From bakkari.abdelkhalek at hotmail.fr Sat Dec 3 17:39:08 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Sat, 3 Dec 2016 22:39:08 +0000 Subject: [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration - Message-ID: Hi, I am a little familiar with ITK. I just need to know how can I apply the model to Image registration 2 to a dicom image series. https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ModelToImageRegistration2_8cxx-example.html#_a13 Thank you inadvance. Kind regards, Abdelkhalek Bakkari Ph.D candidate in Computer Science Institute of Applied Computer Science Lodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From bakkari.abdelkhalek at hotmail.fr Sat Dec 3 18:08:26 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Sat, 3 Dec 2016 23:08:26 +0000 Subject: [ITK-users] [ITK] 3D Binary Mask to Point Set - 3D Image Registration - In-Reply-To: References: , Message-ID: Hi Andras, I am not using just using examples. But, I am creating my own application from existing examples in ITK. ________________________________ From: Andras Lasso Sent: 03 December 2016 23:57 To: Abdelkhalek Bakkari Subject: RE: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration - Hi Abdelkhalek, ITK is a only for algorithm developers or advanced users (who can figure out how to perform simple operations such as applying a transform from the plenty of examples and tests that are included in ITK). If you want to just use algorithms then it's much more efficient to use applications that ITK is integrated into. For example, applying a transform to a DICOM series is a trivial operation in 3D Slicer (drag-and-drop DICOM directory to import your DICOM data, use DICOM module to load DICOM series, drag-and-drop transform file to load transform, using Transforms module apply transform to image). You can also perform all kinds of analysis, segmentation, quantification, and visualization tasks in Slicer (you can visualize the original and transformed volume, original and transformed landmark points, segmented surfaces; or the transformation itself). You can also fully script all operations if you need to process a large number of sequences in batch mode. Andras From: Abdelkhalek Bakkari Sent: Saturday, December 3, 2016 17:39 To: insight-users Subject: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration - Hi, I am a little familiar with ITK. I just need to know how can I apply the model to Image registration 2 to a dicom image series. https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ModelToImageRegistration2_8cxx-example.html#_a13 Thank you inadvance. Kind regards, Abdelkhalek Bakkari Ph.D candidate in Computer Science Institute of Applied Computer Science Lodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From lasso at queensu.ca Sat Dec 3 20:15:56 2016 From: lasso at queensu.ca (Andras Lasso) Date: Sun, 4 Dec 2016 01:15:56 +0000 Subject: [ITK-users] [ITK] 3D Binary Mask to Point Set - 3D Image Registration - In-Reply-To: References: , Message-ID: The point I'm trying to make is that you should not start developing a custom application from scratch before you have a complete, proven, and tested solution. You can develop and test solutions very quickly by using existing application frameworks (3D Slicer, MITK, Paraview, etc). They all allow writing plugins to add custom algorithms or streamlined user interface. Andras From: Abdelkhalek Bakkari [mailto:bakkari.abdelkhalek at hotmail.fr] Sent: December 3, 2016 18:08 To: Andras Lasso ; insight-users Subject: Re: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration - Hi Andras, I am not using just using examples. But, I am creating my own application from existing examples in ITK. ________________________________ From: Andras Lasso > Sent: 03 December 2016 23:57 To: Abdelkhalek Bakkari Subject: RE: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration - Hi Abdelkhalek, ITK is a only for algorithm developers or advanced users (who can figure out how to perform simple operations such as applying a transform from the plenty of examples and tests that are included in ITK). If you want to just use algorithms then it's much more efficient to use applications that ITK is integrated into. For example, applying a transform to a DICOM series is a trivial operation in 3D Slicer (drag-and-drop DICOM directory to import your DICOM data, use DICOM module to load DICOM series, drag-and-drop transform file to load transform, using Transforms module apply transform to image). You can also perform all kinds of analysis, segmentation, quantification, and visualization tasks in Slicer (you can visualize the original and transformed volume, original and transformed landmark points, segmented surfaces; or the transformation itself). You can also fully script all operations if you need to process a large number of sequences in batch mode. Andras From: Abdelkhalek Bakkari Sent: Saturday, December 3, 2016 17:39 To: insight-users Subject: [ITK] [ITK-users] 3D Binary Mask to Point Set - 3D Image Registration - Hi, I am a little familiar with ITK. I just need to know how can I apply the model to Image registration 2 to a dicom image series. https://itk.org/Doxygen/html/Examples_2RegistrationITKv4_2ModelToImageRegistration2_8cxx-example.html#_a13 Thank you inadvance. Kind regards, Abdelkhalek Bakkari Ph.D candidate in Computer Science Institute of Applied Computer Science Lodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgo_2113 at hotmail.com Sun Dec 4 09:15:29 2016 From: cgo_2113 at hotmail.com (CocoM) Date: Sun, 4 Dec 2016 07:15:29 -0700 (MST) Subject: [ITK-users] Optimization in deformable registration Message-ID: <1480860929243-7589502.post@n2.nabble.com> Hi everyone, Being fairly new in ITK, I have kind of a general question about deformable registration. I'm working with the LevelSetMotionRegistrationFilter/Function classes and the example DeformableRegistration5, which is using them. I noticed this example doesn't use any optimizer class. It seems to be the same for the other PDEDeformable methods. So my question is : why? Is that because it's non parametric registration? And I guess there isn't any possibility to use an optimizer class in that kind of problem? Thanks a lot in advance, Marie -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Optimization-in-deformable-registration-tp7589502.html Sent from the ITK Insight Users mailing list archive at Nabble.com. From dzenanz at gmail.com Sun Dec 4 13:04:28 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sun, 4 Dec 2016 13:04:28 -0500 Subject: [ITK-users] Optimization in deformable registration In-Reply-To: <1480860929243-7589502.post@n2.nabble.com> References: <1480860929243-7589502.post@n2.nabble.com> Message-ID: Hi Marie, by looking at the documentation of Level-Set Motion Registration Filter , optimizer is not needed. The whole registration is set up as an iterative process, executing motion equations at each iteration. You need to experiment with it to see which number of iterations produces good results for your case. Regards, D?enan On Sun, Dec 4, 2016 at 9:15 AM, CocoM wrote: > Hi everyone, > > Being fairly new in ITK, I have kind of a general question about deformable > registration. I'm working with the LevelSetMotionRegistrationFilt > er/Function > classes and the example DeformableRegistration5, which is using them. I > noticed this example doesn't use any optimizer class. It seems to be the > same for the other PDEDeformable methods. So my question is : why? Is that > because it's non parametric registration? And I guess there isn't any > possibility to use an optimizer class in that kind of problem? > > Thanks a lot in advance, > > Marie > > > > -- > View this message in context: http://itk-insight-users. > 2283740.n2.nabble.com/Optimization-in-deformable- > registration-tp7589502.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From steve at sumost.ca Sun Dec 4 13:43:37 2016 From: steve at sumost.ca (Steve M. Robbins) Date: Sun, 04 Dec 2016 12:43:37 -0600 Subject: [ITK-users] Picking corresponding anatomical points -- best software for a clinician? Message-ID: <2164522.aeE28Xrt1B@riemann> Hi, I have an urgent need to acquire some data to validate (medical) image registration in a clinical context. To that end, I plan to sit with several clinicians and have them identify salient points in two datasets that will be registered. Then I plan to use the residual errors of these points after registration -- e.g. the median distance -- as a quality metric. What I'm after right now is a really easy-to-use tool with which the clinician can pick the points. So that one can judge the points are indeed corresponding: my present thought is to have an MPR view of each image volume side-by-side; e.g. axial/sagittal/coronal of volume 1 on top of the same slices of volume 2. Or similar. My main requirement is that a clinician who is familar with PACS viewers can learn to use it in a minute or so. The other requirement is that the point coordinates can be saved to a file for later analysis. Despite posting to the ITK list: ITK is not a requirement. My question, briefly, is: what software would you recommend for this scenario? I have briefly looked at 3D Slicer, MITK, Amide, and RegistrationShop. So far, 3D Slicer is the only one that I can even find the functionality I want -- using the LandmarkRegistration module. I realize this next part may come across as whining so let me say up front I mean no denigration of the many fine folks who put hard work into 3D Slicer! If I were the one picking the points, I think the Landmark Registration of 3D Slicer would be fine. However, the clinician will be driving and will typically have limited time and patience -- so I want something reasonably familiar. For example: in navigating through the stacks: I can use the scrool wheel or slider to choose a slice. But then I have to manipulate all three slices to find a point. In other software, one can grab the slice intersection lines and update the other two slices -- e.g. move the coronal and sagittal to intersect a point of interest located on the axial. I can turn on slice intersection lines, but it shows intersections for BOTH volumes, which I don't want as they are not registered. And when I use SHIFT to drag around the lines, both volumes are updated. I need to do one volume at a time. Maybe there is a way to tune the Slicer GUI to my needs? Or maybe a more appropriate module I have overlooked? For any thoughts: thanks in advance, -Steve -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part. URL: From fepegar at gmail.com Sun Dec 4 13:59:52 2016 From: fepegar at gmail.com (=?UTF-8?B?RmVybmFuZG8gUMOpcmV6LUdhcmPDrWE=?=) Date: Sun, 4 Dec 2016 19:59:52 +0100 Subject: [ITK-users] Picking corresponding anatomical points -- best software for a clinician? In-Reply-To: <2164522.aeE28Xrt1B@riemann> References: <2164522.aeE28Xrt1B@riemann> Message-ID: ?Hi Steve, I think you should ask in Slicer mailing list: http://slicer-users.65878.n3.nabble.com/ You should be able to do what you want with some Python scripting. Best, Fernando? 2016-12-04 19:43 GMT+01:00 Steve M. Robbins : > Hi, > > I have an urgent need to acquire some data to validate (medical) image > registration in a clinical context. To that end, I plan to sit with > several > clinicians and have them identify salient points in two datasets that will > be > registered. Then I plan to use the residual errors of these points after > registration -- e.g. the median distance -- as a quality metric. > > What I'm after right now is a really easy-to-use tool with which the > clinician > can pick the points. So that one can judge the points are indeed > corresponding: my present thought is to have an MPR view of each image > volume > side-by-side; e.g. axial/sagittal/coronal of volume 1 on top of the same > slices of volume 2. Or similar. My main requirement is that a clinician > who > is familar with PACS viewers can learn to use it in a minute or so. > > The other requirement is that the point coordinates can be saved to a file > for > later analysis. Despite posting to the ITK list: ITK is not a requirement. > > My question, briefly, is: what software would you recommend for this > scenario? > > I have briefly looked at 3D Slicer, MITK, Amide, and RegistrationShop. So > far, > 3D Slicer is the only one that I can even find the functionality I want -- > using the LandmarkRegistration module. I realize this next part may come > across as whining so let me say up front I mean no denigration of the many > fine > folks who put hard work into 3D Slicer! If I were the one picking the > points, > I think the Landmark Registration of 3D Slicer would be fine. However, the > clinician will be driving and will typically have limited time and > patience -- > so I want something reasonably familiar. For example: in navigating > through > the stacks: I can use the scrool wheel or slider to choose a slice. But > then > I have to manipulate all three slices to find a point. In other software, > one > can grab the slice intersection lines and update the other two slices -- > e.g. > move the coronal and sagittal to intersect a point of interest located on > the > axial. I can turn on slice intersection lines, but it shows > intersections > for BOTH volumes, which I don't want as they are not registered. And when > I > use SHIFT to drag around the lines, both volumes are updated. I need to do > one volume at a time. > > Maybe there is a way to tune the Slicer GUI to my needs? Or maybe a more > appropriate module I have overlooked? > > For any thoughts: thanks in advance, > -Steve > > _____________________________________ > 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 dzenanz at gmail.com Sun Dec 4 19:04:06 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sun, 4 Dec 2016 19:04:06 -0500 Subject: [ITK-users] Picking corresponding anatomical points -- best software for a clinician? In-Reply-To: <2164522.aeE28Xrt1B@riemann> References: <2164522.aeE28Xrt1B@riemann> Message-ID: Hi Steve, in 3DSlicer, pressing shift key (Windows, could be different on Mac) and moving mouse will select other 2 slices corresponding to mouse position. Slicer can also save fiducial points list into a file (comma separated values format). Regards, D?enan On Sun, Dec 4, 2016 at 1:43 PM, Steve M. Robbins wrote: > Hi, > > I have an urgent need to acquire some data to validate (medical) image > registration in a clinical context. To that end, I plan to sit with > several > clinicians and have them identify salient points in two datasets that will > be > registered. Then I plan to use the residual errors of these points after > registration -- e.g. the median distance -- as a quality metric. > > What I'm after right now is a really easy-to-use tool with which the > clinician > can pick the points. So that one can judge the points are indeed > corresponding: my present thought is to have an MPR view of each image > volume > side-by-side; e.g. axial/sagittal/coronal of volume 1 on top of the same > slices of volume 2. Or similar. My main requirement is that a clinician > who > is familar with PACS viewers can learn to use it in a minute or so. > > The other requirement is that the point coordinates can be saved to a file > for > later analysis. Despite posting to the ITK list: ITK is not a requirement. > > My question, briefly, is: what software would you recommend for this > scenario? > > I have briefly looked at 3D Slicer, MITK, Amide, and RegistrationShop. So > far, > 3D Slicer is the only one that I can even find the functionality I want -- > using the LandmarkRegistration module. I realize this next part may come > across as whining so let me say up front I mean no denigration of the many > fine > folks who put hard work into 3D Slicer! If I were the one picking the > points, > I think the Landmark Registration of 3D Slicer would be fine. However, the > clinician will be driving and will typically have limited time and > patience -- > so I want something reasonably familiar. For example: in navigating > through > the stacks: I can use the scrool wheel or slider to choose a slice. But > then > I have to manipulate all three slices to find a point. In other software, > one > can grab the slice intersection lines and update the other two slices -- > e.g. > move the coronal and sagittal to intersect a point of interest located on > the > axial. I can turn on slice intersection lines, but it shows > intersections > for BOTH volumes, which I don't want as they are not registered. And when > I > use SHIFT to drag around the lines, both volumes are updated. I need to do > one volume at a time. > > Maybe there is a way to tune the Slicer GUI to my needs? Or maybe a more > appropriate module I have overlooked? > > For any thoughts: thanks in advance, > -Steve > > _____________________________________ > 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 steve at sumost.ca Sun Dec 4 22:40:18 2016 From: steve at sumost.ca (Steve M. Robbins) Date: Sun, 04 Dec 2016 21:40:18 -0600 Subject: [ITK-users] Picking corresponding anatomical points -- best software for a clinician? In-Reply-To: References: <2164522.aeE28Xrt1B@riemann> Message-ID: <296184501.RM8fqRJEb6@riemann> Dear slicer-users: I originally asked a question in insight-users but it touches on slicer, so I'm cross-posting. On Sunday, December 4, 2016 7:04:06 PM CST D?enan Zuki? wrote: > Hi Steve, > > in 3DSlicer, pressing shift key (Windows, could be different on Mac) and > moving mouse will select other 2 slices corresponding to mouse position. Yes, but when I have two volumes displayed using Landmark Registration module, the shift-mouse-move operation on axial updates the sagital and coronal of BOTH volumes, not just the one I'm operating on. This seems wrong to me when the two volumes are not registered. > Slicer can also save fiducial points list into a file (comma separated > values format). Yes, that is great. > > Regards, > D?enan > > On Sun, Dec 4, 2016 at 1:43 PM, Steve M. Robbins wrote: > > Hi, > > > > I have an urgent need to acquire some data to validate (medical) image > > registration in a clinical context. To that end, I plan to sit with > > several > > clinicians and have them identify salient points in two datasets that will > > be > > registered. Then I plan to use the residual errors of these points after > > registration -- e.g. the median distance -- as a quality metric. > > > > What I'm after right now is a really easy-to-use tool with which the > > clinician > > can pick the points. So that one can judge the points are indeed > > corresponding: my present thought is to have an MPR view of each image > > volume > > side-by-side; e.g. axial/sagittal/coronal of volume 1 on top of the same > > slices of volume 2. Or similar. My main requirement is that a clinician > > who > > is familar with PACS viewers can learn to use it in a minute or so. > > > > The other requirement is that the point coordinates can be saved to a file > > for > > later analysis. Despite posting to the ITK list: ITK is not a > > requirement. > > > > My question, briefly, is: what software would you recommend for this > > scenario? > > > > I have briefly looked at 3D Slicer, MITK, Amide, and RegistrationShop. So > > far, > > 3D Slicer is the only one that I can even find the functionality I want -- > > using the LandmarkRegistration module. I realize this next part may come > > across as whining so let me say up front I mean no denigration of the many > > fine > > folks who put hard work into 3D Slicer! If I were the one picking the > > points, > > I think the Landmark Registration of 3D Slicer would be fine. However, > > the > > clinician will be driving and will typically have limited time and > > patience -- > > so I want something reasonably familiar. For example: in navigating > > through > > the stacks: I can use the scrool wheel or slider to choose a slice. But > > then > > I have to manipulate all three slices to find a point. In other software, > > one > > can grab the slice intersection lines and update the other two slices -- > > e.g. > > move the coronal and sagittal to intersect a point of interest located on > > the > > axial. I can turn on slice intersection lines, but it shows > > intersections > > for BOTH volumes, which I don't want as they are not registered. And when > > I > > use SHIFT to drag around the lines, both volumes are updated. I need to > > do > > one volume at a time. > > > > Maybe there is a way to tune the Slicer GUI to my needs? Or maybe a more > > appropriate module I have overlooked? > > > > For any thoughts: thanks in advance, > > -Steve > > > > _____________________________________ > > 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 -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part. URL: From dzenanz at gmail.com Wed Dec 7 18:37:13 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 7 Dec 2016 18:37:13 -0500 Subject: [ITK-users] Fwd: [Developer Community] Ulzii Luvsanbat posted a new comment on "Compiling ITK triggers internal error" In-Reply-To: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com> References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com> Message-ID: ---------- Forwarded message ---------- From: Date: Wed, Dec 7, 2016 at 6:17 PM Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on "Compiling ITK triggers internal error" To: dzenanz at gmail.com Hi d?enan-zuki?, A new comment on a *Compiling ITK triggers internal error* was posted by Ulzii Luvsanbat on Developer Community: * Hello, Thanks for this report. We'll look into fixing this for VS2017. We're also going to add this open source project to our compiler validation test suites to ensure we don't ship future VS releases that don't compile ITK sources. Thanks, Ulzii Luvsanbat Visual C++ Team * View Ulzii Luvsanbat's new comment If you do not wish to receive these notifications you can update your Notification Settings . This message from Microsoft is an important part of a program, service, or product that you or your company purchased or participate in. Microsoft respects your privacy. Please read our Privacy Statement . -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Dec 8 10:34:22 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 8 Dec 2016 15:34:22 +0000 Subject: [ITK-users] [ITK] Fwd: [Developer Community] Ulzii Luvsanbat posted a new comment on "Compiling ITK triggers internal error" In-Reply-To: References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com> Message-ID: <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov> Thanks for reporting and forwarding that reported issue. That sounds outstanding that they will try to fix the issue for the VS release, and are also consider adding ITK into their compiler validation tests. Based on the Experimental build I did: https://open.cdash.org/viewBuildError.php?buildid=4673717 This looks like the only internal compiler error (ICE) encountered. I hope there are not more ICE encounter after this one. One thing to note is that with this ICE no tests were able to run, so we don?t know if the code generated has any differences or problems. I wonder if there is a little hack that could be done to work around this ICE issue in itkPrometeType.h, to see if there are any other issues later one? Brad On Dec 7, 2016, at 6:37 PM, D?enan Zuki? > wrote: ---------- Forwarded message ---------- From: > Date: Wed, Dec 7, 2016 at 6:17 PM Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on "Compiling ITK triggers internal error" To: dzenanz at gmail.com [https://developercommunity.visualstudio.com/themes/microsoft/images/visual_studio_logo_small.png] Hi d?enan-zuki?, A new comment on a Compiling ITK triggers internal error was posted by Ulzii Luvsanbat on Developer Community: Hello, Thanks for this report. We'll look into fixing this for VS2017. We're also going to add this open source project to our compiler validation test suites to ensure we don't ship future VS releases that don't compile ITK sources. Thanks, Ulzii Luvsanbat Visual C++ Team View Ulzii Luvsanbat's new comment If you do not wish to receive these notifications you can update your Notification Settings. This message from Microsoft is an important part of a program, service, or product that you or your company purchased or participate in. Microsoft respects your privacy. Please read our Privacy Statement. [https://developercommunity.visualstudio.com/themes/microsoft/images/Microsoft-logo_rgb_c-gray4.png] _____________________________________ 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 dzenanz at gmail.com Thu Dec 8 10:37:58 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 8 Dec 2016 10:37:58 -0500 Subject: [ITK-users] [ITK] Fwd: [Developer Community] Ulzii Luvsanbat posted a new comment on "Compiling ITK triggers internal error" In-Reply-To: <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov> References: <6.7.37282.572.COMMENT.a769b2ad82de06fda7e952dd76e9db37@microsoft.com> <303FFB15-F51A-48A3-AD3A-01CEEA30059F@mail.nih.gov> Message-ID: Hopefully they will give me a chance to thoroughly test the fix, in case they don't do it themselves. There will probably be another update to the RC release - there was one already. Regards, D?enan On Thu, Dec 8, 2016 at 10:34 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov> wrote: > Thanks for reporting and forwarding that reported issue. That sounds > outstanding that they will try to fix the issue for the VS release, and are > also consider adding ITK into their compiler validation tests. > > Based on the Experimental build I did: > https://open.cdash.org/viewBuildError.php?buildid=4673717 > > This looks like the only internal compiler error (ICE) encountered. I hope > there are not more ICE encounter after this one. > > One thing to note is that with this ICE no tests were able to run, so we > don?t know if the code generated has any differences or problems. I wonder > if there is a little hack that could be done to work around this ICE issue > in itkPrometeType.h, to see if there are any other issues later one? > > Brad > > On Dec 7, 2016, at 6:37 PM, D?enan Zuki? wrote: > > > ---------- Forwarded message ---------- > From: > Date: Wed, Dec 7, 2016 at 6:17 PM > Subject: [Developer Community] Ulzii Luvsanbat posted a new comment on > "Compiling ITK triggers internal error" > To: dzenanz at gmail.com > > > > > Hi d?enan-zuki?, > > A new comment on a *Compiling ITK triggers internal error* > was > posted by Ulzii Luvsanbat on Developer Community: > > > > * Hello, Thanks for this report. We'll look into fixing this for VS2017. > We're also going to add this open source project to our compiler validation > test suites to ensure we don't ship future VS releases that don't compile > ITK sources. Thanks, Ulzii Luvsanbat Visual C++ Team * > > View Ulzii Luvsanbat's new comment > > > If you do not wish to receive these notifications you can update your Notification > Settings > > . > > This message from Microsoft is an important part of a program, service, or > product that you or your company purchased or participate in. > Microsoft respects your privacy. Please read our Privacy Statement > . > > _____________________________________ > 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 dzenanz at gmail.com Thu Dec 8 14:05:42 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 8 Dec 2016 14:05:42 -0500 Subject: [ITK-users] Fwd: [Developer Community] Ulzii Luvsanbat posted a new solution to "Compiling ITK triggers internal error" In-Reply-To: <6.7.37951.572.SOLUTION.ca0f8282a528bda939595b4871560509@microsoft.com> References: <6.7.37951.572.SOLUTION.ca0f8282a528bda939595b4871560509@microsoft.com> Message-ID: I guess they are nearing release. ---------- Forwarded message ---------- From: Date: Dec 8, 2016 13:23 Subject: [Developer Community] Ulzii Luvsanbat posted a new solution to "Compiling ITK triggers internal error" To: Cc: > > Hi d?enan-zuki?, > > A new solution to the problem "Compiling ITK triggers internal error" was > posted by Ulzii Luvsanbat on Developer Community: > > * Hello, We've validated that with /Od and /O2 compilations with our > latest compiler for VS2017 final release, this bug doesn't exist. As I've > mentioned we'll add ITK and VTK projects into our compiler validation test > suites going forward. Thanks, Ulzii Luvsanbat Visual C++ Team * > > View Ulzii Luvsanbat's new solution > > > If you do not wish to receive these notifications you can update your Notification > Settings > > . > > This message from Microsoft is an important part of a program, service, or > product that you or your company purchased or participate in. > Microsoft respects your privacy. Please read our Privacy Statement > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ndel314 at gmail.com Wed Dec 14 08:56:15 2016 From: ndel314 at gmail.com (Nico Del Piano) Date: Wed, 14 Dec 2016 10:56:15 -0300 Subject: [ITK-users] Error conversion from Message-ID: Hello ITK community, I'm struggling with an error and I don't understand why it's happening: /usr/local/include/ITK-4.11/itkConceptChecking.h:796:28: error: conversion from ?itk::Concept::IsFloatingPoint::Constraints::FalseT {aka itk::Concept::Detail::UniqueType_bool}? to non-scalar type ?itk::Concept::IsFloatingPoint::Constraints::IntegralT {aka itk::Concept::Detail::UniqueType_bool}? requested IntegralT a = FalseT(); ^ /usr/local/include/ITK-4.11/itkConceptChecking.h:797:28: error: conversion from ?itk::Concept::IsFloatingPoint::Constraints::FalseT {aka itk::Concept::Detail::UniqueType_bool}? to non-scalar type ?itk::Concept::IsFloatingPoint::Constraints::ExactT {aka itk::Concept::Detail::UniqueType_bool}? requested ExactT b = FalseT(); Any hint of what could be causing this? If you need the whole error I can paste it. Thanks, Nico. From blowekamp at mail.nih.gov Wed Dec 14 09:03:26 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 14 Dec 2016 14:03:26 +0000 Subject: [ITK-users] Error conversion from In-Reply-To: References: Message-ID: <3ACA34EA-C664-4D0C-BB46-5010BBE0EF71@mail.nih.gov> This error message is suppose to be an improvement from the default to indicate why the code/filter does not work with the template parameters you selected. Here is the key part: > itk::Concept::IsFloatingPoint::Constraints::False This a a concept check to verify the template parameter is a floating point type which is required by the algorithm/filter/code. The type ?short int? is not a floating point type, so it generates a compilation error. I have no clue what is causing it, as you didn?t include any code :) If you look at the all error messages it should indicate the origin of the error. Most likely the cause is: you provided a "short" type for a template parameter (or image type) to a filter or algorithm which requires a floating point type. HTH, Brad > On Dec 14, 2016, at 8:56 AM, Nico Del Piano wrote: > > Hello ITK community, > > I'm struggling with an error and I don't understand why it's happening: > > > /usr/local/include/ITK-4.11/itkConceptChecking.h:796:28: error: > conversion from ?itk::Concept::IsFloatingPoint int>::Constraints::FalseT {aka > itk::Concept::Detail::UniqueType_bool}? to non-scalar type > ?itk::Concept::IsFloatingPoint::Constraints::IntegralT {aka > itk::Concept::Detail::UniqueType_bool}? requested > IntegralT a = FalseT(); > ^ > /usr/local/include/ITK-4.11/itkConceptChecking.h:797:28: error: > conversion from ?itk::Concept::IsFloatingPoint int>::Constraints::FalseT {aka > itk::Concept::Detail::UniqueType_bool}? to non-scalar type > ?itk::Concept::IsFloatingPoint::Constraints::ExactT {aka > itk::Concept::Detail::UniqueType_bool}? requested > ExactT b = FalseT(); > > > Any hint of what could be causing this? If you need the whole error I > can paste it. > > Thanks, > > Nico. > _____________________________________ > 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 aharr8 at uwo.ca Wed Dec 14 10:21:01 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Wed, 14 Dec 2016 10:21:01 -0500 Subject: [ITK-users] [ITK] LBFGSBOptimizerv4 step size Message-ID: Hello, hopefully someone can point me in the right direction. I have been trying to use a LBFGSBOptimizerv4 with some ultrasound images to do a rigid 3D versor transform registration, but can't find anywhere that either allows me to set the step size for the optimizer or documents what the step size is. Does anyone have a reference for this? -- AH ----------------------------------------------------------------------------------------------- *This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Dec 14 14:32:36 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 14 Dec 2016 14:32:36 -0500 Subject: [ITK-users] [ITK] LBFGSBOptimizerv4 step size In-Reply-To: References: Message-ID: There is no mention of step size in source code of this optimizer. It probably does not use fixed step size. Regards On Wed, Dec 14, 2016 at 10:21 AM, Andrew Harris wrote: > Hello, hopefully someone can point me in the right direction. I have been > trying to use a LBFGSBOptimizerv4 with some ultrasound images to do a rigid > 3D versor transform registration, but can't find anywhere that either > allows me to set the step size for the optimizer or documents what the step > size is. Does anyone have a reference for this? > > -- > > AH > > > ------------------------------------------------------------ > ----------------------------------- > > *This email and any attachments thereto may contain private, > confidential, and privileged materials for the sole use of the intended > recipient. Any reviewing, copying, or distribution of this email (or any > attachments thereto) by other than the intended recipient is strictly > prohibited. If you are not the intended recipient, please contact the > sender immediately and permanently destroy this email and any attachments > thereto.* > > _____________________________________ > 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 dzenanz at gmail.com Wed Dec 14 14:45:32 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 14 Dec 2016 14:45:32 -0500 Subject: [ITK-users] [ITK] LBFGSBOptimizerv4 step size In-Reply-To: References: Message-ID: I guess there are a few stopping criteria, by looking at the public functions : SetCostFunctionConvergenceFactor - probably examines changes in cost function value SetMaximumNumberOfCorrections - sounds like iteration count There is probably also some implicit epsilon-like criterion on position changes. Regards, D?enan On Wed, Dec 14, 2016 at 2:38 PM, Andrew Harris wrote: > Thanks for getting back to me. Do you have any idea what the stopping > criteria is for the Broyden-Fletcher implementation? > > -- > > AH > > > ------------------------------------------------------------ > ----------------------------------- > > *This email and any attachments thereto may contain private, > confidential, and privileged materials for the sole use of the intended > recipient. Any reviewing, copying, or distribution of this email (or any > attachments thereto) by other than the intended recipient is strictly > prohibited. If you are not the intended recipient, please contact the > sender immediately and permanently destroy this email and any attachments > thereto.* > > On Wed, Dec 14, 2016 at 2:32 PM, D?enan Zuki? wrote: > >> There is no mention of step size in source code of this optimizer. It >> probably does not use fixed step size. >> >> Regards >> >> On Wed, Dec 14, 2016 at 10:21 AM, Andrew Harris wrote: >> >>> Hello, hopefully someone can point me in the right direction. I have >>> been trying to use a LBFGSBOptimizerv4 with some ultrasound images to do a >>> rigid 3D versor transform registration, but can't find anywhere that either >>> allows me to set the step size for the optimizer or documents what the step >>> size is. Does anyone have a reference for this? >>> >>> -- >>> >>> AH >>> >>> >>> ------------------------------------------------------------ >>> ----------------------------------- >>> >>> *This email and any attachments thereto may contain private, >>> confidential, and privileged materials for the sole use of the intended >>> recipient. Any reviewing, copying, or distribution of this email (or any >>> attachments thereto) by other than the intended recipient is strictly >>> prohibited. If you are not the intended recipient, please contact the >>> sender immediately and permanently destroy this email and any attachments >>> thereto.* >>> >>> _____________________________________ >>> 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 aharr8 at uwo.ca Wed Dec 14 14:38:27 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Wed, 14 Dec 2016 14:38:27 -0500 Subject: [ITK-users] [ITK] LBFGSBOptimizerv4 step size In-Reply-To: References: Message-ID: Thanks for getting back to me. Do you have any idea what the stopping criteria is for the Broyden-Fletcher implementation? -- AH ----------------------------------------------------------------------------------------------- *This email and any attachments thereto may contain private, confidential, and privileged materials for the sole use of the intended recipient. Any reviewing, copying, or distribution of this email (or any attachments thereto) by other than the intended recipient is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently destroy this email and any attachments thereto.* On Wed, Dec 14, 2016 at 2:32 PM, D?enan Zuki? wrote: > There is no mention of step size in source code of this optimizer. It > probably does not use fixed step size. > > Regards > > On Wed, Dec 14, 2016 at 10:21 AM, Andrew Harris wrote: > >> Hello, hopefully someone can point me in the right direction. I have >> been trying to use a LBFGSBOptimizerv4 with some ultrasound images to do a >> rigid 3D versor transform registration, but can't find anywhere that either >> allows me to set the step size for the optimizer or documents what the step >> size is. Does anyone have a reference for this? >> >> -- >> >> AH >> >> >> ------------------------------------------------------------ >> ----------------------------------- >> >> *This email and any attachments thereto may contain private, >> confidential, and privileged materials for the sole use of the intended >> recipient. Any reviewing, copying, or distribution of this email (or any >> attachments thereto) by other than the intended recipient is strictly >> prohibited. If you are not the intended recipient, please contact the >> sender immediately and permanently destroy this email and any attachments >> thereto.* >> >> _____________________________________ >> 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 cr at neuro.ma.uni-heidelberg.de Fri Dec 16 05:26:54 2016 From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith) Date: Fri, 16 Dec 2016 11:26:54 +0100 Subject: [ITK-users] Example with wrong name Message-ID: Hi, I guess WikiExamples/Statistics/HistogramToImageFilterGrayscale.cxx should be renamed to .../ImageToHistogramFilterGrayscale.cxx Regards, Christina -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Fri Dec 16 07:51:07 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 16 Dec 2016 07:51:07 -0500 Subject: [ITK-users] Example with wrong name In-Reply-To: References: Message-ID: Thanks. I'll take care of it. On Dec 16, 2016 5:39 AM, "Chr. Rossmanith" wrote: > Hi, > > I guess WikiExamples/Statistics/HistogramToImageFilterGrayscale.cxx > > should be renamed to .../ImageToHistogramFilterGrayscale.cxx > > Regards, > > Christina > > > > > > _____________________________________ > 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 Sat Dec 17 12:01:10 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 17 Dec 2016 12:01:10 -0500 Subject: [ITK-users] RFI on the NLM Strategic Plan Message-ID: Hi, The National Library of Medicine (NLM) has driven open science and reproducible research long before the recent surge in popularity of the movement. Not only did the NLM start the Insight Toolkit (ITK) project in 1999, but it has continuously enabled it to thrive by supporting community development, maintenance, and algorithmic and technological advances to this day [1] [2]. Open science needs active communities, supported communities, standards, open-source tools, strong ties will commercial / clinical efforts, high-quality practices, transparency, and more - and those are exactly the strengths of our community's toolkits, applications, and projects. We should to encourage the NLM (NIH, DHHS, US Government) to continue to prioritize these efforts via their funding. The NLM has called for Request for Information (RFI) on the strategic plan for the institute: https://grants.nih.gov/grants/guide/notice-files/NOT-LM-17-002.html that is due by January 9th. Please consider letting the NLM know how important their role is in open science and open source. Thanks, Matt [1] https://itk.org/ITK/project/about.html [2] http://journal.frontiersin.org/article/10.3389/fninf.2014.00013/full From fisidoro at ethz.ch Sat Dec 31 05:13:44 2016 From: fisidoro at ethz.ch (D'Isidoro Fabio) Date: Sat, 31 Dec 2016 10:13:44 +0000 Subject: [ITK-users] Itk Python GetParameters Message-ID: <50B858FB5F53124F9E32314E5C1B40943A18A889@MBX112.d.ethz.ch> Hallo, within the context of exploring the domain of an image metric (MeanSquaresImageMetric1.cxx), I want to check the current parameters used for the translation transform: parameters = transform.GetParameters() parameters[0] = dx parameters[1] = dy metric.SetParameters( parameters ) If I then code: print(metric.GetParameters()) I get the proxy of Swig Object, from which I can't see the parameters. [cid:image001.png at 01D26356.608C9950] I have tried in many ways: print(metric.GetParameters()[0]) print(metric.GetParameters()[1]) print(metric.GetTransform().GetParameters()) print(metric.GetTransform().GetParameters().GetElement(0)) but none of them works. How can I get the elements from the Swig Object? Thank you! Fabio -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 3700 bytes Desc: image001.png URL: