achievements). Now, we can really use your help with our follow-on > proposal. Part of the strategy of our proposal is to demonstrate to the > reviewers that VTK plays a critical part in medical innovation. Along this > line, we want to hear from the developers and users of VTK, so that they > can indicate their support for VTK and our proposal.If you?d like to help, > we have included three example letters. Please modify one of them to fit > your circumstances, copy it to your letterhead, sign it, and then send it > (a scanned pdf is fine) directly to me by June 30. These letters in no way > obligate you or your employer, they simply state ?VTK is great and > important to my work.? Also, don?t worry if you are not doing biomedical > research, we want to hear from everybody. Note that this information (i.e., > the names of endorsers) is considered private, only the writers of the VTK > proposal and the NIH review team will see this information.If you have any > questions or concerns, please feel free to contact me directly. Thanks and > we hope to hear from you (by June 30). Feel free to forward this to friends > and family.Sincerely,Will SchroederStephen AylwardKen MartinExample support > letters follow:Example 1=========Dr. Ken MartinKitware, Inc.28 Corporate > DriveClifton Park, NY 12065, USADear Dr. Martin,I am writing to indicate my > support for your NIH proposal for the continued development of VTK. The VTK > standards and software are absolutely critical to my lab, the ___ Lab at > ___ University, and to my collaborators around the world. Even as we speak, > I am working on a project involving complex visualizations using 3D Slicer, > Osirix, ParaView, and ITKSnap (which are largely built on VTK). Several of > my students also use VTK software libraries to write customized user > interfaces and visualizations for my scientific and clinical collaborators. > Our most recent application was for a physiologist who wanted to explore > very specialized data related to the movement of the tongue in speech after > glossectomy surgery.There are many worthy software projects under > development around the world, but very few who can claim to be > foundational. VTK can claim this, and I'm certain it can claim to be at the > core of hundreds of software products that will be used by many biomedical > researchers and thousands more that will be developed and used in-house. > The complexity of visualization tasks has continued to grow with the volume > of data and its connections across scales and from anatomy to function and > from individuals to populations. VTK is keeping up with the demand?leading > the rest, in fact?and should be a high priority for continued > funding.Example 2=========Dr. William J. SchroederKitware, Inc.28 Corporate > DriveClifton Park, NY 12065, USADear Dr. Schroeder,I enthusiastically > endorse your proposed effort to support and improve VTK. We use this open > source software in our work and have found it extremely helpful as we > create new technological solutions. We have developed a software > application that is currently being used by around the world for scientific > data visualization to gain new insights. Your Visualization Toolkit has > provided the software tools needed to develop that application that has > satisfied the needs of a very diverse customer base. We definitely would be > interested in your proposed VR/AR enhancements and improved integration > with web services. VTK fills a vital role in the international community?s > scientific computing infrastructure; additional developments along the > lines that you propose will certainly accelerate innovation.Example > 3=========Dr. Stephen R. AylwardKitware, Inc.101 East Weaver St, Ste > G4Carrboro, NC 27510, USADear Dr. Aylward,I am writing in ardent support > of your NIH proposal to continue the development, enhancement, and > dissemination of the Visualization Toolkit (VTK). Not only do I use it in > several projects myself, but I have found that it fosters the dissemination > and extension of research by allowing the community to efficiently > reproduce research, to easily combine contributions in unexpected ways, and > to transfer research into production. Developing and maintaining a project > as large and complex as VTK while fostering such an active community is a > breathtaking achievement, and I hope Kitware obtains the funding it needs > to keep this work up. * > > > -- > William J. Schroeder, PhD > Kitware, Inc. - Building the World's Technical Computing Software > 28 Corporate Drive > Clifton Park, NY 12065 > will.schroeder at kitware.com > http://www.kitware.com > (518) 881-4902 > -- William J. Schroeder, PhD Kitware, Inc. - Building the World's Technical Computing Software 28 Corporate Drive Clifton Park, NY 12065 will.schroeder at kitware.com http://www.kitware.com (518) 881-4902 -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Jun 26 08:24:08 2018 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 26 Jun 2018 12:24:08 +0000 Subject: [ITK-users] blind deconvolution : how to declare "parametric kernel" In-Reply-To: <1529997065177-0.post@n2.nabble.com> References: <1529997065177-0.post@n2.nabble.com> Message-ID: <0869D40B-4B44-48BE-9C5E-85BBCEA93BB2@mail.nih.gov> As attached to the end, please post in discourse. I'll point you to a couple things: 1) The test for the class may be useful: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/Deconvolution/test/itkParametricBlindLeastSquaresDeconvolutionImageFilterTest.cxx 2) This class may have come from or be related to this IJ: http://www.insight-journal.org/browse/publication/753 Hope that helps, Brad ?On 6/26/18, 3:19 AM, "radouxju" wrote: Dear list, I am trying to compile an application using the itk::ParametricBlindLeastSquaresDeconvolutionImageFilter . My problem is that I don't understand what I should use as type for the TKernelSource in the template of the filter. Basically I would like to use a 2D Gaussian kernel and, if I understand correctly, the filter will update its parameters, but how do I define the size and type of this kernel in my cxx ? -- Sent from: http://itk-insight-users.2283740.n2.nabble.com/ The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there! ________________________________ 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: https://itk.org/mailman/listinfo/insight-users From leenzz.m at gmail.com Wed Jun 27 23:36:36 2018 From: leenzz.m at gmail.com (leena m) Date: Thu, 28 Jun 2018 09:06:36 +0530 Subject: [ITK-users] post a message Message-ID: i'm a beginner in python wen i apply thresholding i'm getting error import SimpleITK as sitk img = sitk.ReadImage("Sub1.png") img=img>20 i'm getting error as RuntimeError Traceback (most recent call last) in () 1 #img = sitk.Image(img.GetSize(), sitk.sitkUInt8)----> 2 img=img>20 ~/sitkpy/lib/python3.5/site-packages/SimpleITK/SimpleITK.py in __gt__(self, other) 4424 return Greater( self, other ) 4425 try:-> 4426 return Greater( self, float(other) ) 4427 except (ValueError, TypeError): 4428 return NotImplemented ~/sitkpy/lib/python3.5/site-packages/SimpleITK/SimpleITK.py in Greater(*args) 34345 34346 """ > 34347 return _SimpleITK.Greater(*args) 34348 class GridImageSource(ImageFilter_0): 34349 """ RuntimeError: Exception thrown in SimpleITK Greater: /tmp/SimpleITK/Code/Common/include/sitkMemberFunctionFactory.hxx:209: sitk::ERROR: Pixel type: vector of 8-bit unsigned integer is not supported in 2D byN3itk6simple18GreaterImageFilterE I applied img = sitk.Image(img.GetSize(), sitk.sitkUInt8) but I'm getting a black image Is there any option like double(img) or im2bw in python.Will normalize work? -------------- next part -------------- An HTML attachment was scrubbed... URL: From drcjaudet at gmail.com Thu Jun 28 11:11:20 2018 From: drcjaudet at gmail.com (Cyril Jaudet) Date: Thu, 28 Jun 2018 17:11:20 +0200 Subject: [ITK-users] Kmeans, Otsu on SPECT image Message-ID: Hello, i want to use Otsu and Kmeans method to segment several lesion on SPECT image. The threshold method is apply on different lesion independently. I write it directly in 3DSlicer. The code for Otsu is working: (write in simpleITK) ####################### label_masked=ThB.Execute(label_PET, 1, 1 ,1, 0) # labelOtsu_parlesion=Otsu.Execute(imagePET,label_masked, 0, 1, 64, True, 1) LabelsOtsu=labelOtsu_parlesion for label in range(2, len(Nlabels)+1): label_masked=ThB.Execute(label_PET, label, label ,label, 0) # labelOtsu_parlesion=Otsu.Execute(imagePET,label_masked, 0, label, 64, True, label) LabelsOtsu=Add.Execute(LabelsOtsu,labelOtsu_parlesion) su.PushToSlicer(LabelsOtsu, 'Otsu_intermediate', 2 ) ################################ I try with Kmeans but i didn't suceed to use a mask directly and is there any kmeans++ avaible? ################################################kmeans#################### label_masked=ThB.Execute(dilatelabelOtsu, 1, 1 ,1, 0) # Image_masked=Mask.Execute(imagePET,label_masked ) labelKmeans_parlesion=Kmeans.Execute(Image_masked) Imagefinal2=labelKmeans_parlesion for label in range(2, len(Nlabels)+1): print label label_masked=ThB.Execute(dilatelabelOtsu, label, label ,label, 0) # Image_masked=Mask.Execute(imagePET,label_masked ) labelKmeans_parlesion=Kmeans.Execute(Image_masked) Imagefinal2=Add.Execute(Imagefinal,labelKmeans_parlesion) su.PushToSlicer(Imagefinal2, 'Kmeans_final', 2 ) ########################################################## Also if you have idea/experience for denoising SPECT image;) Thank you, Cyril Jaudet, Phd -------------- next part -------------- An HTML attachment was scrubbed... URL: From zivrafael.yaniv at nih.gov Thu Jun 28 12:11:12 2018 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Thu, 28 Jun 2018 16:11:12 +0000 Subject: [ITK-users] post a message In-Reply-To: References: Message-ID: <1070D8F7-BB8D-448E-9A6A-7A1E0D2E632A@nih.gov> Hello Leena, The ITK users mailing list is deprecated. In the future, please post questions to the ITK discourse forum https://discourse.itk.org/ With respect to the runtime error, your png image is likely a color image even if it looks grayscale, it is what we call a vector image (multi-channel) in SimpleITK, and the operation of img>20 does not make sense for such images, hence the exception. As it is not clear what you want to do ?threshold a color image? is not a well-defined operation, please post on the discourse forum and provide additional details so that we can help you. You can see all of the relevant information with respect to ?img?, by printing the image ?print(img)? will show you the actual structure of the image you read. hope this helps Ziv From: leena m Date: Wednesday, June 27, 2018 at 11:38 PM To: "insight-users at itk.org" Subject: [ITK-users] post a message i'm a beginner in python wen i apply thresholding i'm getting error import SimpleITK as sitk img = sitk.ReadImage("Sub1.png") img=img>20 i'm getting error as RuntimeError Traceback (most recent call last) in () 1 #img = sitk.Image(img.GetSize(), sitk.sitkUInt8) ----> 2 img=img>20 ~/sitkpy/lib/python3.5/site-packages/SimpleITK/SimpleITK.py in __gt__(self, other) 4424 return Greater( self, other ) 4425 try: -> 4426 return Greater( self, float(other) ) 4427 except (ValueError, TypeError): 4428 return NotImplemented ~/sitkpy/lib/python3.5/site-packages/SimpleITK/SimpleITK.py in Greater(*args) 34345 34346 """ > 34347 return _SimpleITK.Greater(*args) 34348 class GridImageSource(ImageFilter_0): 34349 """ RuntimeError: Exception thrown in SimpleITK Greater: /tmp/SimpleITK/Code/Common/include/sitkMemberFunctionFactory.hxx:209: sitk::ERROR: Pixel type: vector of 8-bit unsigned integer is not supported in 2D byN3itk6simple18GreaterImageFilterE I applied img = sitk.Image(img.GetSize(), sitk.sitkUInt8) but I'm getting a black image Is there any option like double(img) or im2bw in python.Will normalize work? -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Sat Jun 30 04:45:01 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sat, 30 Jun 2018 10:45:01 +0200 Subject: [ITK-users] Interpolation grid In-Reply-To: References: Message-ID: Hi Elli, what you seem to want to do it apply the same transform to both your original image and its mask. There is normal image resampling (read more about it in the software guide ). And there is also hardening of linear transforms (affine, rigid etc), where only the image's meta-data is modified, but pixel data is untouched. Regards, D?enan On Thu, Jun 21, 2018 at 12:03 PM Elisabeth Pfaehler wrote: > Dear all, > > I have one question: > > I have an image and a corresponding mask with a label marking a tumor > region. > I interpolate now both images using tri-linear interpolation. For aligning > mask and image, I set in both cases the output origin to the origin of the > original image. > So far, everything is very fine. But now, I have the task to align the > interpolated image grid of both image and mask so that the grid centers > correspond for image and mask. I do not know if I was very clear with what > I want to do, but is there any way to align interpolated image grids to the > grid center and not the origin using ITK? > > Thanks a lot for your help, > > Elli > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > 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: > https://itk.org/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: