From dzenanz at gmail.com Mon Aug 1 09:38:18 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 1 Aug 2016 09:38:18 -0400 Subject: [ITK] [ITK-dev] ITK wrapping with VS2013 Message-ID: Hi Brad and everybody, I am trying to build ITK with Ultrasound module, FFTW and wrapping for Python. This builds without errors on Linux, but on Windows I run into issues: 165> Building Custom Rule C:/Libs/InsightToolkit-4.10.0/Modules/External/ITKUltrasound/wrapping/CMakeLists.txt ... 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(706): warning 401: Nothing known about base class 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex2 > >'. Ignored. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(706): warning 401: Maybe you forgot to instantiate 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex2 > >' using %template. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(776): warning 401: Nothing known about base class 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex3 > >'. Ignored. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(776): warning 401: Maybe you forgot to instantiate 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex3 > >' using %template. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(720): warning 476: Initialization using std::initializer_list. ... 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(793): warning 476: Initialization using std::initializer_list. 165>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(170,5): error MSB6006: "cmd.exe" exited with code 28. The same error happens with ITK 4.10.0 and ITK git from 10 days ago. Can someone shed some light on the error and how to fix it? Regards, D?enan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From dzenanz at gmail.com Mon Aug 1 09:38:18 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 1 Aug 2016 09:38:18 -0400 Subject: [ITK] [ITK-users] ITK wrapping with VS2013 Message-ID: Hi Brad and everybody, I am trying to build ITK with Ultrasound module, FFTW and wrapping for Python. This builds without errors on Linux, but on Windows I run into issues: 165> Building Custom Rule C:/Libs/InsightToolkit-4.10.0/Modules/External/ITKUltrasound/wrapping/CMakeLists.txt ... 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(706): warning 401: Nothing known about base class 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex2 > >'. Ignored. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(706): warning 401: Maybe you forgot to instantiate 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex2 > >' using %template. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(776): warning 401: Nothing known about base class 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex3 > >'. Ignored. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(776): warning 401: Maybe you forgot to instantiate 'std::_Deque_alloc< false,std::_Deque_base_types< itkIndex3 > >' using %template. 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(720): warning 476: Initialization using std::initializer_list. ... 165>C:\Libs\InsightToolkit-4.10.0-msvc2013\Wrapping\Typedefs\itkSpectra1DSupportWindowImageFilter.i(793): warning 476: Initialization using std::initializer_list. 165>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(170,5): error MSB6006: "cmd.exe" exited with code 28. The same error happens with ITK 4.10.0 and ITK git from 10 days ago. Can someone shed some light on the error and how to fix it? Regards, D?enan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 Mon Aug 1 11:21:16 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 1 Aug 2016 11:21:16 -0400 Subject: [ITK] [ITK-dev] ITK fails to compile after recent update Message-ID: Folks, My clang compile of ITK fails to compile. clang version: Apple clang version 3.0 (tags/Apple/clang-211.12) (based on LLVM 3.0svn) Error: In file included from /Users/lorensen/ProjectsGIT/ITK/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler_detection.h:160: /Users/lorensen/ProjectsGIT/ITK/Modules/ThirdParty/VNL/src/vxl/vcl/compilers/VXL_COMPILER_INFO_Clang_CXX.h:6:8: error: #error Unsupported compiler version # error Unsupported compiler version Bill _______________________________________________ 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://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-developers From jeannasheen at gmail.com Tue Aug 2 21:08:42 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Tue, 2 Aug 2016 18:08:42 -0700 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter Message-ID: Hello, I am trying to process the attached image using the ShapeOpeningLabelMapFilter for the Insight Toolkit. The image is of a retina, and I want to use the image filter to remove the blood vessels from the picture (the blood vessels are the long, skinny, branching lines). I was wondering if the example code for the ShapeOpeningLabelMapFilter (here ) would be able to do this with a little modification, and if so, which attribute would be the most useful to identify and remove the blood vessels. Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: input.png Type: image/png Size: 85575 bytes Desc: not available URL: From tevain at telecom-paristech.fr Wed Aug 3 04:59:21 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Wed, 3 Aug 2016 10:59:21 +0200 (CEST) Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: Message-ID: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Hello Jeanna, I think this will be difficult just with the LabelMap framework. Usually to filter vessels you rely on some measures based on their shape, but in the ShapeLabelObject, the elongation measure is "the ratio of the longest physical size of the region [i.e. the bounding box] on one dimension and its smallest physical size". This is a quite coarse measure, sensitive to rotation, and I doubt it will be useful in your case. Aside from the attribute problem, you also have to detect the vessels prior to filtering them (i.e. getting a binary or a label image of vessels), and the LabelMap framework doesn't do that. I would suggest taking a look at these other methods: -Frangi's vesselness (implemented in itk through these filter : itkHessianToObjectnessMeasureImageFilter or itkHessian3DToVesselnessMeasureImageFilter) -Ranking Orientation Responses of Path Openings, aka RORPO (http://path-openings.github.io/RORPO/) -Fast Marching (itkFastMarchingImageFilter) HTH, Tim ----- Mail original ----- De: "Jeanna S." ?: community at itk.org Envoy?: Mercredi 3 Ao?t 2016 03:08:42 Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter Hello, I am trying to process the attached image using the ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a retina, and I want to use the image filter to remove the blood vessels from the picture (the blood vessels are the long, skinny, branching lines). I was wondering if the example code for the ShapeOpeningLabelMapFilter ( here ) would be able to do this with a little modification, and if so, which attribute would be the most useful to identify and remove the blood vessels. Thanks in advance. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From anton.delehony at gmail.com Fri Aug 5 09:40:53 2016 From: anton.delehony at gmail.com (Anton Delehony) Date: Fri, 5 Aug 2016 09:40:53 -0400 Subject: [ITK] [ITK-users] simpleitk question C# Message-ID: Hi all, I'm a new to C# and simple itk and have a very simple question. in the ImageRegistrationMethodBSpline1.cxx there is the line: std::vector transfromDomainMeshSize(fixed.GetDimension(),8); What is the equivlent line to this in C#? thanks, Anton -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 dzenanz at gmail.com Fri Aug 5 10:05:44 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 5 Aug 2016 10:05:44 -0400 Subject: [ITK] [ITK-users] simpleitk question C# In-Reply-To: References: Message-ID: Hi Anton, I don't know C#'s syntax that well to give you direct translation, but here is another way to write the same C++ code which should be easier to translate: std::vector transfromDomainMeshSize; //C# eqivalent: unsigned int[] transfromDomainMeshSize; transfromDomainMeshSize.resize(8); //my stab in C#: transfromDomainMeshSize=new unsigned int[8]; for (int i=0; i<8; i++) transfromDomainMeshSize[i]=fixed.GetDimension(); HTH, D?enan On Fri, Aug 5, 2016 at 9:40 AM, Anton Delehony wrote: > Hi all, > > I'm a new to C# and simple itk and have a very simple question. > > in the ImageRegistrationMethodBSpline1.cxx there is the line: > > std::vector transfromDomainMeshSize(fixed.GetDimension(),8); > > What is the equivlent line to this in C#? > > thanks, > > Anton > > _____________________________________ > 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 -------------- _____________________________________ 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 brad at lowekamp.net Fri Aug 5 22:06:24 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Fri, 5 Aug 2016 22:06:24 -0400 Subject: [ITK] [ITK-users] simpleitk question C# In-Reply-To: References: Message-ID: Hi This suggestion has the arguments backwards: http://en.cppreference.com/w/cpp/container/vector/vector This line creates an std::vector of Dimension size and fills it with the value of 8. You can use the for loop to fill the array as suggested or use an array initializer if the array size is fixed. HTH Brad > On Aug 5, 2016, at 10:05 AM, D?enan Zuki? wrote: > > Hi Anton, > > I don't know C#'s syntax that well to give you direct translation, but here is another way to write the same C++ code which should be easier to translate: > > std::vector transfromDomainMeshSize; > //C# eqivalent: unsigned int[] transfromDomainMeshSize; > transfromDomainMeshSize.resize(8); > //my stab in C#: transfromDomainMeshSize=new unsigned int[8]; > for (int i=0; i<8; i++) > transfromDomainMeshSize[i]=fixed.GetDimension(); > > HTH, > D?enan > >> On Fri, Aug 5, 2016 at 9:40 AM, Anton Delehony wrote: >> Hi all, >> >> I'm a new to C# and simple itk and have a very simple question. >> >> in the ImageRegistrationMethodBSpline1.cxx there is the line: >> >> std::vector transfromDomainMeshSize(fixed.GetDimension(),8); >> >> What is the equivlent line to this in C#? >> >> thanks, >> >> Anton >> >> _____________________________________ >> 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: -------------- next part -------------- _____________________________________ 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 bakkari.abdelkhalek at hotmail.fr Sat Aug 6 02:35:46 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Sat, 6 Aug 2016 07:35:46 +0100 Subject: [ITK] FW: Manual 3d image segmentation using itk In-Reply-To: References: , Message-ID: Hi, I would like to ask about the functions that may be used with ITK-SNAP for the manual segmentation. Thank you in advance. Kind regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland From: matt.mccormick at kitware.com Date: Wed, 6 Jul 2016 11:42:51 -0400 Subject: Re: [ITK] Manual 3d image segmentation using itk To: bakkari.abdelkhalek at hotmail.fr CC: insight-users at itk.org; community at itk.org Hi, You may want to investigate the open source, ITK-based ITK-SNAP project, which has similiar functionality. HTH, Matt On Wed, Jul 6, 2016 at 11:11 AM, Abdelkhalek Bakkari wrote: Hi, I would like to ask if you could help me with a code source related to Manual interactive 3d image segmentation using itk as described in the video below : https://www.youtube.com/watch?v=7wCC2NaVLjs Thank you in advance. Best regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Virus-free. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Sat Aug 6 19:52:08 2016 From: matthias.b at hotmail.com (Matthias B) Date: Sun, 7 Aug 2016 01:52:08 +0200 Subject: [ITK] Using ITK library in .Net (Visual Studio) Message-ID: Hey, I'm programming in VB.Net, I succesfully added the ITK managed C# library wrapper to my VS project. Now I'm able to use the ITK C# functions in VB.Net. My goal is to use a regional maxima filter (ITK) on a 2D-array that I declared in VB.Net I have really no idea how to do this and if this is even possible. Hope somebody can help me with this. Thank you, Matthias Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Sat Aug 6 19:52:28 2016 From: matthias.b at hotmail.com (Matthias B) Date: Sun, 7 Aug 2016 01:52:28 +0200 Subject: [ITK] Using ITK library in .Net (Visual Studio) Message-ID: Hey, I'm programming in VB.Net, I succesfully added the ITK managed C# library wrapper to my VS project. Now I'm able to use the ITK C# functions in VB.Net. My goal is to use a regional maxima filter (ITK) on a 2D-array that I declared in VB.Net I have really no idea how to do this and if this is even possible. Hope somebody can help me with this. Thank you, Matthias Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeannasheen at gmail.com Sat Aug 6 23:53:05 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Sat, 6 Aug 2016 20:53:05 -0700 Subject: [ITK] ITK ImageFileReader Example Library Not Loaded Message-ID: Hello, I am trying to run the ITK ImageFileReader example (here ). CMake can successfully configure and generate the executable, but when I try to run the executable, I get the following error: dyld: Library not loaded: libvtkDomainsChemistryOpenGL2-7.0.1.dylib Referenced from: /Users/JJ/Desktop/ITKstuffs/ImageFileReader/build/ImageFileReader.app/Contents/MacOS/./ImageFileReader Reason: image not found Trace/BPT trap: 5 A search of the files on my computer reveals that libvtkDomainsChemistryOpenGL2-7.0.1.dylib is in /Users/JJ/Desktop/ITKstuffs/Install/vtk/lib. I can open the executable file generated by CMake in my text editor, and I think I found where libvtkDomainsChemistryOpenGL2-7.0.1.dylib is being referenced. There are 2 lines that state: 0 /usr/lib/libz.1.dylib H libvtkDomainsChemistryOpenGL2-7.0.1.dylib I do not know why the program is looking for the libraries in user/lib, because when I configured and generated the code in CMake I changed the CMAKE_INSTALL_PREFIX to /Users/JJ/Desktop/ITKstuffs/Install. If anyone has any suggestions on how to fix this problem, they would be much appreciated. I would also like to know where to put the image file to be read and how to tell the program where the image to be read is (e.g. do I pass the file name and path when I run the executable?). Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dan.muel at gmail.com Sun Aug 7 01:30:29 2016 From: dan.muel at gmail.com (Dan Mueller) Date: Sun, 7 Aug 2016 15:00:29 +0930 Subject: [ITK] Using ITK library in .Net (Visual Studio) In-Reply-To: References: Message-ID: Hi Matthias, To import the 2d array into SimpleITK you can use the ImportAsXXX function. You need to make sure you match your pixel types correctly (e.g. if your buffer is float, using ImportAsFloat, etc). Here is some C# code that might help you. using System; using System.Runtime.InteropServices; using sitk = itk.simple.SimpleITK; using simple = itk.simple; namespace itk.simple { public class ImageProcessing { public static void Main(string[] args) { try { var size = new simple.VectorUInt32(2) { 256, 256 }; var spacing = new simple.VectorDouble(2) { 1.0, 1.0 }; var buffer = new float[size[0] * size[1]]; GCHandle bufferPinned = GCHandle.Alloc(buffer, GCHandleType.Pinned); // Pin managed array IntPtr bufferPtr = bufferPinned.AddrOfPinnedObject(); // Get address of array // Import buffer as SimpleITK image var input = sitk.ImportAsFloat(bufferPtr, size, spacing); // Compute regional maxima var maxima = sitk.RegionalMaxima(input, backgroundValue: 0, foregroundValue: 255, fullyConnected: true); sitk.WriteImage(maxima, @"C:\Temp\maxima.mha"); bufferPinned.Free(); // Free pinned array } catch (Exception ex) { Console.WriteLine(ex); } } } } Hope this helps. Cheers, Dan On 7 August 2016 at 09:22, Matthias B wrote: > Hey, > > I'm programming in VB.Net, I succesfully added the ITK managed C# library > wrapper to my VS project. > Now I'm able to use the ITK C# functions in VB.Net. > > My goal is to use a regional maxima filter (ITK) on a 2D-array that I > declared in VB.Net > > I have really no idea how to do this and if this is even possible. > > Hope somebody can help me with this. > > Thank you, Matthias > > > Virusvrij. > www.avast.com > > <#m_-7220795038837665703_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeannasheen at gmail.com Sun Aug 7 19:13:08 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Sun, 7 Aug 2016 16:13:08 -0700 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Hi Timothee, Thank you for replying. I will look into these methods. Jeanna On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain wrote: > Hello Jeanna, > > I think this will be difficult just with the LabelMap framework. > Usually to filter vessels you rely on some measures based on their shape, > but in the ShapeLabelObject, the elongation measure is "the ratio of the > longest physical size of the region [i.e. the bounding box] on one > dimension and its smallest physical size". This is a quite coarse measure, > sensitive to rotation, and I doubt it will be useful in your case. > Aside from the attribute problem, you also have to detect the vessels > prior to filtering them (i.e. getting a binary or a label image of > vessels), and the LabelMap framework doesn't do that. > > I would suggest taking a look at these other methods: > -Frangi's vesselness (implemented in itk through these filter : > itkHessianToObjectnessMeasureImageFilter or itkHessian3DToVesselnessMeasur > eImageFilter) > -Ranking Orientation Responses of Path Openings, aka RORPO ( > http://path-openings.github.io/RORPO/) > -Fast Marching (itkFastMarchingImageFilter) > > HTH, > > Tim > > ----- Mail original ----- > De: "Jeanna S." > ?: community at itk.org > Envoy?: Mercredi 3 Ao?t 2016 03:08:42 > Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter > > Hello, > > I am trying to process the attached image using the > ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a > retina, and I want to use the image filter to remove the blood vessels from > the picture (the blood vessels are the long, skinny, branching lines). I > was wondering if the example code for the ShapeOpeningLabelMapFilter ( here > ) would be able to do this with a little modification, and if so, which > attribute would be the most useful to identify and remove the blood vessels. > > Thanks in advance. > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeannasheen at gmail.com Sun Aug 7 19:16:59 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Sun, 7 Aug 2016 16:16:59 -0700 Subject: [ITK] ITK ImageFileReader Example Library Not Loaded In-Reply-To: References: Message-ID: Hello, I have already found a solution to my problem here . It seems all I have to do is type "export DYLD_LIBRARY_PATH=" followed by the install path in the Terminal. On Sat, Aug 6, 2016 at 8:53 PM, Jeanna S. wrote: > Hello, > > I am trying to run the ITK ImageFileReader example (here > ). CMake can > successfully configure and generate the executable, but when I try to run > the executable, I get the following error: > > dyld: Library not loaded: libvtkDomainsChemistryOpenGL2-7.0.1.dylib > > Referenced from: /Users/JJ/Desktop/ITKstuffs/ImageFileReader/build/ > ImageFileReader.app/Contents/MacOS/./ImageFileReader > > Reason: image not found > > Trace/BPT trap: 5 > > A search of the files on my computer reveals that > libvtkDomainsChemistryOpenGL2-7.0.1.dylib is in > /Users/JJ/Desktop/ITKstuffs/Install/vtk/lib. > > I can open the executable file generated by CMake in my text editor, and I > think I found where libvtkDomainsChemistryOpenGL2-7.0.1.dylib is being > referenced. There are 2 lines that state: > > 0 /usr/lib/libz.1.dylib > > H libvtkDomainsChemistryOpenGL2-7.0.1.dylib > > I do not know why the program is looking for the libraries in user/lib, > because when I configured and generated the code in CMake I changed the CMAKE_INSTALL_PREFIX > to /Users/JJ/Desktop/ITKstuffs/Install. > > If anyone has any suggestions on how to fix this problem, they would be > much appreciated. > > I would also like to know where to put the image file to be read and how > to tell the program where the image to be read is (e.g. do I pass the file > name and path when I run the executable?). > > Thanks in advance. > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeannasheen at gmail.com Mon Aug 8 00:44:34 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Sun, 7 Aug 2016 21:44:34 -0700 Subject: [ITK] ITK LaplacianRecursiveGaussianImageFilter Example Message-ID: Hello, I am trying to run the ITK LaplacianRecursiveGaussianImageFilter Example ( here ), but I keep getting this error: libc++abi.dylib: terminating with uncaught exception of type itk::ExceptionObject: /Users/JJ/Desktop/ITKstuffs/ITK/Modules/Core/Common/include/itkImageBase.hxx:326: itk::ERROR: Image(0x7fd8a4970e70): itk::ImageBase::CopyInformation() cannot cast PKN3itk10DataObjectE to PKN3itk9ImageBaseILj2EEE I also once got this error: libpng warning: iCCP: known incorrect sRGB profile followed by the above error. Does anybody know why this error is happening and/or can provide an image that will work with the example? Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Aug 8 09:08:46 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 8 Aug 2016 09:08:46 -0400 Subject: [ITK] ITK LaplacianRecursiveGaussianImageFilter Example In-Reply-To: References: Message-ID: Hi Jeanna, you can safely ignore "libpng warning: iCCP: known incorrect sRGB profile". LaplacianRecursiveGaussianImageFilter works for me: [image: Inline image 1] I am not a Mac user, but your error stinks of version mixing: either the ITK libraries in your path are a different version from the one your program is compiled with, or have been compiled with a different compiler version (this is sometimes a problem with Visual Studio versions). Regards, D?enan On Mon, Aug 8, 2016 at 12:44 AM, Jeanna S. wrote: > Hello, > > I am trying to run the ITK LaplacianRecursiveGaussianImageFilter Example ( > here > ), > but I keep getting this error: > > libc++abi.dylib: terminating with uncaught exception of type > itk::ExceptionObject: /Users/JJ/Desktop/ITKstuffs/ITK/Modules/Core/Common/ > include/itkImageBase.hxx:326: > > itk::ERROR: Image(0x7fd8a4970e70): itk::ImageBase::CopyInformation() > cannot cast PKN3itk10DataObjectE to PKN3itk9ImageBaseILj2EEE > > I also once got this error: > > libpng warning: iCCP: known incorrect sRGB profile > > followed by the above error. > > Does anybody know why this error is happening and/or can provide an image > that will work with the example? > > Thanks in advance. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2016-08-08 09.05.38.png Type: image/png Size: 220650 bytes Desc: not available URL: From dzenanz at gmail.com Mon Aug 8 09:15:25 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 8 Aug 2016 09:15:25 -0400 Subject: [ITK] FW: Manual 3d image segmentation using itk In-Reply-To: References: Message-ID: Hi Abdelkhalek, the manual does a pretty good job of explaining the built-in functions. It is also very graphical. Regards, D?enan On Sat, Aug 6, 2016 at 2:35 AM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > Hi, > > I would like to ask about the functions that may be used with ITK-SNAP for > the manual segmentation. > > Thank you in advance. > > Kind regards, > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > > ------------------------------ > From: matt.mccormick at kitware.com > Date: Wed, 6 Jul 2016 11:42:51 -0400 > Subject: Re: [ITK] Manual 3d image segmentation using itk > To: bakkari.abdelkhalek at hotmail.fr > CC: insight-users at itk.org; community at itk.org > > > Hi, > > You may want to investigate the open source, ITK-based ITK-SNAP project, > which has similiar functionality. > > HTH, > Matt > > On Wed, Jul 6, 2016 at 11:11 AM, Abdelkhalek Bakkari < > bakkari.abdelkhalek at hotmail.fr> wrote: > > Hi, > > I would like to ask if you could help me with a code source related > to Manual interactive 3d image segmentation using itk as described in the > video below : > https://www.youtube.com/watch?v=7wCC2NaVLjs > > Thank you in advance. > > Best regards, > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > Virus-free. > www.avast.com > > <#m_4781774733812301522_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeannasheen at gmail.com Mon Aug 8 12:38:25 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Mon, 8 Aug 2016 09:38:25 -0700 Subject: [ITK] ITK LaplacianRecursiveGaussianImageFilter Example In-Reply-To: References: Message-ID: Hello D?enan, Thanks for your reply. Would you happen to know any way to fix the error, if it is in fact caused by version mixing? Jeanna On Mon, Aug 8, 2016 at 6:08 AM, D?enan Zuki? wrote: > Hi Jeanna, > > you can safely ignore "libpng warning: iCCP: known incorrect sRGB profile". > > LaplacianRecursiveGaussianImageFilter works for me: > [image: Inline image 1] > > I am not a Mac user, but your error stinks of version mixing: either the > ITK libraries in your path are a different version from the one your > program is compiled with, or have been compiled with a different compiler > version (this is sometimes a problem with Visual Studio versions). > > Regards, > D?enan > > On Mon, Aug 8, 2016 at 12:44 AM, Jeanna S. wrote: > >> Hello, >> >> I am trying to run the ITK LaplacianRecursiveGaussianImageFilter Example >> (here >> ), >> but I keep getting this error: >> >> libc++abi.dylib: terminating with uncaught exception of type >> itk::ExceptionObject: /Users/JJ/Desktop/ITKstuffs/IT >> K/Modules/Core/Common/include/itkImageBase.hxx:326: >> >> itk::ERROR: Image(0x7fd8a4970e70): itk::ImageBase::CopyInformation() >> cannot cast PKN3itk10DataObjectE to PKN3itk9ImageBaseILj2EEE >> >> I also once got this error: >> >> libpng warning: iCCP: known incorrect sRGB profile >> >> followed by the above error. >> >> Does anybody know why this error is happening and/or can provide an image >> that will work with the example? >> >> Thanks in advance. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2016-08-08 09.05.38.png Type: image/png Size: 220650 bytes Desc: not available URL: From dzenanz at gmail.com Mon Aug 8 12:41:19 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 8 Aug 2016 12:41:19 -0400 Subject: [ITK] ITK LaplacianRecursiveGaussianImageFilter Example In-Reply-To: References: Message-ID: The best way to fix that is by not using dynamic libraries. When configuring ITK with CMake make sure that BUILD_SHARED_LIBS is OFF. Regards, D?enan On Mon, Aug 8, 2016 at 12:38 PM, Jeanna S. wrote: > Hello D?enan, > > Thanks for your reply. Would you happen to know any way to fix the error, > if it is in fact caused by version mixing? > > Jeanna > > On Mon, Aug 8, 2016 at 6:08 AM, D?enan Zuki? wrote: > >> Hi Jeanna, >> >> you can safely ignore "libpng warning: iCCP: known incorrect sRGB >> profile". >> >> LaplacianRecursiveGaussianImageFilter works for me: >> [image: Inline image 1] >> >> I am not a Mac user, but your error stinks of version mixing: either the >> ITK libraries in your path are a different version from the one your >> program is compiled with, or have been compiled with a different compiler >> version (this is sometimes a problem with Visual Studio versions). >> >> Regards, >> D?enan >> >> On Mon, Aug 8, 2016 at 12:44 AM, Jeanna S. wrote: >> >>> Hello, >>> >>> I am trying to run the ITK LaplacianRecursiveGaussianImageFilter >>> Example (here >>> ), >>> but I keep getting this error: >>> >>> libc++abi.dylib: terminating with uncaught exception of type >>> itk::ExceptionObject: /Users/JJ/Desktop/ITKstuffs/IT >>> K/Modules/Core/Common/include/itkImageBase.hxx:326: >>> >>> itk::ERROR: Image(0x7fd8a4970e70): itk::ImageBase::CopyInformation() >>> cannot cast PKN3itk10DataObjectE to PKN3itk9ImageBaseILj2EEE >>> >>> I also once got this error: >>> >>> libpng warning: iCCP: known incorrect sRGB profile >>> >>> followed by the above error. >>> >>> Does anybody know why this error is happening and/or can provide an >>> image that will work with the example? >>> >>> Thanks in advance. >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >> > > > -- > when the rich wage war, it's the poor who die > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2016-08-08 09.05.38.png Type: image/png Size: 220650 bytes Desc: not available URL: From jeannasheen at gmail.com Mon Aug 8 13:27:29 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Mon, 8 Aug 2016 10:27:29 -0700 Subject: [ITK] ITK LaplacianRecursiveGaussianImageFilter Example In-Reply-To: References: Message-ID: Alright, now the example works after I switched BUILD_SHARED_LIBS to OFF. Thanks for your help. Jeanna On Mon, Aug 8, 2016 at 9:41 AM, D?enan Zuki? wrote: > The best way to fix that is by not using dynamic libraries. When > configuring ITK with CMake make sure that BUILD_SHARED_LIBS is OFF. > > Regards, > D?enan > > On Mon, Aug 8, 2016 at 12:38 PM, Jeanna S. wrote: > >> Hello D?enan, >> >> Thanks for your reply. Would you happen to know any way to fix the error, >> if it is in fact caused by version mixing? >> >> Jeanna >> >> On Mon, Aug 8, 2016 at 6:08 AM, D?enan Zuki? wrote: >> >>> Hi Jeanna, >>> >>> you can safely ignore "libpng warning: iCCP: known incorrect sRGB >>> profile". >>> >>> LaplacianRecursiveGaussianImageFilter works for me: >>> [image: Inline image 1] >>> >>> I am not a Mac user, but your error stinks of version mixing: either the >>> ITK libraries in your path are a different version from the one your >>> program is compiled with, or have been compiled with a different compiler >>> version (this is sometimes a problem with Visual Studio versions). >>> >>> Regards, >>> D?enan >>> >>> On Mon, Aug 8, 2016 at 12:44 AM, Jeanna S. >>> wrote: >>> >>>> Hello, >>>> >>>> I am trying to run the ITK LaplacianRecursiveGaussianImageFilter >>>> Example (here >>>> ), >>>> but I keep getting this error: >>>> >>>> libc++abi.dylib: terminating with uncaught exception of type >>>> itk::ExceptionObject: /Users/JJ/Desktop/ITKstuffs/IT >>>> K/Modules/Core/Common/include/itkImageBase.hxx:326: >>>> >>>> itk::ERROR: Image(0x7fd8a4970e70): itk::ImageBase::CopyInformation() >>>> cannot cast PKN3itk10DataObjectE to PKN3itk9ImageBaseILj2EEE >>>> >>>> I also once got this error: >>>> >>>> libpng warning: iCCP: known incorrect sRGB profile >>>> >>>> followed by the above error. >>>> >>>> Does anybody know why this error is happening and/or can provide an >>>> image that will work with the example? >>>> >>>> Thanks in advance. >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >>>> >>> >> >> >> -- >> when the rich wage war, it's the poor who die >> > > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2016-08-08 09.05.38.png Type: image/png Size: 220650 bytes Desc: not available URL: From jeannasheen at gmail.com Mon Aug 8 19:37:51 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Mon, 8 Aug 2016 16:37:51 -0700 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Hi Timothee, I'm using the itk:HessianToObjectnessMeasureImageFilter that you suggested. I was wondering if there is any way for me to view the image on the screen after it has been run through the filter, and if you have any examples of the filter working on an image. Thanks, Jeanna On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. wrote: > Hi Timothee, > > Thank you for replying. I will look into these methods. > > Jeanna > > On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < > tevain at telecom-paristech.fr> wrote: > >> Hello Jeanna, >> >> I think this will be difficult just with the LabelMap framework. >> Usually to filter vessels you rely on some measures based on their shape, >> but in the ShapeLabelObject, the elongation measure is "the ratio of the >> longest physical size of the region [i.e. the bounding box] on one >> dimension and its smallest physical size". This is a quite coarse measure, >> sensitive to rotation, and I doubt it will be useful in your case. >> Aside from the attribute problem, you also have to detect the vessels >> prior to filtering them (i.e. getting a binary or a label image of >> vessels), and the LabelMap framework doesn't do that. >> >> I would suggest taking a look at these other methods: >> -Frangi's vesselness (implemented in itk through these filter : >> itkHessianToObjectnessMeasureImageFilter or >> itkHessian3DToVesselnessMeasureImageFilter) >> -Ranking Orientation Responses of Path Openings, aka RORPO ( >> http://path-openings.github.io/RORPO/) >> -Fast Marching (itkFastMarchingImageFilter) >> >> HTH, >> >> Tim >> >> ----- Mail original ----- >> De: "Jeanna S." >> ?: community at itk.org >> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >> >> Hello, >> >> I am trying to process the attached image using the >> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >> retina, and I want to use the image filter to remove the blood vessels from >> the picture (the blood vessels are the long, skinny, branching lines). I >> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >> ) would be able to do this with a little modification, and if so, which >> attribute would be the most useful to identify and remove the blood vessels. >> >> Thanks in advance. >> >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > > > > -- > when the rich wage war, it's the poor who die > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeannasheen at gmail.com Mon Aug 8 21:38:46 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Mon, 8 Aug 2016 18:38:46 -0700 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Actually, I found a way to display the images to the screen. However, I am still not quite sure how to detect the blood vessels in my image. When I apply the itkHessianToObjectnessMeasureImageFilter on my image, it just turns out black. I was wondering if this is because there is not enough contrast between the vessels and the background. If so, is there any setting or threshold on the filter I can change so that it can detect the blood vessels? Thanks, Jeanna On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. wrote: > Hi Timothee, > > I'm using the itk:HessianToObjectnessMeasureImageFilter that you > suggested. I was wondering if there is any way for me to view the image on > the screen after it has been run through the filter, and if you have any > examples of the filter working on an image. > > Thanks, > Jeanna > > On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. wrote: > >> Hi Timothee, >> >> Thank you for replying. I will look into these methods. >> >> Jeanna >> >> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < >> tevain at telecom-paristech.fr> wrote: >> >>> Hello Jeanna, >>> >>> I think this will be difficult just with the LabelMap framework. >>> Usually to filter vessels you rely on some measures based on their >>> shape, but in the ShapeLabelObject, the elongation measure is "the ratio of >>> the longest physical size of the region [i.e. the bounding box] on one >>> dimension and its smallest physical size". This is a quite coarse measure, >>> sensitive to rotation, and I doubt it will be useful in your case. >>> Aside from the attribute problem, you also have to detect the vessels >>> prior to filtering them (i.e. getting a binary or a label image of >>> vessels), and the LabelMap framework doesn't do that. >>> >>> I would suggest taking a look at these other methods: >>> -Frangi's vesselness (implemented in itk through these filter : >>> itkHessianToObjectnessMeasureImageFilter or >>> itkHessian3DToVesselnessMeasureImageFilter) >>> -Ranking Orientation Responses of Path Openings, aka RORPO ( >>> http://path-openings.github.io/RORPO/) >>> -Fast Marching (itkFastMarchingImageFilter) >>> >>> HTH, >>> >>> Tim >>> >>> ----- Mail original ----- >>> De: "Jeanna S." >>> ?: community at itk.org >>> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >>> >>> Hello, >>> >>> I am trying to process the attached image using the >>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >>> retina, and I want to use the image filter to remove the blood vessels from >>> the picture (the blood vessels are the long, skinny, branching lines). I >>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >>> ) would be able to do this with a little modification, and if so, which >>> attribute would be the most useful to identify and remove the blood vessels. >>> >>> Thanks in advance. >>> >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >> >> >> >> -- >> when the rich wage war, it's the poor who die >> > > > > -- > when the rich wage war, it's the poor who die > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Tue Aug 9 07:20:41 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Tue, 9 Aug 2016 11:20:41 +0000 Subject: [ITK] finite differences approximation & MultipleValuedCostFunction Message-ID: Hello, I wondered if ITK already included some methods to compute finite differences approximation and in particular for MultipleValuedCostFunction ? Thanks for any help, Fran?ois. From dzenanz at gmail.com Tue Aug 9 09:29:47 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 9 Aug 2016 09:29:47 -0400 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Hi Jeanna, output of this filter is in [0,1] range, and if your output image type is not float then you will get an all-black image. Here is an example invocation: typedef itk::HessianToObjectnessMeasureImageFilter< HessianImageType, FloatImageType > ObjectnessFilterType; ObjectnessFilterType::Pointer objectnessFilter = ObjectnessFilterType::New(); objectnessFilter->SetBrightObject(true); objectnessFilter->SetScaleObjectnessMeasure(false); objectnessFilter->SetObjectDimension(2.5); objectnessFilter->SetAlpha(0.5); objectnessFilter->SetBeta(1.0); objectnessFilter->SetGamma(5.0); objectnessFilter->SetInput(hc->GetOutput()); objectnessFilter->Update(); FloatImageType::Pointer objectness = objectnessFilter->GetOutput(); On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. wrote: > Actually, I found a way to display the images to the screen. However, I > am still not quite sure how to detect the blood vessels in my image. When I > apply the itkHessianToObjectnessMeasureImageFilter on my image, it just > turns out black. I was wondering if this is because there is not enough > contrast between the vessels and the background. If so, is there any > setting or threshold on the filter I can change so that it can detect the > blood vessels? > > Thanks, > Jeanna > > On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. wrote: > >> Hi Timothee, >> >> I'm using the itk:HessianToObjectnessMeasureImageFilter that you >> suggested. I was wondering if there is any way for me to view the image on >> the screen after it has been run through the filter, and if you have any >> examples of the filter working on an image. >> >> Thanks, >> Jeanna >> >> On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. wrote: >> >>> Hi Timothee, >>> >>> Thank you for replying. I will look into these methods. >>> >>> Jeanna >>> >>> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < >>> tevain at telecom-paristech.fr> wrote: >>> >>>> Hello Jeanna, >>>> >>>> I think this will be difficult just with the LabelMap framework. >>>> Usually to filter vessels you rely on some measures based on their >>>> shape, but in the ShapeLabelObject, the elongation measure is "the ratio of >>>> the longest physical size of the region [i.e. the bounding box] on one >>>> dimension and its smallest physical size". This is a quite coarse measure, >>>> sensitive to rotation, and I doubt it will be useful in your case. >>>> Aside from the attribute problem, you also have to detect the vessels >>>> prior to filtering them (i.e. getting a binary or a label image of >>>> vessels), and the LabelMap framework doesn't do that. >>>> >>>> I would suggest taking a look at these other methods: >>>> -Frangi's vesselness (implemented in itk through these filter : >>>> itkHessianToObjectnessMeasureImageFilter or >>>> itkHessian3DToVesselnessMeasureImageFilter) >>>> -Ranking Orientation Responses of Path Openings, aka RORPO ( >>>> http://path-openings.github.io/RORPO/) >>>> -Fast Marching (itkFastMarchingImageFilter) >>>> >>>> HTH, >>>> >>>> Tim >>>> >>>> ----- Mail original ----- >>>> De: "Jeanna S." >>>> ?: community at itk.org >>>> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >>>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >>>> >>>> Hello, >>>> >>>> I am trying to process the attached image using the >>>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >>>> retina, and I want to use the image filter to remove the blood vessels from >>>> the picture (the blood vessels are the long, skinny, branching lines). I >>>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >>>> ) would be able to do this with a little modification, and if so, which >>>> attribute would be the most useful to identify and remove the blood vessels. >>>> >>>> Thanks in advance. >>>> >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >>> >>> >>> >>> -- >>> when the rich wage war, it's the poor who die >>> >> >> >> >> -- >> when the rich wage war, it's the poor who die >> > > > > -- > when the rich wage war, it's the poor who die > > _______________________________________________ > 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 Tue Aug 9 09:33:38 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 9 Aug 2016 09:33:38 -0400 Subject: [ITK] finite differences approximation & MultipleValuedCostFunction In-Reply-To: References: Message-ID: Hi Fran?ois, have you seen this list? Regards, D?enan On Tue, Aug 9, 2016 at 7:20 AM, wrote: > Hello, > > I wondered if ITK already included some methods to compute finite > differences approximation and in particular for MultipleValuedCostFunction ? > > Thanks for any help, > Fran?ois. > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Tue Aug 9 09:46:08 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Tue, 9 Aug 2016 13:46:08 +0000 Subject: [ITK] finite differences approximation & MultipleValuedCostFunction References: Message-ID: Le 09/08/2016 ? 15:34, D?enan Zuki? a ?crit : Hi Fran?ois, have you seen this list? Regards, D?enan On Tue, Aug 9, 2016 at 7:20 AM, > wrote: Hello, I wondered if ITK already included some methods to compute finite differences approximation and in particular for MultipleValuedCostFunction ? Thanks for any help, Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community I've actually seen this, but what I'd like to do is computing for the 1 ... i parameters of a transformation : df/dpi = (f(pi + epsilon) - f(pi + epsilon))/ (2*epsilon) where : * f is a MultipleValuedCostFunction * pi , the ith parameter -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Tue Aug 9 11:50:45 2016 From: matthias.b at hotmail.com (Matthias B) Date: Tue, 9 Aug 2016 17:50:45 +0200 Subject: [ITK] Determine surface area of certain region in image Message-ID: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80).The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Aug 9 11:58:56 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 9 Aug 2016 15:58:56 +0000 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: Message-ID: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Hello, You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. HTH, Brad [1] http://hdl.handle.net/1926/584 [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb [4] http://hdl.handle.net/10380/3342 On Aug 9, 2016, at 11:50 AM, Matthias B > wrote: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80). The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. [https://ipmcdn.avast.com/images/2016/icons/icon-envelope-tick-round-orange_184x116-v1.png] Virusvrij. www.avast.com _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Wed Aug 10 02:40:11 2016 From: matthias.b at hotmail.com (Matthias B) Date: Wed, 10 Aug 2016 08:40:11 +0200 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> References: , <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Message-ID: Thank you for answering! At this moment I get the perimeter in pixel units (not the surface area of my X,Y-data) of my labeled image.I have also really no idea how to use my 3D data with a labeled image. I see no way how to add 3D data to a LabelMap for example. This is what I have at the moment.Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter()labelShapeStatistics.Execute(labelImage)Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Thanks for any help, Matthias From: blowekamp at mail.nih.gov To: matthias.b at hotmail.com CC: community at itk.org Subject: Re: [ITK] Determine surface area of certain region in image Date: Tue, 9 Aug 2016 15:58:56 +0000 Hello, You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. HTH, Brad [1] http://hdl.handle.net/1926/584 [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb [4] http://hdl.handle.net/10380/3342 On Aug 9, 2016, at 11:50 AM, Matthias B wrote: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80). The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. Virusvrij. www.avast.com _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Wed Aug 10 07:15:24 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Wed, 10 Aug 2016 11:15:24 +0000 Subject: [ITK] reading private tags returns weird strings Message-ID: Hi, I'm trying to read private dicom tags using : ImageIOType::Pointer dicomIO = ImageIOType::New(); ... dicomIO->SetLoadPrivateTags(true); std::string offsetFromBottomStr; std::string offsetFromBottom = "0863|1041"; dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); The value offsetFromBottomStr returned is AICTQw== How does it come and how can I fix this ? Thank you, Fran?ois. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 07:59:18 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 07:59:18 -0400 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Hi Jeanna, by taking a look at the output, you need objectnessFilter->SetBrightObject(false); and a larger size of objectnessFilter->SetObjectDimension(); HTH, D?enan On Wed, Aug 10, 2016 at 12:01 AM, Jeanna S. wrote: > Thanks for letting me know. I've changed the output image type to float > and now it no longer shows up as just black. I've attached my output image > (the image on the left is the input image; the image on the right is the > output image). However, the filter seems not to detect blood vessels like I > hoped, even after testing various values of Alpha, Beta, and Gamma. I was > wondering if anybody has suggestions on how to improve the vessel detection? > > Thanks, > Jeanna > > On Tue, Aug 9, 2016 at 6:29 AM, D?enan Zuki? wrote: > >> Hi Jeanna, >> >> output of this filter is in [0,1] range, and if your output image type is >> not float then you will get an all-black image. Here is an example >> invocation: >> >> typedef itk::HessianToObjectnessMeasureImageFilter< >> HessianImageType, FloatImageType > ObjectnessFilterType; >> ObjectnessFilterType::Pointer objectnessFilter = >> ObjectnessFilterType::New(); >> objectnessFilter->SetBrightObject(true); >> objectnessFilter->SetScaleObjectnessMeasure(false); >> objectnessFilter->SetObjectDimension(2.5); >> objectnessFilter->SetAlpha(0.5); >> objectnessFilter->SetBeta(1.0); >> objectnessFilter->SetGamma(5.0); >> objectnessFilter->SetInput(hc->GetOutput()); >> objectnessFilter->Update(); >> FloatImageType::Pointer objectness = objectnessFilter->GetOutput(); >> >> On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. wrote: >> >>> Actually, I found a way to display the images to the screen. However, I >>> am still not quite sure how to detect the blood vessels in my image. When I >>> apply the itkHessianToObjectnessMeasureImageFilter on my image, it just >>> turns out black. I was wondering if this is because there is not enough >>> contrast between the vessels and the background. If so, is there any >>> setting or threshold on the filter I can change so that it can detect the >>> blood vessels? >>> >>> Thanks, >>> Jeanna >>> >>> On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. wrote: >>> >>>> Hi Timothee, >>>> >>>> I'm using the itk:HessianToObjectnessMeasureImageFilter that you >>>> suggested. I was wondering if there is any way for me to view the image on >>>> the screen after it has been run through the filter, and if you have any >>>> examples of the filter working on an image. >>>> >>>> Thanks, >>>> Jeanna >>>> >>>> On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. >>>> wrote: >>>> >>>>> Hi Timothee, >>>>> >>>>> Thank you for replying. I will look into these methods. >>>>> >>>>> Jeanna >>>>> >>>>> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < >>>>> tevain at telecom-paristech.fr> wrote: >>>>> >>>>>> Hello Jeanna, >>>>>> >>>>>> I think this will be difficult just with the LabelMap framework. >>>>>> Usually to filter vessels you rely on some measures based on their >>>>>> shape, but in the ShapeLabelObject, the elongation measure is "the ratio of >>>>>> the longest physical size of the region [i.e. the bounding box] on one >>>>>> dimension and its smallest physical size". This is a quite coarse measure, >>>>>> sensitive to rotation, and I doubt it will be useful in your case. >>>>>> Aside from the attribute problem, you also have to detect the vessels >>>>>> prior to filtering them (i.e. getting a binary or a label image of >>>>>> vessels), and the LabelMap framework doesn't do that. >>>>>> >>>>>> I would suggest taking a look at these other methods: >>>>>> -Frangi's vesselness (implemented in itk through these filter : >>>>>> itkHessianToObjectnessMeasureImageFilter or >>>>>> itkHessian3DToVesselnessMeasureImageFilter) >>>>>> -Ranking Orientation Responses of Path Openings, aka RORPO ( >>>>>> http://path-openings.github.io/RORPO/) >>>>>> -Fast Marching (itkFastMarchingImageFilter) >>>>>> >>>>>> HTH, >>>>>> >>>>>> Tim >>>>>> >>>>>> ----- Mail original ----- >>>>>> De: "Jeanna S." >>>>>> ?: community at itk.org >>>>>> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >>>>>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >>>>>> >>>>>> Hello, >>>>>> >>>>>> I am trying to process the attached image using the >>>>>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >>>>>> retina, and I want to use the image filter to remove the blood vessels from >>>>>> the picture (the blood vessels are the long, skinny, branching lines). I >>>>>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >>>>>> ) would be able to do this with a little modification, and if so, which >>>>>> attribute would be the most useful to identify and remove the blood vessels. >>>>>> >>>>>> Thanks in advance. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Community mailing list >>>>>> Community at itk.org >>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> when the rich wage war, it's the poor who die >>>>> >>>> >>>> >>>> >>>> -- >>>> when the rich wage war, it's the poor who die >>>> >>> >>> >>> >>> -- >>> when the rich wage war, it's the poor who die >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >> > > > -- > when the rich wage war, it's the poor who die > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 08:32:53 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 08:32:53 -0400 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Message-ID: Hi Matthias, perimeter should be surface area in 3D (which you can divide by 2 to eliminate back side if you have a very flat object). In 2D image, it is the circumference. In 2D image, you can get object's surface area by counting how many pixels it has and then multiplying that by the size of each pixel (spacing[0]*spacing[1]). Regards, D?enan On Wed, Aug 10, 2016 at 2:40 AM, Matthias B wrote: > Thank you for answering! > > At this moment I get the perimeter in pixel units (not the surface area of > my X,Y-data) of my labeled image. > I have also really no idea how to use my 3D data with a labeled image. I > see no way how to add 3D data to a LabelMap for example. > > This is what I have at the moment. > Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() > labelShapeStatistics.Execute(labelImage) > Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) > > Thanks for any help, Matthias > > > > ------------------------------ > From: blowekamp at mail.nih.gov > To: matthias.b at hotmail.com > CC: community at itk.org > Subject: Re: [ITK] Determine surface area of certain region in image > Date: Tue, 9 Aug 2016 15:58:56 +0000 > > > Hello, > > You should look into the label map framework [1]. In particular the > LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. > > HTH, > Brad > > [1] http://hdl.handle.net/1926/584 > [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilt > er.html > [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html# > aff1209e925293c15775520ef89e97afb > [4] http://hdl.handle.net/10380/3342 > > On Aug 9, 2016, at 11:50 AM, Matthias B wrote: > > Hello ITK-community, > > At the moment I'm working with 3D Images with following structure: > 100x80x3. Every pixel contains a X,Y,Z value. > I want to calculate the surface area of a certain region that I have > defined with a boolean 2D-Image (100x80). > The surface area should only be calculated with the X,Y-data. > > In Matlab I have experience with this by using the function bwboundaries > on the boolean image. This function determines the indices of the the > boundaries in clockwise direction. Next I take the corresponding X,Y > values of the indices so I can calculate the surface area with the function > polyarea. > > Is this possbile with the ITK-library? > > Thank you for your help guys. > > > > Virusvrij. www.avast.com > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > _______________________________________________ > 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 Wed Aug 10 08:34:40 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 08:34:40 -0400 Subject: [ITK] reading private tags returns weird strings In-Reply-To: References: Message-ID: Hi Francois, is this base64 encoded? You should perhaps do base64 decode on the return string to get the binary value. Regards, D?enan On Wed, Aug 10, 2016 at 7:15 AM, wrote: > Hi, > > I'm trying to read private dicom tags using : > > ImageIOType::Pointer dicomIO = ImageIOType::New(); > ... > dicomIO->SetLoadPrivateTags(true); > std::string offsetFromBottomStr; > > std::string offsetFromBottom = "0863|1041"; > dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); > > The value *offsetFromBottomStr *returned is *AICTQw==* > How does it come and how can I fix this ? > > Thank you, > Fran?ois. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Wed Aug 10 08:47:14 2016 From: matthias.b at hotmail.com (Matthias B) Date: Wed, 10 Aug 2016 14:47:14 +0200 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov>, , Message-ID: Thank you for answering D?enan, ok, the perimeter attribute is what I need. Problem is that I don't see a way where I can1. Choose a label image to define the region2. Choose the 3D Image where the label will be aplied At this moment it looks for me that the label image already contains the 3D data, which confuses me. From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 08:32:53 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; community at itk.org Hi Matthias, perimeter should be surface area in 3D (which you can divide by 2 to eliminate back side if you have a very flat object). In 2D image, it is the circumference. In 2D image, you can get object's surface area by counting how many pixels it has and then multiplying that by the size of each pixel (spacing[0]*spacing[1]). Regards,D?enan On Wed, Aug 10, 2016 at 2:40 AM, Matthias B wrote: Thank you for answering! At this moment I get the perimeter in pixel units (not the surface area of my X,Y-data) of my labeled image.I have also really no idea how to use my 3D data with a labeled image. I see no way how to add 3D data to a LabelMap for example. This is what I have at the moment.Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter()labelShapeStatistics.Execute(labelImage)Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Thanks for any help, Matthias From: blowekamp at mail.nih.gov To: matthias.b at hotmail.com CC: community at itk.org Subject: Re: [ITK] Determine surface area of certain region in image Date: Tue, 9 Aug 2016 15:58:56 +0000 Hello, You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. HTH, Brad [1] http://hdl.handle.net/1926/584 [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb [4] http://hdl.handle.net/10380/3342 On Aug 9, 2016, at 11:50 AM, Matthias B wrote: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80). The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. Virusvrij. www.avast.com _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 09:14:35 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 09:14:35 -0400 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Message-ID: The 3D image where the label will be applied is need for statistics such as mean, min and max values. If you don't care about those, you can supply the same image as both label and original (intensity) image. Or you can supply an empty (all black) image there. HTH, D?enan On Wed, Aug 10, 2016 at 8:47 AM, Matthias B wrote: > Thank you for answering D?enan, > > ok, the perimeter attribute is what I need. > > Problem is that I don't see a way where I can > 1. Choose a label image to define the region > 2. Choose the 3D Image where the label will be aplied > > At this moment it looks for me that the label image already contains the > 3D data, which confuses me. > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 08:32:53 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; community at itk.org > > > Hi Matthias, > > perimeter should be surface area in 3D (which you can divide by 2 to > eliminate back side if you have a very flat object). In 2D image, it is the > circumference. In 2D image, you can get object's surface area by counting > how many pixels it has and then multiplying that by the size of each pixel > (spacing[0]*spacing[1]). > > Regards, > D?enan > > On Wed, Aug 10, 2016 at 2:40 AM, Matthias B > wrote: > > Thank you for answering! > > At this moment I get the perimeter in pixel units (not the surface area of > my X,Y-data) of my labeled image. > I have also really no idea how to use my 3D data with a labeled image. I > see no way how to add 3D data to a LabelMap for example. > > This is what I have at the moment. > Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() > labelShapeStatistics.Execute(labelImage) > Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) > > Thanks for any help, Matthias > > > > ------------------------------ > From: blowekamp at mail.nih.gov > To: matthias.b at hotmail.com > CC: community at itk.org > Subject: Re: [ITK] Determine surface area of certain region in image > Date: Tue, 9 Aug 2016 15:58:56 +0000 > > > Hello, > > You should look into the label map framework [1]. In particular the > LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. > > HTH, > Brad > > [1] http://hdl.handle.net/1926/584 > [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToSha > peLabelMapFilter.html > [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObjec > t.html#aff1209e925293c15775520ef89e97afb > [4] http://hdl.handle.net/10380/3342 > > On Aug 9, 2016, at 11:50 AM, Matthias B wrote: > > Hello ITK-community, > > At the moment I'm working with 3D Images with following structure: > 100x80x3. Every pixel contains a X,Y,Z value. > I want to calculate the surface area of a certain region that I have > defined with a boolean 2D-Image (100x80). > The surface area should only be calculated with the X,Y-data. > > In Matlab I have experience with this by using the function bwboundaries > on the boolean image. This function determines the indices of the the > boundaries in clockwise direction. Next I take the corresponding X,Y > values of the indices so I can calculate the surface area with the function > polyarea. > > Is this possbile with the ITK-library? > > Thank you for your help guys. > > > > Virusvrij. www.avast.com > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > Virusvrij. > www.avast.com > > <#m_4192781686007042514_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Wed Aug 10 09:19:29 2016 From: matthias.b at hotmail.com (Matthias B) Date: Wed, 10 Aug 2016 15:19:29 +0200 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov>, , , Message-ID: I understand, but how do I add the label on the 3D image programmatically?preferable in C#, but C++ is also ok. Thank you for your help From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:14:35 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org The 3D image where the label will be applied is need for statistics such as mean, min and max values. If you don't care about those, you can supply the same image as both label and original (intensity) image. Or you can supply an empty (all black) image there. HTH,D?enan On Wed, Aug 10, 2016 at 8:47 AM, Matthias B wrote: Thank you for answering D?enan, ok, the perimeter attribute is what I need. Problem is that I don't see a way where I can1. Choose a label image to define the region2. Choose the 3D Image where the label will be aplied At this moment it looks for me that the label image already contains the 3D data, which confuses me. From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 08:32:53 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; community at itk.org Hi Matthias, perimeter should be surface area in 3D (which you can divide by 2 to eliminate back side if you have a very flat object). In 2D image, it is the circumference. In 2D image, you can get object's surface area by counting how many pixels it has and then multiplying that by the size of each pixel (spacing[0]*spacing[1]). Regards,D?enan On Wed, Aug 10, 2016 at 2:40 AM, Matthias B wrote: Thank you for answering! At this moment I get the perimeter in pixel units (not the surface area of my X,Y-data) of my labeled image.I have also really no idea how to use my 3D data with a labeled image. I see no way how to add 3D data to a LabelMap for example. This is what I have at the moment.Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter()labelShapeStatistics.Execute(labelImage)Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Thanks for any help, Matthias From: blowekamp at mail.nih.gov To: matthias.b at hotmail.com CC: community at itk.org Subject: Re: [ITK] Determine surface area of certain region in image Date: Tue, 9 Aug 2016 15:58:56 +0000 Hello, You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. HTH, Brad [1] http://hdl.handle.net/1926/584 [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb [4] http://hdl.handle.net/10380/3342 On Aug 9, 2016, at 11:50 AM, Matthias B wrote: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80). The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. Virusvrij. www.avast.com _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Aug 10 09:26:05 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 10 Aug 2016 13:26:05 +0000 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Message-ID: What do you mean by ?add the label on the 3D image?? Do you have an example? Are you talking about composing the label image (binary image) with the grayscale image? Brad On Aug 10, 2016, at 9:19 AM, Matthias B > wrote: I understand, but how do I add the label on the 3D image programmatically? preferable in C#, but C++ is also ok. Thank you for your help ________________________________ From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:14:35 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org The 3D image where the label will be applied is need for statistics such as mean, min and max values. If you don't care about those, you can supply the same image as both label and original (intensity) image. Or you can supply an empty (all black) image there. HTH, D?enan On Wed, Aug 10, 2016 at 8:47 AM, Matthias B > wrote: Thank you for answering D?enan, ok, the perimeter attribute is what I need. Problem is that I don't see a way where I can 1. Choose a label image to define the region 2. Choose the 3D Image where the label will be aplied At this moment it looks for me that the label image already contains the 3D data, which confuses me. ________________________________ From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 08:32:53 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; community at itk.org Hi Matthias, perimeter should be surface area in 3D (which you can divide by 2 to eliminate back side if you have a very flat object). In 2D image, it is the circumference. In 2D image, you can get object's surface area by counting how many pixels it has and then multiplying that by the size of each pixel (spacing[0]*spacing[1]). Regards, D?enan On Wed, Aug 10, 2016 at 2:40 AM, Matthias B > wrote: Thank you for answering! At this moment I get the perimeter in pixel units (not the surface area of my X,Y-data) of my labeled image. I have also really no idea how to use my 3D data with a labeled image. I see no way how to add 3D data to a LabelMap for example. This is what I have at the moment. Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() labelShapeStatistics.Execute(labelImage) Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Thanks for any help, Matthias ________________________________ From: blowekamp at mail.nih.gov To: matthias.b at hotmail.com CC: community at itk.org Subject: Re: [ITK] Determine surface area of certain region in image Date: Tue, 9 Aug 2016 15:58:56 +0000 Hello, You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. HTH, Brad [1] http://hdl.handle.net/1926/584 [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb [4] http://hdl.handle.net/10380/3342 On Aug 9, 2016, at 11:50 AM, Matthias B > wrote: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80). The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. [https://ipmcdn.avast.com/images/2016/icons/icon-envelope-tick-round-orange_184x116-v1.png] Virusvrij. www.avast.com _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community [https://ipmcdn.avast.com/images/2016/icons/icon-envelope-tick-round-orange_184x116-v1.png] Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 09:27:05 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 09:27:05 -0400 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Message-ID: Sorry, I have confused LabelShapeStatistics with LabelStatistics filter. With label shape statistics, there is no intensity image, only the label image which you are already using as input. You generally don't mix (add) label and intensity images, you just keep them separate and know which two are a pair. For label statistics, you simply set two inputs like in this example . Regards On Wed, Aug 10, 2016 at 9:19 AM, Matthias B wrote: > I understand, but how do I add the label on the 3D image programmatically? > preferable in C#, but C++ is also ok. > > Thank you for your help > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:14:35 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org > > > The 3D image where the label will be applied is need for statistics such > as mean, min and max values. If you don't care about those, you can supply > the same image as both label and original (intensity) image. Or you can > supply an empty (all black) image there. > > HTH, > D?enan > > On Wed, Aug 10, 2016 at 8:47 AM, Matthias B > wrote: > > Thank you for answering D?enan, > > ok, the perimeter attribute is what I need. > > Problem is that I don't see a way where I can > 1. Choose a label image to define the region > 2. Choose the 3D Image where the label will be aplied > > At this moment it looks for me that the label image already contains the > 3D data, which confuses me. > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 08:32:53 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; community at itk.org > > > Hi Matthias, > > perimeter should be surface area in 3D (which you can divide by 2 to > eliminate back side if you have a very flat object). In 2D image, it is the > circumference. In 2D image, you can get object's surface area by counting > how many pixels it has and then multiplying that by the size of each pixel > (spacing[0]*spacing[1]). > > Regards, > D?enan > > On Wed, Aug 10, 2016 at 2:40 AM, Matthias B > wrote: > > Thank you for answering! > > At this moment I get the perimeter in pixel units (not the surface area of > my X,Y-data) of my labeled image. > I have also really no idea how to use my 3D data with a labeled image. I > see no way how to add 3D data to a LabelMap for example. > > This is what I have at the moment. > Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() > labelShapeStatistics.Execute(labelImage) > Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) > > Thanks for any help, Matthias > > > > ------------------------------ > From: blowekamp at mail.nih.gov > To: matthias.b at hotmail.com > CC: community at itk.org > Subject: Re: [ITK] Determine surface area of certain region in image > Date: Tue, 9 Aug 2016 15:58:56 +0000 > > > Hello, > > You should look into the label map framework [1]. In particular the > LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. > > HTH, > Brad > > [1] http://hdl.handle.net/1926/584 > [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToSha > peLabelMapFilter.html > [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObjec > t.html#aff1209e925293c15775520ef89e97afb > [4] http://hdl.handle.net/10380/3342 > > On Aug 9, 2016, at 11:50 AM, Matthias B wrote: > > Hello ITK-community, > > At the moment I'm working with 3D Images with following structure: > 100x80x3. Every pixel contains a X,Y,Z value. > I want to calculate the surface area of a certain region that I have > defined with a boolean 2D-Image (100x80). > The surface area should only be calculated with the X,Y-data. > > In Matlab I have experience with this by using the function bwboundaries > on the boolean image. This function determines the indices of the the > boundaries in clockwise direction. Next I take the corresponding X,Y > values of the indices so I can calculate the surface area with the function > polyarea. > > Is this possbile with the ITK-library? > > Thank you for your help guys. > > > > Virusvrij. www.avast.com > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > Virusvrij. > www.avast.com > > <#m_1512104202195024141_m_4192781686007042514_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Wed Aug 10 09:48:52 2016 From: matthias.b at hotmail.com (Matthias B) Date: Wed, 10 Aug 2016 15:48:52 +0200 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov>, , , , Message-ID: I think an example is the best way to solve my problem. Let us take following 3D Data with name 3DImage as itk.simple.imageXdata={{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4}}Ydata={{2,2,2,2,2},{1,1,1,1,1},{0,0,0,0,0},{-1,-1,-1,-1,-1},{-2,-2,-2,-2,-2}}Zdata={{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}} and LabelImage as itk.simple.imageLabelImage={{{0,0,0,0,0},{0,1,1,1,0},{0,1,1,1,0},{0,1,1,1,0},{0,0,0,0,0}} The surface area with label 1 should be 12.Which steps (C# or C++) do I need to take to solve this? Thank you guys From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:27:05 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: community at itk.org; dan.muel at gmail.com; blowekamp at mail.nih.gov Sorry, I have confused LabelShapeStatistics with LabelStatistics filter. With label shape statistics, there is no intensity image, only the label image which you are already using as input. You generally don't mix (add) label and intensity images, you just keep them separate and know which two are a pair. For label statistics, you simply set two inputs like in this example. Regards On Wed, Aug 10, 2016 at 9:19 AM, Matthias B wrote: I understand, but how do I add the label on the 3D image programmatically?preferable in C#, but C++ is also ok. Thank you for your help From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:14:35 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org The 3D image where the label will be applied is need for statistics such as mean, min and max values. If you don't care about those, you can supply the same image as both label and original (intensity) image. Or you can supply an empty (all black) image there. HTH,D?enan On Wed, Aug 10, 2016 at 8:47 AM, Matthias B wrote: Thank you for answering D?enan, ok, the perimeter attribute is what I need. Problem is that I don't see a way where I can1. Choose a label image to define the region2. Choose the 3D Image where the label will be aplied At this moment it looks for me that the label image already contains the 3D data, which confuses me. From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 08:32:53 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; community at itk.org Hi Matthias, perimeter should be surface area in 3D (which you can divide by 2 to eliminate back side if you have a very flat object). In 2D image, it is the circumference. In 2D image, you can get object's surface area by counting how many pixels it has and then multiplying that by the size of each pixel (spacing[0]*spacing[1]). Regards,D?enan On Wed, Aug 10, 2016 at 2:40 AM, Matthias B wrote: Thank you for answering! At this moment I get the perimeter in pixel units (not the surface area of my X,Y-data) of my labeled image.I have also really no idea how to use my 3D data with a labeled image. I see no way how to add 3D data to a LabelMap for example. This is what I have at the moment.Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter()labelShapeStatistics.Execute(labelImage)Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Thanks for any help, Matthias From: blowekamp at mail.nih.gov To: matthias.b at hotmail.com CC: community at itk.org Subject: Re: [ITK] Determine surface area of certain region in image Date: Tue, 9 Aug 2016 15:58:56 +0000 Hello, You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. HTH, Brad [1] http://hdl.handle.net/1926/584 [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb [4] http://hdl.handle.net/10380/3342 On Aug 9, 2016, at 11:50 AM, Matthias B wrote: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80). The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. Virusvrij. www.avast.com _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Wed Aug 10 09:58:17 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Wed, 10 Aug 2016 13:58:17 +0000 Subject: [ITK] reading private tags returns weird strings References: Message-ID: Le 10/08/2016 ? 14:35, D?enan Zuki? a ?crit : Hi Francois, is this base64 encoded? You should perhaps do base64 decode on the return string to get the binary value. Regards, D?enan On Wed, Aug 10, 2016 at 7:15 AM, > wrote: Hi, I'm trying to read private dicom tags using : ImageIOType::Pointer dicomIO = ImageIOType::New(); ... dicomIO->SetLoadPrivateTags(true); std::string offsetFromBottomStr; std::string offsetFromBottom = "0863|1041"; dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); The value offsetFromBottomStr returned is AICTQw== How does it come and how can I fix this ? Thank you, Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Thanks for your answer. You might be right, they say here private tags and encodes the with Base64 into strings. Unfortunately, AICTQw== should correspond to 295 and according to https://www.base64decode.org/, AICTQw== is a C. Besides, I don't understand how does itksysBase64_Decode works (I'm not sure I should use this method too). -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 09:58:32 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 09:58:32 -0400 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Message-ID: 3DImage of size 5x5x3, and LabelImage 5x5. Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() labelShapeStatistics.Execute(labelImage) Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Dim pixelCount = labelShapeStatistics.GetNumberOfPixels(1) //=9 in your example Dim sp = labelImage.GetSpacing() Dim surfaceArea=pixelCount*sp[0]*sp[1] //sp[0]*sp[1] should be =1.25 to yield a total of 12 which you want HTH, D?enan On Wed, Aug 10, 2016 at 9:48 AM, Matthias B wrote: > I think an example is the best way to solve my problem. > > Let us take following 3D Data with name 3DImage as itk.simple.image > Xdata={{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4}, > {-4,-2,0,2,4}} > Ydata={{2,2,2,2,2},{1,1,1,1,1},{0,0,0,0,0},{-1,-1,-1,-1,-1}, > {-2,-2,-2,-2,-2}} > Zdata={{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}} > > and LabelImage as itk.simple.image > LabelImage={{{0,0,0,0,0},{0,1,1,1,0},{0,1,1,1,0},{0,1,1,1,0},{0,0,0,0,0}} > > The surface area with label 1 should be 12. > Which steps (C# or C++) do I need to take to solve this? > > Thank you guys > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:27:05 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: community at itk.org; dan.muel at gmail.com; blowekamp at mail.nih.gov > > > Sorry, I have confused LabelShapeStatistics > > with LabelStatistics > > filter. > > With label shape statistics, there is no intensity image, only the label > image which you are already using as input. > > You generally don't mix (add) label and intensity images, you just keep > them separate and know which two are a pair. For label statistics, you > simply set two inputs like in this example > > . > > Regards > > On Wed, Aug 10, 2016 at 9:19 AM, Matthias B > wrote: > > I understand, but how do I add the label on the 3D image programmatically? > preferable in C#, but C++ is also ok. > > Thank you for your help > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:14:35 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org > > > The 3D image where the label will be applied is need for statistics such > as mean, min and max values. If you don't care about those, you can supply > the same image as both label and original (intensity) image. Or you can > supply an empty (all black) image there. > > HTH, > D?enan > > On Wed, Aug 10, 2016 at 8:47 AM, Matthias B > wrote: > > Thank you for answering D?enan, > > ok, the perimeter attribute is what I need. > > Problem is that I don't see a way where I can > 1. Choose a label image to define the region > 2. Choose the 3D Image where the label will be aplied > > At this moment it looks for me that the label image already contains the > 3D data, which confuses me. > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 08:32:53 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; community at itk.org > > > Hi Matthias, > > perimeter should be surface area in 3D (which you can divide by 2 to > eliminate back side if you have a very flat object). In 2D image, it is the > circumference. In 2D image, you can get object's surface area by counting > how many pixels it has and then multiplying that by the size of each pixel > (spacing[0]*spacing[1]). > > Regards, > D?enan > > On Wed, Aug 10, 2016 at 2:40 AM, Matthias B > wrote: > > Thank you for answering! > > At this moment I get the perimeter in pixel units (not the surface area of > my X,Y-data) of my labeled image. > I have also really no idea how to use my 3D data with a labeled image. I > see no way how to add 3D data to a LabelMap for example. > > This is what I have at the moment. > Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() > labelShapeStatistics.Execute(labelImage) > Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) > > Thanks for any help, Matthias > > > > ------------------------------ > From: blowekamp at mail.nih.gov > To: matthias.b at hotmail.com > CC: community at itk.org > Subject: Re: [ITK] Determine surface area of certain region in image > Date: Tue, 9 Aug 2016 15:58:56 +0000 > > > Hello, > > You should look into the label map framework [1]. In particular the > LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. > > HTH, > Brad > > [1] http://hdl.handle.net/1926/584 > [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToSha > peLabelMapFilter.html > [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObjec > t.html#aff1209e925293c15775520ef89e97afb > [4] http://hdl.handle.net/10380/3342 > > On Aug 9, 2016, at 11:50 AM, Matthias B wrote: > > Hello ITK-community, > > At the moment I'm working with 3D Images with following structure: > 100x80x3. Every pixel contains a X,Y,Z value. > I want to calculate the surface area of a certain region that I have > defined with a boolean 2D-Image (100x80). > The surface area should only be calculated with the X,Y-data. > > In Matlab I have experience with this by using the function bwboundaries > on the boolean image. This function determines the indices of the the > boundaries in clockwise direction. Next I take the corresponding X,Y > values of the indices so I can calculate the surface area with the function > polyarea. > > Is this possbile with the ITK-library? > > Thank you for your help guys. > > > > Virusvrij. www.avast.com > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > Virusvrij. > www.avast.com > > <#m_876262044166110828_m_1512104202195024141_m_4192781686007042514_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 10:04:42 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 10:04:42 -0400 Subject: [ITK] reading private tags returns weird strings In-Reply-To: References: Message-ID: In fact, this decodes to 00 80 93 43 - four bytes given here in hexadecimal notation. The decoder you linked does not seem to work correctly. I don't know why you expect 295 there. On Wed, Aug 10, 2016 at 9:58 AM, wrote: > Le 10/08/2016 ? 14:35, D?enan Zuki? a ?crit : > > Hi Francois, > > is this base64 encoded? You should perhaps do base64 decode on the return > string to get the binary value. > > Regards, > D?enan > > On Wed, Aug 10, 2016 at 7:15 AM, wrote: > >> Hi, >> >> I'm trying to read private dicom tags using : >> >> ImageIOType::Pointer dicomIO = ImageIOType::New(); >> ... >> dicomIO->SetLoadPrivateTags(true); >> std::string offsetFromBottomStr; >> >> std::string offsetFromBottom = "0863|1041"; >> dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); >> >> The value *offsetFromBottomStr *returned is *AICTQw==* >> How does it come and how can I fix this ? >> >> Thank you, >> Fran?ois. >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> > Thanks for your answer. You might be right, they say here > > *private tags and encodes the with Base64 into strings. *Unfortunately, *AICTQw== > *should correspond to 295 and according to https://www.base64decode.org/, > *AICTQw==* is a C. > Besides, I don't understand how does itksysBase64_Decode works (I'm not > sure I should use this method too). > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Wed Aug 10 10:13:40 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Wed, 10 Aug 2016 14:13:40 +0000 Subject: [ITK] reading private tags returns weird strings References: Message-ID: Le 10/08/2016 ? 16:05, D?enan Zuki? a ?crit : In fact, this decodes to 00 80 93 43 - four bytes given here in hexadecimal notation. The decoder you linked does not seem to work correctly. I don't know why you expect 295 there. On Wed, Aug 10, 2016 at 9:58 AM, > wrote: Le 10/08/2016 ? 14:35, D?enan Zuki? a ?crit : Hi Francois, is this base64 encoded? You should perhaps do base64 decode on the return string to get the binary value. Regards, D?enan On Wed, Aug 10, 2016 at 7:15 AM, > wrote: Hi, I'm trying to read private dicom tags using : ImageIOType::Pointer dicomIO = ImageIOType::New(); ... dicomIO->SetLoadPrivateTags(true); std::string offsetFromBottomStr; std::string offsetFromBottom = "0863|1041"; dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); The value offsetFromBottomStr returned is AICTQw== How does it come and how can I fix this ? Thank you, Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Thanks for your answer. You might be right, they say here private tags and encodes the with Base64 into strings. Unfortunately, AICTQw== should correspond to 295 and according to https://www.base64decode.org/, AICTQw== is a C. Besides, I don't understand how does itksysBase64_Decode works (I'm not sure I should use this method too). In fact I have previously red the dicom using matlab and the value of the private tag 0863 1041 is 295. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 10:22:56 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 10:22:56 -0400 Subject: [ITK] reading private tags returns weird strings In-Reply-To: References: Message-ID: Does Matlab have special support for those private tags? They may have special encoding besides base64 applied by ITK DICOM dictionary. On Wed, Aug 10, 2016 at 10:13 AM, wrote: > Le 10/08/2016 ? 16:05, D?enan Zuki? a ?crit : > > In fact, this decodes > to 00 80 93 > 43 - four bytes given here in hexadecimal notation. The decoder you linked > does not seem to work correctly. I don't know why you expect 295 there. > > On Wed, Aug 10, 2016 at 9:58 AM, wrote: > >> Le 10/08/2016 ? 14:35, D?enan Zuki? a ?crit : >> >> Hi Francois, >> >> is this base64 encoded? You should perhaps do base64 decode on the return >> string to get the binary value. >> >> Regards, >> D?enan >> >> On Wed, Aug 10, 2016 at 7:15 AM, wrote: >> >>> Hi, >>> >>> I'm trying to read private dicom tags using : >>> >>> ImageIOType::Pointer dicomIO = ImageIOType::New(); >>> ... >>> dicomIO->SetLoadPrivateTags(true); >>> std::string offsetFromBottomStr; >>> >>> std::string offsetFromBottom = "0863|1041"; >>> dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); >>> >>> The value *offsetFromBottomStr *returned is *AICTQw==* >>> How does it come and how can I fix this ? >>> >>> Thank you, >>> Fran?ois. >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >> Thanks for your answer. You might be right, they say here >> >> *private tags and encodes the with Base64 into strings. *Unfortunately, *AICTQw== >> *should correspond to 295 and according to https://www.base64decode.org/, >> *AICTQw==* is a C. >> Besides, I don't understand how does itksysBase64_Decode works (I'm not >> sure I should use this method too). >> > > In fact I have previously red the dicom using matlab and the value of the > private tag 0863 1041 is 295. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Wed Aug 10 10:41:00 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Wed, 10 Aug 2016 14:41:00 +0000 Subject: [ITK] reading private tags returns weird strings References: Message-ID: Le 10/08/2016 ? 16:23, D?enan Zuki? a ?crit : Does Matlab have special support for those private tags? They may have special encoding besides base64 applied by ITK DICOM dictionary. On Wed, Aug 10, 2016 at 10:13 AM, > wrote: Le 10/08/2016 ? 16:05, D?enan Zuki? a ?crit : In fact, this decodes to 00 80 93 43 - four bytes given here in hexadecimal notation. The decoder you linked does not seem to work correctly. I don't know why you expect 295 there. On Wed, Aug 10, 2016 at 9:58 AM, > wrote: Le 10/08/2016 ? 14:35, D?enan Zuki? a ?crit : Hi Francois, is this base64 encoded? You should perhaps do base64 decode on the return string to get the binary value. Regards, D?enan On Wed, Aug 10, 2016 at 7:15 AM, > wrote: Hi, I'm trying to read private dicom tags using : ImageIOType::Pointer dicomIO = ImageIOType::New(); ... dicomIO->SetLoadPrivateTags(true); std::string offsetFromBottomStr; std::string offsetFromBottom = "0863|1041"; dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); The value offsetFromBottomStr returned is AICTQw== How does it come and how can I fix this ? Thank you, Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Thanks for your answer. You might be right, they say here private tags and encodes the with Base64 into strings. Unfortunately, AICTQw== should correspond to 295 and according to https://www.base64decode.org/, AICTQw== is a C. Besides, I don't understand how does itksysBase64_Decode works (I'm not sure I should use this method too). In fact I have previously red the dicom using matlab and the value of the private tag 0863 1041 is 295. I don't know, it doesn't seem really matlab specific, this tool also gets a dicom inspector module which displays 295. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 10:43:35 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 10:43:35 -0400 Subject: [ITK] reading private tags returns weird strings In-Reply-To: References: Message-ID: Can you share (either with the list or just me) this DICOM image (optionally anonymized) and a runnable example which you use to read it? On Wed, Aug 10, 2016 at 10:41 AM, wrote: > Le 10/08/2016 ? 16:23, D?enan Zuki? a ?crit : > > Does Matlab have special support for those private tags? They may have > special encoding besides base64 applied by ITK DICOM dictionary. > > On Wed, Aug 10, 2016 at 10:13 AM, wrote: > >> Le 10/08/2016 ? 16:05, D?enan Zuki? a ?crit : >> >> In fact, this decodes >> to 00 80 93 >> 43 - four bytes given here in hexadecimal notation. The decoder you linked >> does not seem to work correctly. I don't know why you expect 295 there. >> >> On Wed, Aug 10, 2016 at 9:58 AM, wrote: >> >>> Le 10/08/2016 ? 14:35, D?enan Zuki? a ?crit : >>> >>> Hi Francois, >>> >>> is this base64 encoded? You should perhaps do base64 decode on the >>> return string to get the binary value. >>> >>> Regards, >>> D?enan >>> >>> On Wed, Aug 10, 2016 at 7:15 AM, wrote: >>> >>>> Hi, >>>> >>>> I'm trying to read private dicom tags using : >>>> >>>> ImageIOType::Pointer dicomIO = ImageIOType::New(); >>>> ... >>>> dicomIO->SetLoadPrivateTags(true); >>>> std::string offsetFromBottomStr; >>>> >>>> std::string offsetFromBottom = "0863|1041"; >>>> dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); >>>> >>>> The value *offsetFromBottomStr *returned is *AICTQw==* >>>> How does it come and how can I fix this ? >>>> >>>> Thank you, >>>> Fran?ois. >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >>>> >>> Thanks for your answer. You might be right, they say here >>> >>> *private tags and encodes the with Base64 into strings. *Unfortunately, *AICTQw== >>> *should correspond to 295 and according to https://www.base64decode.org/, >>> *AICTQw==* is a C. >>> Besides, I don't understand how does itksysBase64_Decode works (I'm not >>> sure I should use this method too). >>> >> >> In fact I have previously red the dicom using matlab and the value of the >> private tag 0863 1041 is 295. >> > > I don't know, it doesn't seem really matlab specific, this tool > also gets a dicom inspector > module which displays 295. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Wed Aug 10 11:11:55 2016 From: matthias.b at hotmail.com (Matthias B) Date: Wed, 10 Aug 2016 17:11:55 +0200 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov>, , , , , Message-ID: Thank you for the code sp[0] and sp[1] is both 1 in my code. I don't get how I would get 12 in your example.The 3DImage is also never used. The spacing is also never absolute in my situation. Ydata could also be like this={{3,2.5,2.1,2.5,2.2},{1.4,1.2,1.3,1.1,1.1},...} From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:58:32 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: dan.muel at gmail.com; community at itk.org; blowekamp at mail.nih.gov 3DImage of size 5x5x3, and LabelImage 5x5. Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() labelShapeStatistics.Execute(labelImage) Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Dim pixelCount = labelShapeStatistics.GetNumberOfPixels(1) //=9 in your example Dim sp = labelImage.GetSpacing() Dim surfaceArea=pixelCount*sp[0]*sp[1] //sp[0]*sp[1] should be =1.25 to yield a total of 12 which you want HTH,D?enan On Wed, Aug 10, 2016 at 9:48 AM, Matthias B wrote: I think an example is the best way to solve my problem. Let us take following 3D Data with name 3DImage as itk.simple.imageXdata={{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4}}Ydata={{2,2,2,2,2},{1,1,1,1,1},{0,0,0,0,0},{-1,-1,-1,-1,-1},{-2,-2,-2,-2,-2}}Zdata={{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}} and LabelImage as itk.simple.imageLabelImage={{{0,0,0,0,0},{0,1,1,1,0},{0,1,1,1,0},{0,1,1,1,0},{0,0,0,0,0}} The surface area with label 1 should be 12.Which steps (C# or C++) do I need to take to solve this? Thank you guys From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:27:05 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: community at itk.org; dan.muel at gmail.com; blowekamp at mail.nih.gov Sorry, I have confused LabelShapeStatistics with LabelStatistics filter. With label shape statistics, there is no intensity image, only the label image which you are already using as input. You generally don't mix (add) label and intensity images, you just keep them separate and know which two are a pair. For label statistics, you simply set two inputs like in this example. Regards On Wed, Aug 10, 2016 at 9:19 AM, Matthias B wrote: I understand, but how do I add the label on the 3D image programmatically?preferable in C#, but C++ is also ok. Thank you for your help From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:14:35 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org The 3D image where the label will be applied is need for statistics such as mean, min and max values. If you don't care about those, you can supply the same image as both label and original (intensity) image. Or you can supply an empty (all black) image there. HTH,D?enan On Wed, Aug 10, 2016 at 8:47 AM, Matthias B wrote: Thank you for answering D?enan, ok, the perimeter attribute is what I need. Problem is that I don't see a way where I can1. Choose a label image to define the region2. Choose the 3D Image where the label will be aplied At this moment it looks for me that the label image already contains the 3D data, which confuses me. From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 08:32:53 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; community at itk.org Hi Matthias, perimeter should be surface area in 3D (which you can divide by 2 to eliminate back side if you have a very flat object). In 2D image, it is the circumference. In 2D image, you can get object's surface area by counting how many pixels it has and then multiplying that by the size of each pixel (spacing[0]*spacing[1]). Regards,D?enan On Wed, Aug 10, 2016 at 2:40 AM, Matthias B wrote: Thank you for answering! At this moment I get the perimeter in pixel units (not the surface area of my X,Y-data) of my labeled image.I have also really no idea how to use my 3D data with a labeled image. I see no way how to add 3D data to a LabelMap for example. This is what I have at the moment.Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter()labelShapeStatistics.Execute(labelImage)Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Thanks for any help, Matthias From: blowekamp at mail.nih.gov To: matthias.b at hotmail.com CC: community at itk.org Subject: Re: [ITK] Determine surface area of certain region in image Date: Tue, 9 Aug 2016 15:58:56 +0000 Hello, You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. HTH, Brad [1] http://hdl.handle.net/1926/584 [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb [4] http://hdl.handle.net/10380/3342 On Aug 9, 2016, at 11:50 AM, Matthias B wrote: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80). The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. Virusvrij. www.avast.com _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 11:19:28 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 11:19:28 -0400 Subject: [ITK] Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Message-ID: There are nine 1s in the LabelImage, which means that your object with label 1 is 9 pixels big. Content of the 3DImage is irrelevant. If the example LabelImage content you provided does not reflect what you want, you need to come up with a better LabelImage (a different, better segmentation), derived from 3DImage. On Wed, Aug 10, 2016 at 11:11 AM, Matthias B wrote: > Thank you for the code > > sp[0] and sp[1] is both 1 in my code. I don't get how I would get 12 in > your example. > The 3DImage is also never used. > > The spacing is also never absolute in my situation. > Ydata could also be like this={{3,2.5,2.1,2.5,2.2},{1. > 4,1.2,1.3,1.1,1.1},...} > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:58:32 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: dan.muel at gmail.com; community at itk.org; blowekamp at mail.nih.gov > > > 3DImage of size 5x5x3, and LabelImage 5x5. > > Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() > labelShapeStatistics.Execute(labelImage) > Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) > Dim pixelCount = labelShapeStatistics.GetNumberOfPixels(1) //=9 in your > example > Dim sp = labelImage.GetSpacing() > Dim surfaceArea=pixelCount*sp[0]*sp[1] //sp[0]*sp[1] should be =1.25 to > yield a total of 12 which you want > > HTH, > D?enan > > On Wed, Aug 10, 2016 at 9:48 AM, Matthias B > wrote: > > I think an example is the best way to solve my problem. > > Let us take following 3D Data with name 3DImage as itk.simple.image > Xdata={{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4}, > {-4,-2,0,2,4}} > Ydata={{2,2,2,2,2},{1,1,1,1,1},{0,0,0,0,0},{-1,-1,-1,-1,-1}, > {-2,-2,-2,-2,-2}} > Zdata={{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}} > > and LabelImage as itk.simple.image > LabelImage={{{0,0,0,0,0},{0,1,1,1,0},{0,1,1,1,0},{0,1,1,1,0},{0,0,0,0,0}} > > The surface area with label 1 should be 12. > Which steps (C# or C++) do I need to take to solve this? > > Thank you guys > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:27:05 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: community at itk.org; dan.muel at gmail.com; blowekamp at mail.nih.gov > > > Sorry, I have confused LabelShapeStatistics > > with LabelStatistics > > filter. > > With label shape statistics, there is no intensity image, only the label > image which you are already using as input. > > You generally don't mix (add) label and intensity images, you just keep > them separate and know which two are a pair. For label statistics, you > simply set two inputs like in this example > > . > > Regards > > On Wed, Aug 10, 2016 at 9:19 AM, Matthias B > wrote: > > I understand, but how do I add the label on the 3D image programmatically? > preferable in C#, but C++ is also ok. > > Thank you for your help > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:14:35 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org > > > The 3D image where the label will be applied is need for statistics such > as mean, min and max values. If you don't care about those, you can supply > the same image as both label and original (intensity) image. Or you can > supply an empty (all black) image there. > > HTH, > D?enan > > On Wed, Aug 10, 2016 at 8:47 AM, Matthias B > wrote: > > Thank you for answering D?enan, > > ok, the perimeter attribute is what I need. > > Problem is that I don't see a way where I can > 1. Choose a label image to define the region > 2. Choose the 3D Image where the label will be aplied > > At this moment it looks for me that the label image already contains the > 3D data, which confuses me. > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 08:32:53 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; community at itk.org > > > Hi Matthias, > > perimeter should be surface area in 3D (which you can divide by 2 to > eliminate back side if you have a very flat object). In 2D image, it is the > circumference. In 2D image, you can get object's surface area by counting > how many pixels it has and then multiplying that by the size of each pixel > (spacing[0]*spacing[1]). > > Regards, > D?enan > > On Wed, Aug 10, 2016 at 2:40 AM, Matthias B > wrote: > > Thank you for answering! > > At this moment I get the perimeter in pixel units (not the surface area of > my X,Y-data) of my labeled image. > I have also really no idea how to use my 3D data with a labeled image. I > see no way how to add 3D data to a LabelMap for example. > > This is what I have at the moment. > Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() > labelShapeStatistics.Execute(labelImage) > Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) > > Thanks for any help, Matthias > > > > ------------------------------ > From: blowekamp at mail.nih.gov > To: matthias.b at hotmail.com > CC: community at itk.org > Subject: Re: [ITK] Determine surface area of certain region in image > Date: Tue, 9 Aug 2016 15:58:56 +0000 > > > Hello, > > You should look into the label map framework [1]. In particular the > LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. > > HTH, > Brad > > [1] http://hdl.handle.net/1926/584 > [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToSha > peLabelMapFilter.html > [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObjec > t.html#aff1209e925293c15775520ef89e97afb > [4] http://hdl.handle.net/10380/3342 > > On Aug 9, 2016, at 11:50 AM, Matthias B wrote: > > Hello ITK-community, > > At the moment I'm working with 3D Images with following structure: > 100x80x3. Every pixel contains a X,Y,Z value. > I want to calculate the surface area of a certain region that I have > defined with a boolean 2D-Image (100x80). > The surface area should only be calculated with the X,Y-data. > > In Matlab I have experience with this by using the function bwboundaries > on the boolean image. This function determines the indices of the the > boundaries in clockwise direction. Next I take the corresponding X,Y > values of the indices so I can calculate the surface area with the function > polyarea. > > Is this possbile with the ITK-library? > > Thank you for your help guys. > > > > Virusvrij. www.avast.com > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > Virusvrij. > www.avast.com > > <#m_-24046198973060639_m_876262044166110828_m_1512104202195024141_m_4192781686007042514_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 10 11:43:53 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 11:43:53 -0400 Subject: [ITK] reading private tags returns weird strings In-Reply-To: References: Message-ID: For posterity: the value Francois was looking for was a float, and the four bytes 00 80 93 43 indeed encode the float value 295.0 The code to convert to float: float * fDecoded = (float *)&decoded[0]; std::cout << "float = " << (*fDecoded) << std::endl; On Wed, Aug 10, 2016 at 10:43 AM, D?enan Zuki? wrote: > Can you share (either with the list or just me) this DICOM image > (optionally anonymized) and a runnable example which you use to read it? > > On Wed, Aug 10, 2016 at 10:41 AM, wrote: > >> Le 10/08/2016 ? 16:23, D?enan Zuki? a ?crit : >> >> Does Matlab have special support for those private tags? They may have >> special encoding besides base64 applied by ITK DICOM dictionary. >> >> On Wed, Aug 10, 2016 at 10:13 AM, wrote: >> >>> Le 10/08/2016 ? 16:05, D?enan Zuki? a ?crit : >>> >>> In fact, this decodes >>> to 00 80 93 >>> 43 - four bytes given here in hexadecimal notation. The decoder you linked >>> does not seem to work correctly. I don't know why you expect 295 there. >>> >>> On Wed, Aug 10, 2016 at 9:58 AM, wrote: >>> >>>> Le 10/08/2016 ? 14:35, D?enan Zuki? a ?crit : >>>> >>>> Hi Francois, >>>> >>>> is this base64 encoded? You should perhaps do base64 decode on the >>>> return string to get the binary value. >>>> >>>> Regards, >>>> D?enan >>>> >>>> On Wed, Aug 10, 2016 at 7:15 AM, wrote: >>>> >>>>> Hi, >>>>> >>>>> I'm trying to read private dicom tags using : >>>>> >>>>> ImageIOType::Pointer dicomIO = ImageIOType::New(); >>>>> ... >>>>> dicomIO->SetLoadPrivateTags(true); >>>>> std::string offsetFromBottomStr; >>>>> >>>>> std::string offsetFromBottom = "0863|1041"; >>>>> dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); >>>>> >>>>> The value *offsetFromBottomStr *returned is *AICTQw==* >>>>> How does it come and how can I fix this ? >>>>> >>>>> Thank you, >>>>> Fran?ois. >>>>> >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>>>> >>>> Thanks for your answer. You might be right, they say here >>>> >>>> *private tags and encodes the with Base64 into strings. *Unfortunately, >>>> *AICTQw== *should correspond to 295 and according to >>>> https://www.base64decode.org/, *AICTQw==* is a C. >>>> Besides, I don't understand how does itksysBase64_Decode works (I'm not >>>> sure I should use this method too). >>>> >>> >>> In fact I have previously red the dicom using matlab and the value of >>> the private tag 0863 1041 is 295. >>> >> >> I don't know, it doesn't seem really matlab specific, this tool >> also gets a dicom inspector >> module which displays 295. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Wed Aug 10 11:51:22 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Wed, 10 Aug 2016 15:51:22 +0000 Subject: [ITK] reading private tags returns weird strings References: Message-ID: Le 10/08/2016 ? 17:44, D?enan Zuki? a ?crit : For posterity: the value Francois was looking for was a float, and the four bytes 00 80 93 43 indeed encode the float value 295.0 The code to convert to float: float * fDecoded = (float *)&decoded[0]; std::cout << "float = " << (*fDecoded) << std::endl; On Wed, Aug 10, 2016 at 10:43 AM, D?enan Zuki? > wrote: Can you share (either with the list or just me) this DICOM image (optionally anonymized) and a runnable example which you use to read it? On Wed, Aug 10, 2016 at 10:41 AM, > wrote: Le 10/08/2016 ? 16:23, D?enan Zuki? a ?crit : Does Matlab have special support for those private tags? They may have special encoding besides base64 applied by ITK DICOM dictionary. On Wed, Aug 10, 2016 at 10:13 AM, > wrote: Le 10/08/2016 ? 16:05, D?enan Zuki? a ?crit : In fact, this decodes to 00 80 93 43 - four bytes given here in hexadecimal notation. The decoder you linked does not seem to work correctly. I don't know why you expect 295 there. On Wed, Aug 10, 2016 at 9:58 AM, > wrote: Le 10/08/2016 ? 14:35, D?enan Zuki? a ?crit : Hi Francois, is this base64 encoded? You should perhaps do base64 decode on the return string to get the binary value. Regards, D?enan On Wed, Aug 10, 2016 at 7:15 AM, > wrote: Hi, I'm trying to read private dicom tags using : ImageIOType::Pointer dicomIO = ImageIOType::New(); ... dicomIO->SetLoadPrivateTags(true); std::string offsetFromBottomStr; std::string offsetFromBottom = "0863|1041"; dicomIO->GetValueFromTag(offsetFromBottom, offsetFromBottomStr); The value offsetFromBottomStr returned is AICTQw== How does it come and how can I fix this ? Thank you, Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Thanks for your answer. You might be right, they say here private tags and encodes the with Base64 into strings. Unfortunately, AICTQw== should correspond to 295 and according to https://www.base64decode.org/, AICTQw== is a C. Besides, I don't understand how does itksysBase64_Decode works (I'm not sure I should use this method too). In fact I have previously red the dicom using matlab and the value of the private tag 0863 1041 is 295. I don't know, it doesn't seem really matlab specific, this tool also gets a dicom inspector module which displays 295. OK !!! Thank you very much for your help ! So the final solution was: int dlen = gdcm::Base64::GetDecodeLength(offsetFromBottomStr.c_str(), offsetFromBottomStr.size() ); std::string decoded; decoded.resize( dlen ); gdcm::Base64::Decode( &decoded[0], decoded.size(), offsetFromBottomStr.c_str(), offsetFromBottomStr.size() ); float * fDecoded = (float *)&decoded[0]; std::cout << "float = " << (*fDecoded) << std::endl; -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthias.b at hotmail.com Wed Aug 10 12:16:16 2016 From: matthias.b at hotmail.com (Matthias B) Date: Wed, 10 Aug 2016 18:16:16 +0200 Subject: [ITK] FW: Determine surface area of certain region in image In-Reply-To: References: , <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov>, , , , , , , , , , , Message-ID: From: matthias.b at hotmail.com To: dzenanz at gmail.com Subject: RE: [ITK] Determine surface area of certain region in image Date: Wed, 10 Aug 2016 18:15:39 +0200 I'm sorry, I really don't get it D?enan, Maybe another approach, I'm working with a 3D camera with a resolution of 5 by 5. Every pixel contains a X, Y and Z component, let's say in centimeters.I put an object int front of the camera right in the center of the image, the object covers 3x3 pixels.. Now I want to have the surface area of this object, I now the object is located on the image like this {{0,0,0,0,0},{0,1,1,1,0},{0,1,1,1,0},{0,1,1,1,0},{0,0,0,0,0}} Xdata={{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4}}Ydata={{3,2.5,2.1,2.5,2.2},{1.4,1.2,1.3,1.1,1.1},{0,0,0,0,0},{-3,-2.5,-2.1,-2.5,-2.2},{-1.4,-1.2,-1.3,-1.1,-1.1}}Zdata={{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}} So, is it possible to get the object surface area in real world, so in cm2 with the ITK library? Thank you for your effort From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 11:19:28 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: dan.muel at gmail.com; community at itk.org; blowekamp at mail.nih.gov There are nine 1s in the LabelImage, which means that your object with label 1 is 9 pixels big. Content of the 3DImage is irrelevant. If the example LabelImage content you provided does not reflect what you want, you need to come up with a better LabelImage (a different, better segmentation), derived from 3DImage. On Wed, Aug 10, 2016 at 11:11 AM, Matthias B wrote: Thank you for the code sp[0] and sp[1] is both 1 in my code. I don't get how I would get 12 in your example.The 3DImage is also never used. The spacing is also never absolute in my situation. Ydata could also be like this={{3,2.5,2.1,2.5,2.2},{1.4,1.2,1.3,1.1,1.1},...} From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:58:32 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: dan.muel at gmail.com; community at itk.org; blowekamp at mail.nih.gov 3DImage of size 5x5x3, and LabelImage 5x5. Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() labelShapeStatistics.Execute(labelImage) Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Dim pixelCount = labelShapeStatistics.GetNumberOfPixels(1) //=9 in your example Dim sp = labelImage.GetSpacing() Dim surfaceArea=pixelCount*sp[0]*sp[1] //sp[0]*sp[1] should be =1.25 to yield a total of 12 which you want HTH,D?enan On Wed, Aug 10, 2016 at 9:48 AM, Matthias B wrote: I think an example is the best way to solve my problem. Let us take following 3D Data with name 3DImage as itk.simple.imageXdata={{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4}}Ydata={{2,2,2,2,2},{1,1,1,1,1},{0,0,0,0,0},{-1,-1,-1,-1,-1},{-2,-2,-2,-2,-2}}Zdata={{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}} and LabelImage as itk.simple.imageLabelImage={{{0,0,0,0,0},{0,1,1,1,0},{0,1,1,1,0},{0,1,1,1,0},{0,0,0,0,0}} The surface area with label 1 should be 12.Which steps (C# or C++) do I need to take to solve this? Thank you guys From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:27:05 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: community at itk.org; dan.muel at gmail.com; blowekamp at mail.nih.gov Sorry, I have confused LabelShapeStatistics with LabelStatistics filter. With label shape statistics, there is no intensity image, only the label image which you are already using as input. You generally don't mix (add) label and intensity images, you just keep them separate and know which two are a pair. For label statistics, you simply set two inputs like in this example. Regards On Wed, Aug 10, 2016 at 9:19 AM, Matthias B wrote: I understand, but how do I add the label on the 3D image programmatically?preferable in C#, but C++ is also ok. Thank you for your help From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 09:14:35 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org The 3D image where the label will be applied is need for statistics such as mean, min and max values. If you don't care about those, you can supply the same image as both label and original (intensity) image. Or you can supply an empty (all black) image there. HTH,D?enan On Wed, Aug 10, 2016 at 8:47 AM, Matthias B wrote: Thank you for answering D?enan, ok, the perimeter attribute is what I need. Problem is that I don't see a way where I can1. Choose a label image to define the region2. Choose the 3D Image where the label will be aplied At this moment it looks for me that the label image already contains the 3D data, which confuses me. From: dzenanz at gmail.com Date: Wed, 10 Aug 2016 08:32:53 -0400 Subject: Re: [ITK] Determine surface area of certain region in image To: matthias.b at hotmail.com CC: blowekamp at mail.nih.gov; community at itk.org Hi Matthias, perimeter should be surface area in 3D (which you can divide by 2 to eliminate back side if you have a very flat object). In 2D image, it is the circumference. In 2D image, you can get object's surface area by counting how many pixels it has and then multiplying that by the size of each pixel (spacing[0]*spacing[1]). Regards,D?enan On Wed, Aug 10, 2016 at 2:40 AM, Matthias B wrote: Thank you for answering! At this moment I get the perimeter in pixel units (not the surface area of my X,Y-data) of my labeled image.I have also really no idea how to use my 3D data with a labeled image. I see no way how to add 3D data to a LabelMap for example. This is what I have at the moment.Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter()labelShapeStatistics.Execute(labelImage)Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) Thanks for any help, Matthias From: blowekamp at mail.nih.gov To: matthias.b at hotmail.com CC: community at itk.org Subject: Re: [ITK] Determine surface area of certain region in image Date: Tue, 9 Aug 2016 15:58:56 +0000 Hello, You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. HTH, Brad [1] http://hdl.handle.net/1926/584 [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb [4] http://hdl.handle.net/10380/3342 On Aug 9, 2016, at 11:50 AM, Matthias B wrote: Hello ITK-community, At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value. I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80). The surface area should only be calculated with the X,Y-data. In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can calculate the surface area with the function polyarea. Is this possbile with the ITK-library? Thank you for your help guys. Virusvrij. www.avast.com _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community Virusvrij. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Aug 10 13:14:28 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 10 Aug 2016 17:14:28 +0000 Subject: [ITK] [ITK-dev] Midas mirror script Message-ID: <2C043DCE-BEA2-44CC-AAD5-96B75EDF2A16@mail.nih.gov> Hello, I am looking to mirror the SimpleITK directory of the midas3.kitware.com MIDAS server. Are there any scripts around to aid in this? Thanks, Brad -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From dzenanz at gmail.com Wed Aug 10 13:28:58 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 10 Aug 2016 13:28:58 -0400 Subject: [ITK] FW: Determine surface area of certain region in image In-Reply-To: References: <44C41E29-B376-471E-B200-8B9B39E1B61D@mail.nih.gov> Message-ID: OK, now I understand your question (I think). 3DImage contains 3D coordinates of points, laid out in approximate grid pattern when view along z axis. LabelImage contains information which points are part of an object's surface. You want to calculate area of this surface. [image: Inline image 1] Option 1: calculate surface of the cross-hatched area. Option 2: calculate surface of the dotted area (similar to ITK's pixel area definition in Defining origin and spacing ). Option 2 would be easier to do using ITK. Calculate each point's surface coverage by examining how far away it is from the neighbors using 3D coordinates, and then simply sum up all those areas. Area of each point coverage would be a 4 triangles or quadrilaterals formed with 4 neighbors. Option 1 is more like creating a triangular surface patch, and then calculating its surface area. Easiest would be iterating the triangles and summing their surface areas using vector cross product. Alternatively, you could convert it to a data structure of some mesh library like e.g. vtkPolyData, and then use that library's algorithms to calculate the surface area e.g. vtkMassProperties . But to do either I think you should use iterators to access individual pixels, and SimpleITK doesn't have them. Have you considered using regular ITK? On Wed, Aug 10, 2016 at 12:16 PM, Matthias B wrote: > > > ------------------------------ > From: matthias.b at hotmail.com > To: dzenanz at gmail.com > Subject: RE: [ITK] Determine surface area of certain region in image > Date: Wed, 10 Aug 2016 18:15:39 +0200 > > > I'm sorry, I really don't get it D?enan, > > Maybe another approach, I'm working with a 3D camera with a resolution of > 5 by 5. Every pixel contains a X, Y and Z component, let's say in > centimeters. > I put an object int front of the camera right in the center of the image, > the object covers 3x3 pixels.. > > Now I want to have the surface area of this object, I now the object is > located on the image like this {{0,0,0,0,0},{0,1,1,1,0},{0,1,1,1,0}, > {0,1,1,1,0},{0,0,0,0,0}} > > Xdata={{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4}, > {-4,-2,0,2,4}} > Ydata={{3,2.5,2.1,2.5,2.2},{1.4,1.2,1.3,1.1,1.1},{0,0,0,0,0}, > {-3,-2.5,-2.1,-2.5,-2.2},{-1.4,-1.2,-1.3,-1.1,-1.1}} > Zdata={{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}} > > So, is it possible to get the object surface area in real world, so in cm2 > with the ITK library? > > Thank you for your effort > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 11:19:28 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: dan.muel at gmail.com; community at itk.org; blowekamp at mail.nih.gov > > There are nine 1s in the LabelImage, which means that your object with > label 1 is 9 pixels big. Content of the 3DImage is irrelevant. If the > example LabelImage content you provided does not reflect what you want, you > need to come up with a better LabelImage (a different, better > segmentation), derived from 3DImage. > > On Wed, Aug 10, 2016 at 11:11 AM, Matthias B > wrote: > > Thank you for the code > > sp[0] and sp[1] is both 1 in my code. I don't get how I would get 12 in > your example. > The 3DImage is also never used. > > The spacing is also never absolute in my situation. > Ydata could also be like this={{3,2.5,2.1,2.5,2.2},{1.4 > ,1.2,1.3,1.1,1.1},...} > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:58:32 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: dan.muel at gmail.com; community at itk.org; blowekamp at mail.nih.gov > > > 3DImage of size 5x5x3, and LabelImage 5x5. > > Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() > labelShapeStatistics.Execute(labelImage) > Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) > Dim pixelCount = labelShapeStatistics.GetNumberOfPixels(1) //=9 in your > example > Dim sp = labelImage.GetSpacing() > Dim surfaceArea=pixelCount*sp[0]*sp[1] //sp[0]*sp[1] should be =1.25 to > yield a total of 12 which you want > > HTH, > D?enan > > On Wed, Aug 10, 2016 at 9:48 AM, Matthias B > wrote: > > I think an example is the best way to solve my problem. > > Let us take following 3D Data with name 3DImage as itk.simple.image > Xdata={{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4},{-4,-2,0,2,4}, > {-4,-2,0,2,4}} > Ydata={{2,2,2,2,2},{1,1,1,1,1},{0,0,0,0,0},{-1,-1,-1,-1,-1}, > {-2,-2,-2,-2,-2}} > Zdata={{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}} > > and LabelImage as itk.simple.image > LabelImage={{{0,0,0,0,0},{0,1,1,1,0},{0,1,1,1,0},{0,1,1,1,0},{0,0,0,0,0}} > > The surface area with label 1 should be 12. > Which steps (C# or C++) do I need to take to solve this? > > Thank you guys > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:27:05 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: community at itk.org; dan.muel at gmail.com; blowekamp at mail.nih.gov > > > Sorry, I have confused LabelShapeStatistics > > with LabelStatistics > > filter. > > With label shape statistics, there is no intensity image, only the label > image which you are already using as input. > > You generally don't mix (add) label and intensity images, you just keep > them separate and know which two are a pair. For label statistics, you > simply set two inputs like in this example > > . > > Regards > > On Wed, Aug 10, 2016 at 9:19 AM, Matthias B > wrote: > > I understand, but how do I add the label on the 3D image programmatically? > preferable in C#, but C++ is also ok. > > Thank you for your help > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 09:14:35 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org > > > The 3D image where the label will be applied is need for statistics such > as mean, min and max values. If you don't care about those, you can supply > the same image as both label and original (intensity) image. Or you can > supply an empty (all black) image there. > > HTH, > D?enan > > On Wed, Aug 10, 2016 at 8:47 AM, Matthias B > wrote: > > Thank you for answering D?enan, > > ok, the perimeter attribute is what I need. > > Problem is that I don't see a way where I can > 1. Choose a label image to define the region > 2. Choose the 3D Image where the label will be aplied > > At this moment it looks for me that the label image already contains the > 3D data, which confuses me. > > ------------------------------ > From: dzenanz at gmail.com > Date: Wed, 10 Aug 2016 08:32:53 -0400 > Subject: Re: [ITK] Determine surface area of certain region in image > To: matthias.b at hotmail.com > CC: blowekamp at mail.nih.gov; community at itk.org > > > Hi Matthias, > > perimeter should be surface area in 3D (which you can divide by 2 to > eliminate back side if you have a very flat object). In 2D image, it is the > circumference. In 2D image, you can get object's surface area by counting > how many pixels it has and then multiplying that by the size of each pixel > (spacing[0]*spacing[1]). > > Regards, > D?enan > > On Wed, Aug 10, 2016 at 2:40 AM, Matthias B > wrote: > > Thank you for answering! > > At this moment I get the perimeter in pixel units (not the surface area of > my X,Y-data) of my labeled image. > I have also really no idea how to use my 3D data with a labeled image. I > see no way how to add 3D data to a LabelMap for example. > > This is what I have at the moment. > Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter() > labelShapeStatistics.Execute(labelImage) > Dim perimeterValue= labelShapeStatistics.GetPerimeter(1) > > Thanks for any help, Matthias > > > > ------------------------------ > From: blowekamp at mail.nih.gov > To: matthias.b at hotmail.com > CC: community at itk.org > Subject: Re: [ITK] Determine surface area of certain region in image > Date: Tue, 9 Aug 2016 15:58:56 +0000 > > > Hello, > > You should look into the label map framework [1]. In particular the > LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4]. > > HTH, > Brad > > [1] http://hdl.handle.net/1926/584 > [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToSha > peLabelMapFilter.html > [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObjec > t.html#aff1209e925293c15775520ef89e97afb > [4] http://hdl.handle.net/10380/3342 > > On Aug 9, 2016, at 11:50 AM, Matthias B wrote: > > Hello ITK-community, > > At the moment I'm working with 3D Images with following structure: > 100x80x3. Every pixel contains a X,Y,Z value. > I want to calculate the surface area of a certain region that I have > defined with a boolean 2D-Image (100x80). > The surface area should only be calculated with the X,Y-data. > > In Matlab I have experience with this by using the function bwboundaries > on the boolean image. This function determines the indices of the the > boundaries in clockwise direction. Next I take the corresponding X,Y > values of the indices so I can calculate the surface area with the function > polyarea. > > Is this possbile with the ITK-library? > > Thank you for your help guys. > > > > Virusvrij. www.avast.com > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > > > Virusvrij. > www.avast.com > > <#m_4865192857103803213_m_-24046198973060639_m_876262044166110828_m_1512104202195024141_m_4192781686007042514_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: xyObject.png Type: image/png Size: 39697 bytes Desc: not available URL: From dzenanz at gmail.com Thu Aug 11 07:51:52 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 11 Aug 2016 07:51:52 -0400 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Hi Jeanna, since this is a 2D image, you may pay some extra computation to get better results. Try using multi-scale approach, and then filter out smaller vessels. Regards On Wed, Aug 10, 2016 at 9:30 PM, Jeanna S. wrote: > Hi D?enan, > > I actually found that I had to put objectnessFilter-> > SetScaleObjectnessMeasure(false);. I already had objectnessFilter-> > SetBrightObject(false); and objectnessFilter->SetObjectDimension(1);. > Now the output, which I've attached, is much better, though it still shows > some of the blobs. Thanks for all your help. > > Jeanna > > On Wed, Aug 10, 2016 at 4:59 AM, D?enan Zuki? wrote: > >> Hi Jeanna, >> >> by taking a look at the output, you need objectnessFilter->SetBrightObj >> ect(false); and a larger size of objectnessFilter->SetObjectDimension(); >> >> HTH, >> D?enan >> >> On Wed, Aug 10, 2016 at 12:01 AM, Jeanna S. >> wrote: >> >>> Thanks for letting me know. I've changed the output image type to float >>> and now it no longer shows up as just black. I've attached my output image >>> (the image on the left is the input image; the image on the right is the >>> output image). However, the filter seems not to detect blood vessels like I >>> hoped, even after testing various values of Alpha, Beta, and Gamma. I was >>> wondering if anybody has suggestions on how to improve the vessel detection? >>> >>> Thanks, >>> Jeanna >>> >>> On Tue, Aug 9, 2016 at 6:29 AM, D?enan Zuki? wrote: >>> >>>> Hi Jeanna, >>>> >>>> output of this filter is in [0,1] range, and if your output image type >>>> is not float then you will get an all-black image. Here is an example >>>> invocation: >>>> >>>> typedef itk::HessianToObjectnessMeasureImageFilter< >>>> HessianImageType, FloatImageType > ObjectnessFilterType; >>>> ObjectnessFilterType::Pointer objectnessFilter = >>>> ObjectnessFilterType::New(); >>>> objectnessFilter->SetBrightObject(true); >>>> objectnessFilter->SetScaleObjectnessMeasure(false); >>>> objectnessFilter->SetObjectDimension(2.5); >>>> objectnessFilter->SetAlpha(0.5); >>>> objectnessFilter->SetBeta(1.0); >>>> objectnessFilter->SetGamma(5.0); >>>> objectnessFilter->SetInput(hc->GetOutput()); >>>> objectnessFilter->Update(); >>>> FloatImageType::Pointer objectness = objectnessFilter->GetOutput(); >>>> >>>> On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. >>>> wrote: >>>> >>>>> Actually, I found a way to display the images to the screen. However, I >>>>> am still not quite sure how to detect the blood vessels in my image. When I >>>>> apply the itkHessianToObjectnessMeasureImageFilter on my image, it >>>>> just turns out black. I was wondering if this is because there is not >>>>> enough contrast between the vessels and the background. If so, is there any >>>>> setting or threshold on the filter I can change so that it can detect the >>>>> blood vessels? >>>>> >>>>> Thanks, >>>>> Jeanna >>>>> >>>>> On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. >>>>> wrote: >>>>> >>>>>> Hi Timothee, >>>>>> >>>>>> I'm using the itk:HessianToObjectnessMeasureImageFilter that you >>>>>> suggested. I was wondering if there is any way for me to view the image on >>>>>> the screen after it has been run through the filter, and if you have any >>>>>> examples of the filter working on an image. >>>>>> >>>>>> Thanks, >>>>>> Jeanna >>>>>> >>>>>> On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. >>>>>> wrote: >>>>>> >>>>>>> Hi Timothee, >>>>>>> >>>>>>> Thank you for replying. I will look into these methods. >>>>>>> >>>>>>> Jeanna >>>>>>> >>>>>>> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < >>>>>>> tevain at telecom-paristech.fr> wrote: >>>>>>> >>>>>>>> Hello Jeanna, >>>>>>>> >>>>>>>> I think this will be difficult just with the LabelMap framework. >>>>>>>> Usually to filter vessels you rely on some measures based on their >>>>>>>> shape, but in the ShapeLabelObject, the elongation measure is "the ratio of >>>>>>>> the longest physical size of the region [i.e. the bounding box] on one >>>>>>>> dimension and its smallest physical size". This is a quite coarse measure, >>>>>>>> sensitive to rotation, and I doubt it will be useful in your case. >>>>>>>> Aside from the attribute problem, you also have to detect the >>>>>>>> vessels prior to filtering them (i.e. getting a binary or a label image of >>>>>>>> vessels), and the LabelMap framework doesn't do that. >>>>>>>> >>>>>>>> I would suggest taking a look at these other methods: >>>>>>>> -Frangi's vesselness (implemented in itk through these filter : >>>>>>>> itkHessianToObjectnessMeasureImageFilter or >>>>>>>> itkHessian3DToVesselnessMeasureImageFilter) >>>>>>>> -Ranking Orientation Responses of Path Openings, aka RORPO ( >>>>>>>> http://path-openings.github.io/RORPO/) >>>>>>>> -Fast Marching (itkFastMarchingImageFilter) >>>>>>>> >>>>>>>> HTH, >>>>>>>> >>>>>>>> Tim >>>>>>>> >>>>>>>> ----- Mail original ----- >>>>>>>> De: "Jeanna S." >>>>>>>> ?: community at itk.org >>>>>>>> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >>>>>>>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >>>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> I am trying to process the attached image using the >>>>>>>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >>>>>>>> retina, and I want to use the image filter to remove the blood vessels from >>>>>>>> the picture (the blood vessels are the long, skinny, branching lines). I >>>>>>>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >>>>>>>> ) would be able to do this with a little modification, and if so, which >>>>>>>> attribute would be the most useful to identify and remove the blood vessels. >>>>>>>> >>>>>>>> Thanks in advance. >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Community mailing list >>>>>>>> Community at itk.org >>>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> when the rich wage war, it's the poor who die >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> when the rich wage war, it's the poor who die >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> when the rich wage war, it's the poor who die >>>>> >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>>>> >>>> >>> >>> >>> -- >>> when the rich wage war, it's the poor who die >>> >> >> > > > -- > when the rich wage war, it's the poor who die > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Fri Aug 12 10:36:26 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Fri, 12 Aug 2016 14:36:26 +0000 Subject: [ITK] define different regions on a mesh Message-ID: Hello, I have a list of indices of vertices and their corresponding labels. I have a corresponding itk mesh. I'd like to get some pointers for the different regions (a different one for each label) I'd like these regions to reference the faces (cells) and vertices (pointset) Would you have any idea how to do this ? Thanks, Fran?ois. From dzenanz at gmail.com Fri Aug 12 14:23:42 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 12 Aug 2016 14:23:42 -0400 Subject: [ITK] define different regions on a mesh In-Reply-To: References: Message-ID: Hi Francois, what do you mean by pointer? Pointer to an itk::MeshCell? Or MeshRegion ? I have not used itk::Mesh and associated classes a lot, so I doubt I will be able to help you. But I might be able to tell you that something is not possible. And clarifying your question will might enable others to help you. Regards, D?enan On Fri, Aug 12, 2016 at 10:36 AM, wrote: > Hello, > > I have a list of indices of vertices and their corresponding labels. > I have a corresponding itk mesh. > > I'd like to get some pointers for the different regions (a different one > for each label) > I'd like these regions to reference the faces (cells) and vertices > (pointset) > > Would you have any idea how to do this ? > > Thanks, > Fran?ois. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From taylor at braun-jones.org Mon Aug 15 18:21:37 2016 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 15 Aug 2016 18:21:37 -0400 Subject: [ITK] [ITK-dev] Unable to login to review.source.kitware.com Message-ID: Hi all, I'm trying to login to Kitware's Gerrit instance in order to submit an ITK patch and getting the following message after I approve access to my GitHub account information: [image: Inline image 1] Any ideas? The GitHub account I'm using is nocnokneo with primary email address taylor at braun-jones.org Thanks in advance, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 10932 bytes Desc: not available URL: -------------- next part -------------- _______________________________________________ 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://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-developers From taylor at braun-jones.org Mon Aug 15 18:32:00 2016 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 15 Aug 2016 18:32:00 -0400 Subject: [ITK] [ITK-dev] Unable to login to review.source.kitware.com In-Reply-To: References: Message-ID: On Mon, Aug 15, 2016 at 6:21 PM, Taylor Braun-Jones wrote: > > I'm trying to login to Kitware's Gerrit instance in order to submit an ITK patch and getting the following message after I approve access to my GitHub account information: > > Any ideas? The GitHub account I'm using is nocnokneo with primary email address taylor at braun-jones.org I just noticed the note on the ITK wiki about OAuth access: > OAuth currently requests R/W access to GitHub repositories. However, none of the repositories will be modified. My Github account is a member of a private Github organization with private repos. Could this be the source of the problem? _______________________________________________ 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://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-developers From zj19872008 at sina.com Mon Aug 15 23:15:59 2016 From: zj19872008 at sina.com (zj19872008 at sina.com) Date: Tue, 16 Aug 2016 11:15:59 +0800 Subject: [ITK] image fusion with itk Message-ID: <20160816031559.271D8C600B9@webmail.sinamail.sina.com.cn> Hi All, Is there a class in ITK for image fusion ? I want to fuse CT and MRI images, I want to overlay them and create a vector image. Thanking in advance, Regards, zj -------------- next part -------------- An HTML attachment was scrubbed... URL: From Francois.GIRINON at ensam.eu Tue Aug 16 02:54:09 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Tue, 16 Aug 2016 06:54:09 +0000 Subject: [ITK] define different regions on a mesh Message-ID: Hi Dzenan, You 're right it wasn't that clear. This is exactly what I want to do : ItkMesh myMesh (the value of the points of the myMesh are regularly updated) For each myMeshRegions regionsCells = myMesh - > myMeshRegions[iRegion] - >GetCellsValue() regionsPoints = myMesh - > myMeshRegions[iRegion] - >GetPointsValue() Thank you, Fran?ois. Le 12 ao?t 2016 8:24 PM, D?enan Zuki? a ?crit : Hi Francois, what do you mean by pointer? Pointer to an itk::MeshCell? Or MeshRegion? I have not used itk::Mesh and associated classes a lot, so I doubt I will be able to help you. But I might be able to tell you that something is not possible. And clarifying your question will might enable others to help you. Regards, D?enan On Fri, Aug 12, 2016 at 10:36 AM, > wrote: Hello, I have a list of indices of vertices and their corresponding labels. I have a corresponding itk mesh. I'd like to get some pointers for the different regions (a different one for each label) I'd like these regions to reference the faces (cells) and vertices (pointset) Would you have any idea how to do this ? Thanks, Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From matimontg at gmail.com Tue Aug 16 09:42:36 2016 From: matimontg at gmail.com (Matias Montroull) Date: Tue, 16 Aug 2016 13:42:36 +0000 Subject: [ITK] image fusion with itk In-Reply-To: <20160816031559.271D8C600B9@webmail.sinamail.sina.com.cn> References: <20160816031559.271D8C600B9@webmail.sinamail.sina.com.cn> Message-ID: You mean Registration? El mar., 16 de ago. de 2016 a la(s) 00:37, escribi?: > Hi All, > > Is there a class in ITK for image fusion ? > I want to fuse CT and MRI images, I want to overlay them and > create a vector image. > Thanking in advance, > > Regards, > > zj > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Matias -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Aug 16 10:18:02 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 16 Aug 2016 10:18:02 -0400 Subject: [ITK] define different regions on a mesh In-Reply-To: References: Message-ID: Hi Francois, by looking at the source code of MeshRegion , it seems to be just a stub class. As regular ITK mesh is meant to represent a closed object and not a surface patch, I would suggest to not use ITK to represent your mesh, but rather some other library which has a more extensive set of classes for dealing with polygonal meshes such as VTK . Regards, D?enan On Tue, Aug 16, 2016 at 2:54 AM, wrote: > Hi Dzenan, > > You 're right it wasn't that clear. > > This is exactly what I want to do : > ItkMesh myMesh > (the value of the points of the myMesh are regularly updated) > > For each myMeshRegions > regionsCells = myMesh - > myMeshRegions[iRegion] - >GetCellsValue() > regionsPoints = myMesh - > myMeshRegions[iRegion] - >GetPointsValue() > > Thank you, > Fran?ois. > Le 12 ao?t 2016 8:24 PM, D?enan Zuki? a ?crit : > > Hi Francois, > > what do you mean by pointer? Pointer to an itk::MeshCell? Or MeshRegion > ? > > I have not used itk::Mesh and associated classes a lot, so I doubt I will > be able to help you. But I might be able to tell you that something is not > possible. And clarifying your question will might enable others to help you. > > Regards, > D?enan > > On Fri, Aug 12, 2016 at 10:36 AM, wrote: > > Hello, > > I have a list of indices of vertices and their corresponding labels. > I have a corresponding itk mesh. > > I'd like to get some pointers for the different regions (a different one > for each label) > I'd like these regions to reference the faces (cells) and vertices > (pointset) > > Would you have any idea how to do this ? > > Thanks, > Fran?ois. > > _______________________________________________ > 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 Tue Aug 16 10:23:24 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 16 Aug 2016 10:23:24 -0400 Subject: [ITK] [ITK-dev] Unable to login to review.source.kitware.com In-Reply-To: References: Message-ID: Hi Taylor, did the issue go away by now? Regards, D?enan On Mon, Aug 15, 2016 at 6:32 PM, Taylor Braun-Jones wrote: > On Mon, Aug 15, 2016 at 6:21 PM, Taylor Braun-Jones > wrote: > > > > I'm trying to login to Kitware's Gerrit instance in order to submit an > ITK patch and getting the following message after I approve access to my > GitHub account information: > > > > Any ideas? The GitHub account I'm using is nocnokneo with primary email > address taylor at braun-jones.org > > I just noticed the note on the ITK wiki about OAuth access: > > > OAuth currently requests R/W access to GitHub repositories. However, > none of the repositories will be modified. > > My Github account is a member of a private Github organization with > private repos. Could this be the source of the problem? > _______________________________________________ > 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://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-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From dzenanz at gmail.com Tue Aug 16 10:25:01 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 16 Aug 2016 10:25:01 -0400 Subject: [ITK] image fusion with itk In-Reply-To: References: <20160816031559.271D8C600B9@webmail.sinamail.sina.com.cn> Message-ID: Hi ZJ, there is such a filter, it is called itk::ComposeImageFilter . Regards, D?enan On Tue, Aug 16, 2016 at 9:42 AM, Matias Montroull wrote: > You mean Registration? > > El mar., 16 de ago. de 2016 a la(s) 00:37, escribi?: > >> Hi All, >> >> Is there a class in ITK for image fusion ? I want to fuse CT and MRI images, >> I want to overlay them and create a vector image. >> Thanking in advance, >> >> Regards, >> >> zj >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > -- > Matias > > _______________________________________________ > 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 Aug 16 11:00:37 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Aug 2016 11:00:37 -0400 Subject: [ITK] [ITK-dev] Unable to login to review.source.kitware.com In-Reply-To: References: Message-ID: Hi Taylor, The error comes up for folks with an older account where a sign in did not occur during the transition from OpenID to GitHub OAuth. The administrators will reset your old account, and you will be good to go. Thanks, Matt On Mon, Aug 15, 2016 at 6:21 PM, Taylor Braun-Jones wrote: > Hi all, > > I'm trying to login to Kitware's Gerrit instance in order to submit an ITK > patch and getting the following message after I approve access to my GitHub > account information: > > [image: Inline image 1] > > Any ideas? The GitHub account I'm using is nocnokneo with primary email > address taylor at braun-jones.org > > Thanks in advance, > Taylor > > _______________________________________________ > 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://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-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 10932 bytes Desc: not available URL: -------------- next part -------------- _______________________________________________ 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://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-developers From taylor at braun-jones.org Tue Aug 16 11:15:12 2016 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Tue, 16 Aug 2016 11:15:12 -0400 Subject: [ITK] [ITK-dev] Unable to login to review.source.kitware.com In-Reply-To: References: Message-ID: On Tue, Aug 16, 2016 at 11:00 AM, Matt McCormick wrote: > The error comes up for folks with an older account where a sign in did not > occur during the transition from OpenID to GitHub OAuth. > > The administrators will reset your old account, and you will be good to go. > Great, thank you. I'll wait for that account reset to go through. Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From zj19872008 at sina.com Tue Aug 16 22:01:49 2016 From: zj19872008 at sina.com (zj19872008 at sina.com) Date: Wed, 17 Aug 2016 10:01:49 +0800 Subject: [ITK] =?gbk?b?u9i4tKO6UmU6ICBpbWFnZSBmdXNpb24gd2l0aCBpdGs=?= Message-ID: <20160817020149.0D2BF2A0A07@webmail.sinamail.sina.com.cn> I want to fuse the two images into one after Registration. Thanks.----- ???? ----- ????Matias Montroull ????zj19872008 at sina.com, community ???Re: [ITK] image fusion with itk ???2016?08?16? 21?42? You mean Registration? El mar., 16 de ago. de 2016 a la(s) 00:37, escribi?: Hi All, Is there a class in ITK for image fusion ? I want to fuse CT and MRI images, I want to overlay them and create a vector image. Thanking in advance, Regards, zj_______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -- Matias -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 17 07:16:47 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 17 Aug 2016 07:16:47 -0400 Subject: [ITK] =?utf-8?b?5Zue5aSN77yaUmU6IGltYWdlIGZ1c2lvbiB3aXRoIGl0aw==?= In-Reply-To: <20160817020149.0D2BF2A0A07@webmail.sinamail.sina.com.cn> References: <20160817020149.0D2BF2A0A07@webmail.sinamail.sina.com.cn> Message-ID: Then you need to resample one of the images onto the image grid of the other before applying compose filter. Regards, D?enan On Tue, Aug 16, 2016 at 10:01 PM, wrote: > I want to fuse the two images into one after Registration. > > Thanks. > ----- ???? ----- > ????Matias Montroull > ????zj19872008 at sina.com, community > ???Re: [ITK] image fusion with itk > ???2016?08?16? 21?42? > > You mean Registration? > > El mar., 16 de ago. de 2016 a la(s) 00:37, escribi?: > > Hi All, > > Is there a class in ITK for image fusion ? I want to fuse CT and MRI images, > I want to overlay them and create a vector image. > Thanking in advance, > > Regards, > > zj > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -- > Matias > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.giord at gmail.com Wed Aug 17 10:26:20 2016 From: marco.giord at gmail.com (marco giordano) Date: Wed, 17 Aug 2016 16:26:20 +0200 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild Message-ID: Hi there, I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this: -- Fetching " http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 " -- [download 100% complete] -- Fetching " https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 " -- Fetching " https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") Call Stack (most recent call first): /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object) make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1 make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 Any help is welcome. Regards -- Marco -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 Wed Aug 17 10:48:59 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Aug 2016 10:48:59 -0400 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hi Marco, Your CMake needs HTTPS support. The binaries from cmake.org have this enabled or set CMAKE_USE_OPENSSL in CMake's build configuration. HTH, Matt On Wed, Aug 17, 2016 at 10:26 AM, marco giordano wrote: > Hi there, > > I just downloaded SimpleTK and I tried to build it on a linux cluster > (running Scientific Linux release 6.5- Carbon) using the superbuild. > > I use cmake 3.3.1. The Generation of build files is fine, then when I try to > build i get this: > > -- Fetching > "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- [download 100% complete] > -- Fetching > "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- Fetching > "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" > CMake Error at > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 > (message): > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > ("Unsupported protocol") > > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 > ("Unsupported protocol") > Call Stack (most recent call first): > > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 > (_ExternalData_download_object) > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error > 1 > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > Any help is welcome. > Regards > -- > Marco > > _____________________________________ > 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 blowekamp at mail.nih.gov Wed Aug 17 10:51:52 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 17 Aug 2016 14:51:52 +0000 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hello! OK, so it looks like you are using the current master branch of SimpleITK. I know this because you have the latest SimpleITK feature where CMake downloads the Superbuild dependencies with the CMake ?ExternalData? module. This enables some interesting options for your situation. You are on a cluster. On compute clusters, frequently the nodes don?t have access to the internet. So when cmake tries to download the URLS below it times out or errors. You can verify this with some command like ?wget https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. The alternative is that your version of CMake doesn?t support HTTPS. Yo can test this with the following script: https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake Frequently, there are nodes on a cluster which have access to the internet for situations like this. You may be able to just use one of them. With the new ExternalData download module you may be able to pre-download these dependencies on the log in node. If you set the environment variable ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache downloads to this directory. I assume your home directory is available on the log in nodes. You can configure the SuperBuild there and build just the ?SuperBuildSimpleITKSource? target. This will download the dependencies to the ExternaData directory. Then you can build in a cluster node, which should use this cache. Also note when testing is enabled for the actual SimpleITK sub-project, a bunch of testing data is downloaded too. You can disable testing to avoid this, download and un-tar a Data archive [1], or replace the above procedure for this subproject. HTH, Brad [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Source/ > On Aug 17, 2016, at 10:26 AM, marco giordano wrote: > > Hi there, > > I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. > > I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this: > > -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- [download 100% complete] > -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- Fetching "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" > CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") > Call Stack (most recent call first): > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object) > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1 > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > Any help is welcome. > Regards > -- > Marco > _____________________________________ > 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 aharr8 at uwo.ca Wed Aug 17 14:52:08 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Wed, 17 Aug 2016 14:52:08 -0400 Subject: [ITK] [ITK-users] CorrelationImageToImageMetricv4 returns with very low correlation values Message-ID: Hello, I am attempting to register two 3D images using the CorrelationImageToImageMetricv4, the LBFGSBOptimizer, and a 3DVersorRigidRegistration. Even if I put the same volumes in to the registration for both the fixed and moving image, I get a very low value for correlation. One thought I had was I might be setting the origins incorrectly, as previously in the project the origin was defined as the centre of the image cubes and I have attempted to stay with that convention, and I haven?t found an example in the ITK examples where the origin is set to something other than 0. The other issue might be that the original data is a char array so I had to create a cast filter to change the image to floats, and the origins might be getting confused between the two. If anyone has any thoughts they would be welcome, I can provide source code if that would be helpful. -- 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: -------------- next part -------------- _____________________________________ 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 blowekamp at mail.nih.gov Wed Aug 17 15:08:52 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 17 Aug 2016 19:08:52 +0000 Subject: [ITK] [ITK-users] CorrelationImageToImageMetricv4 returns with very low correlation values In-Reply-To: References: Message-ID: <1269FEDC-93AE-4349-A5EB-E4021AFAB399@mail.nih.gov> Hello, You seem to need a way to interactively explore your program, images and registration setup. All ITK registration metrics are designed to be minimized. So the correlations are negative if I recall correctly. You may want to look into Slicer3D (https://www.slicer.org) for a image visualizer which is aware of ITK?s image geometry. You also may want to look into using an interactive programing environment such as Python to better understand the image geometry and the properties of what you are trying to setup. You may find the SimpleITK Notebooks on Image Registration useful: http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/ HTH, Brad On Aug 17, 2016, at 2:52 PM, Andrew Harris > wrote: Hello, I am attempting to register two 3D images using the CorrelationImageToImageMetricv4, the LBFGSBOptimizer, and a 3DVersorRigidRegistration. Even if I put the same volumes in to the registration for both the fixed and moving image, I get a very low value for correlation. One thought I had was I might be setting the origins incorrectly, as previously in the project the origin was defined as the centre of the image cubes and I have attempted to stay with that convention, and I haven?t found an example in the ITK examples where the origin is set to something other than 0. The other issue might be that the original data is a char array so I had to create a cast filter to change the image to floats, and the origins might be getting confused between the two. If anyone has any thoughts they would be welcome, I can provide source code if that would be helpful. -- 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: -------------- next part -------------- _____________________________________ 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 c.spanakis83 at gmail.com Thu Aug 18 05:19:40 2016 From: c.spanakis83 at gmail.com (Constantinus Spanakis) Date: Thu, 18 Aug 2016 12:19:40 +0300 Subject: [ITK] Best similarity measure for deformable image registration Message-ID: Hello. I am working on deformable image registration and I am puzzled by the variety of the similarity measures that ITK has and I don't know which to use. Any susggestions? -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.zaffino at yahoo.it Thu Aug 18 05:33:03 2016 From: p.zaffino at yahoo.it (Paolo Zaffino) Date: Thu, 18 Aug 2016 11:33:03 +0200 Subject: [ITK] Best similarity measure for deformable image registration In-Reply-To: References: Message-ID: Hi, monomodal or multimodal registration? Paolo On 18/08/2016 11:19, Constantinus Spanakis wrote: > Hello. I am working on deformable image registration and I am puzzled > by the variety of the similarity measures that ITK has and I don't > know which to use. Any susggestions? > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.giord at gmail.com Thu Aug 18 05:37:57 2016 From: marco.giord at gmail.com (marco giordano) Date: Thu, 18 Aug 2016 11:37:57 +0200 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hi there, I checked the internet connection on the node and seems fine (I can download with wget the https://midas3.kitware.com/ midas/api/rest?method=midas.bitstream.download&checksum= 2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?). I run the script SSLTest.cmake but it fails (it downloads a LICENSE file but it is empty): CMake Error at SSLTest.cmake:5 (file): file DOWNLOAD HASH mismatch for file: [/home/mgiordano/code/SimpleITK/LICENSE] expected hash: [f8c925402b90f74566f71e64eea7bb9d83daac69cde71408ffd6c043be6a4991] actual hash: [e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855] status: [1;"Unsupported protocol"] So I assume the HTTPS is not supported. Now if I understand correctly the alternative is to download the modules manually in $HOME/ExternalData and point to that folder through the variable ExternalData_OBJECT_STORES. The question is what do I need to download, is that the only the two links above or there is more ? Is it maybe an option to change version of Cmake that can support that or/and how do I enable the support ? Any help is appreciated. Regards, Marco 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov>: > Hello! > > OK, so it looks like you are using the current master branch of SimpleITK. > I know this because you have the latest SimpleITK feature where CMake > downloads the Superbuild dependencies with the CMake ?ExternalData? module. > This enables some interesting options for your situation. > > You are on a cluster. On compute clusters, frequently the nodes don?t have > access to the internet. So when cmake tries to download the URLS below it > times out or errors. You can verify this with some command like ?wget > https://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. > The alternative is that your version of CMake doesn?t support HTTPS. Yo can > test this with the following script: https://github.com/conda- > forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake > > Frequently, there are nodes on a cluster which have access to the internet > for situations like this. You may be able to just use one of them. > > With the new ExternalData download module you may be able to pre-download > these dependencies on the log in node. If you set the environment variable > ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache > downloads to this directory. I assume your home directory is available on > the log in nodes. You can configure the SuperBuild there and build just the > ?SuperBuildSimpleITKSource? target. This will download the dependencies to > the ExternaData directory. Then you can build in a cluster node, which > should use this cache. > > Also note when testing is enabled for the actual SimpleITK sub-project, a > bunch of testing data is downloaded too. You can disable testing to avoid > this, download and un-tar a Data archive [1], or replace the above > procedure for this subproject. > > HTH, > Brad > > [1] https://sourceforge.net/projects/simpleitk/files/ > SimpleITK/0.10.0/Source/ > > > > On Aug 17, 2016, at 10:26 AM, marco giordano > wrote: > > > > Hi there, > > > > I just downloaded SimpleTK and I tried to build it on a linux cluster > (running Scientific Linux release 6.5- Carbon) using the superbuild. > > > > I use cmake 3.3.1. The Generation of build files is fine, then when I > try to build i get this: > > > > -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > " > > -- [download 100% complete] > > -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > " > > -- Fetching "https://itk.org/files/ExternalData/MD5/ > 2e115fe26e435e33b0d5c022e4490567" > > CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/ > Modules/ExternalData.cmake:1012 (message): > > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > > > http://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > ("Unsupported protocol") > > https://midas3.kitware.com/midas/api/rest?method=midas. > bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 > ("Unsupported protocol") > > https://itk.org/files/ExternalData/MD5/ > 2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") > > Call Stack (most recent call first): > > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/ > Modules/ExternalData.cmake:1034 (_ExternalData_download_object) > > > > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] > Error 1 > > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > > > Any help is welcome. > > Regards > > -- > > Marco > > _____________________________________ > > 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 > > -- Marco Giordano SKYPE:marcogiord81 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 richard.beare at gmail.com Thu Aug 18 06:14:43 2016 From: richard.beare at gmail.com (Richard Beare) Date: Thu, 18 Aug 2016 20:14:43 +1000 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: A related problem, which I've never found a solution for, is that some cluster software (probably the curl library) is built without ssl support at a critical point. You may have the same issue. Maybe the configuration info for curl will tell you one way or another whether this is the case and you can request a reinstall. On Thu, Aug 18, 2016 at 7:37 PM, marco giordano wrote: > Hi there, > I checked the internet connection on the node and seems fine (I can > download with wget the https://midas3.kitware.com/mid > as/api/rest?method=midas.bitstream.download&checksum=2e115fe > 26e435e33b0d5c022e4490567&algorithm=MD5?). > > I run the script SSLTest.cmake > > but it fails (it downloads a LICENSE file but it is empty): > CMake Error at SSLTest.cmake:5 (file): > file DOWNLOAD HASH mismatch > > for file: [/home/mgiordano/code/SimpleITK/LICENSE] > expected hash: [f8c925402b90f74566f71e64eea7bb > 9d83daac69cde71408ffd6c043be6a4991] > actual hash: [e3b0c44298fc1c149afbf4c8996fb9 > 2427ae41e4649b934ca495991b7852b855] > status: [1;"Unsupported protocol"] > > So I assume the HTTPS is not supported. Now if I understand correctly the > alternative is to download the modules manually in $HOME/ExternalData and > point to that folder through the variable ExternalData_OBJECT_STORES. The > question is what do I need to download, is that the only the two links > above or there is more ? Is it maybe an option to change version of Cmake > that can support that or/and how do I enable the support ? > > Any help is appreciated. > Regards, > Marco > > 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < > blowekamp at mail.nih.gov>: > >> Hello! >> >> OK, so it looks like you are using the current master branch of >> SimpleITK. I know this because you have the latest SimpleITK feature where >> CMake downloads the Superbuild dependencies with the CMake ?ExternalData? >> module. This enables some interesting options for your situation. >> >> You are on a cluster. On compute clusters, frequently the nodes don?t >> have access to the internet. So when cmake tries to download the URLS below >> it times out or errors. You can verify this with some command like ?wget >> https://midas3.kitware.com/midas/api/rest?method=midas.bitst >> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. >> The alternative is that your version of CMake doesn?t support HTTPS. Yo can >> test this with the following script: https://github.com/conda-forge >> /cmake-feedstock/blob/master/recipe/SSLTest.cmake >> >> Frequently, there are nodes on a cluster which have access to the >> internet for situations like this. You may be able to just use one of them. >> >> With the new ExternalData download module you may be able to pre-download >> these dependencies on the log in node. If you set the environment variable >> ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache >> downloads to this directory. I assume your home directory is available on >> the log in nodes. You can configure the SuperBuild there and build just the >> ?SuperBuildSimpleITKSource? target. This will download the dependencies to >> the ExternaData directory. Then you can build in a cluster node, which >> should use this cache. >> >> Also note when testing is enabled for the actual SimpleITK sub-project, a >> bunch of testing data is downloaded too. You can disable testing to avoid >> this, download and un-tar a Data archive [1], or replace the above >> procedure for this subproject. >> >> HTH, >> Brad >> >> [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/ >> 0.10.0/Source/ >> >> >> > On Aug 17, 2016, at 10:26 AM, marco giordano >> wrote: >> > >> > Hi there, >> > >> > I just downloaded SimpleTK and I tried to build it on a linux cluster >> (running Scientific Linux release 6.5- Carbon) using the superbuild. >> > >> > I use cmake 3.3.1. The Generation of build files is fine, then when I >> try to build i get this: >> > >> > -- Fetching "http://midas3.kitware.com/mid >> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >> 26e435e33b0d5c022e4490567&algorithm=MD5" >> > -- [download 100% complete] >> > -- Fetching "https://midas3.kitware.com/mi >> das/api/rest?method=midas.bitstream.download&checksum=2e115f >> e26e435e33b0d5c022e4490567&algorithm=MD5" >> > -- Fetching "https://itk.org/files/Externa >> lData/MD5/2e115fe26e435e33b0d5c022e4490567" >> > CMake Error at /cm/shared/apps/cmake/3.3.1/in >> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): >> > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: >> > >> > http://midas3.kitware.com/midas/api/rest?method=midas.bitst >> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >> ("Unsupported protocol") >> > https://midas3.kitware.com/midas/api/rest?method=midas.bits >> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >> ("Unsupported protocol") >> > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5 >> c022e4490567 ("Unsupported protocol") >> > Call Stack (most recent call first): >> > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 >> (_ExternalData_download_object) >> > >> > >> > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] >> Error 1 >> > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 >> > >> > Any help is welcome. >> > Regards >> > -- >> > Marco >> > _____________________________________ >> > 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 >> >> > > > -- > Marco Giordano > SKYPE:marcogiord81 > > _____________________________________ > 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 -------------- _____________________________________ 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 insight-users at itk.org Thu Aug 18 07:09:21 2016 From: insight-users at itk.org (Paolo Zaffino via Insight-users) Date: Thu, 18 Aug 2016 13:09:21 +0200 Subject: [ITK] [ITK-users] Best similarity measure for deformable image registration In-Reply-To: References: Message-ID: <04164068-d766-bc76-d3f9-c8a595e3ab9d@yahoo.it> In this case I would suggest mutual information (there are different "versions"). I would also try different settings for the numbers of bins and for the sampling percentage. HTH. Paolo On 18/08/2016 12:18, Constantinus Spanakis wrote: > Helo Paolo. Sorry for omitting details. It's about 3D multimodal > registration > > On Thu, Aug 18, 2016 at 12:33 PM, Paolo Zaffino > wrote: > > Hi, > monomodal or multimodal registration? > > Paolo > > > On 18/08/2016 11:19, Constantinus Spanakis wrote: >> Hello. I am working on deformable image registration and I am >> puzzled by the variety of the similarity measures that ITK has >> and I don't know which to use. Any susggestions? >> >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 dzenanz at gmail.com Thu Aug 18 08:53:48 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 18 Aug 2016 08:53:48 -0400 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hi Marco, as Matt said, you can build CMake from source and while configuring it turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead of the system one. Regards, D?enan On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare wrote: > A related problem, which I've never found a solution for, is that some > cluster software (probably the curl library) is built without ssl support > at a critical point. You may have the same issue. Maybe the configuration > info for curl will tell you one way or another whether this is the case and > you can request a reinstall. > > On Thu, Aug 18, 2016 at 7:37 PM, marco giordano > wrote: > >> Hi there, >> I checked the internet connection on the node and seems fine (I can >> download with wget the https://midas3.kitware.com/mid >> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >> 26e435e33b0d5c022e4490567&algorithm=MD5?). >> >> I run the script SSLTest.cmake >> >> but it fails (it downloads a LICENSE file but it is empty): >> CMake Error at SSLTest.cmake:5 (file): >> file DOWNLOAD HASH mismatch >> >> for file: [/home/mgiordano/code/SimpleITK/LICENSE] >> expected hash: [f8c925402b90f74566f71e64eea7b >> b9d83daac69cde71408ffd6c043be6a4991] >> actual hash: [e3b0c44298fc1c149afbf4c8996fb >> 92427ae41e4649b934ca495991b7852b855] >> status: [1;"Unsupported protocol"] >> >> So I assume the HTTPS is not supported. Now if I understand correctly the >> alternative is to download the modules manually in $HOME/ExternalData and >> point to that folder through the variable ExternalData_OBJECT_STORES. The >> question is what do I need to download, is that the only the two links >> above or there is more ? Is it maybe an option to change version of Cmake >> that can support that or/and how do I enable the support ? >> >> Any help is appreciated. >> Regards, >> Marco >> >> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < >> blowekamp at mail.nih.gov>: >> >>> Hello! >>> >>> OK, so it looks like you are using the current master branch of >>> SimpleITK. I know this because you have the latest SimpleITK feature where >>> CMake downloads the Superbuild dependencies with the CMake ?ExternalData? >>> module. This enables some interesting options for your situation. >>> >>> You are on a cluster. On compute clusters, frequently the nodes don?t >>> have access to the internet. So when cmake tries to download the URLS below >>> it times out or errors. You can verify this with some command like ?wget >>> https://midas3.kitware.com/midas/api/rest?method=midas.bitst >>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. >>> The alternative is that your version of CMake doesn?t support HTTPS. Yo can >>> test this with the following script: https://github.com/conda-forge >>> /cmake-feedstock/blob/master/recipe/SSLTest.cmake >>> >>> Frequently, there are nodes on a cluster which have access to the >>> internet for situations like this. You may be able to just use one of them. >>> >>> With the new ExternalData download module you may be able to >>> pre-download these dependencies on the log in node. If you set the >>> environment variable ExternalData_OBJECT_STORES to say >>> ?${HOME}/.ExternalData?, it will cache downloads to this directory. I >>> assume your home directory is available on the log in nodes. You can >>> configure the SuperBuild there and build just the >>> ?SuperBuildSimpleITKSource? target. This will download the dependencies to >>> the ExternaData directory. Then you can build in a cluster node, which >>> should use this cache. >>> >>> Also note when testing is enabled for the actual SimpleITK sub-project, >>> a bunch of testing data is downloaded too. You can disable testing to avoid >>> this, download and un-tar a Data archive [1], or replace the above >>> procedure for this subproject. >>> >>> HTH, >>> Brad >>> >>> [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0 >>> .10.0/Source/ >>> >>> >>> > On Aug 17, 2016, at 10:26 AM, marco giordano >>> wrote: >>> > >>> > Hi there, >>> > >>> > I just downloaded SimpleTK and I tried to build it on a linux cluster >>> (running Scientific Linux release 6.5- Carbon) using the superbuild. >>> > >>> > I use cmake 3.3.1. The Generation of build files is fine, then when I >>> try to build i get this: >>> > >>> > -- Fetching "http://midas3.kitware.com/mid >>> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >>> 26e435e33b0d5c022e4490567&algorithm=MD5" >>> > -- [download 100% complete] >>> > -- Fetching "https://midas3.kitware.com/mi >>> das/api/rest?method=midas.bitstream.download&checksum=2e115f >>> e26e435e33b0d5c022e4490567&algorithm=MD5" >>> > -- Fetching "https://itk.org/files/Externa >>> lData/MD5/2e115fe26e435e33b0d5c022e4490567" >>> > CMake Error at /cm/shared/apps/cmake/3.3.1/in >>> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): >>> > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: >>> > >>> > http://midas3.kitware.com/midas/api/rest?method=midas.bitst >>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >>> ("Unsupported protocol") >>> > https://midas3.kitware.com/midas/api/rest?method=midas.bits >>> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >>> ("Unsupported protocol") >>> > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5 >>> c022e4490567 ("Unsupported protocol") >>> > Call Stack (most recent call first): >>> > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 >>> (_ExternalData_download_object) >>> > >>> > >>> > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] >>> Error 1 >>> > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error >>> 2 >>> > >>> > Any help is welcome. >>> > Regards >>> > -- >>> > Marco >>> > _____________________________________ >>> > 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 >>> >>> >> >> >> -- >> Marco Giordano >> SKYPE:marcogiord81 >> >> _____________________________________ >> 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: -------------- next part -------------- _____________________________________ 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 blowekamp at mail.nih.gov Thu Aug 18 09:28:41 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 18 Aug 2016 13:28:41 +0000 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: And for the lazier there are now CMake binaries for Linux i386 and x86_64. https://cmake.org/download/ On Aug 18, 2016, at 8:53 AM, D?enan Zuki? wrote: Hi Marco, as Matt said, you can build CMake from source and while configuring it turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead of the system one. Regards, D?enan On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare > wrote: A related problem, which I've never found a solution for, is that some cluster software (probably the curl library) is built without ssl support at a critical point. You may have the same issue. Maybe the configuration info for curl will tell you one way or another whether this is the case and you can request a reinstall. On Thu, Aug 18, 2016 at 7:37 PM, marco giordano > wrote: Hi there, I checked the internet connection on the node and seems fine (I can download with wget the https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?). I run the script SSLTest.cmake but it fails (it downloads a LICENSE file but it is empty): CMake Error at SSLTest.cmake:5 (file): file DOWNLOAD HASH mismatch for file: [/home/mgiordano/code/SimpleITK/LICENSE] expected hash: [f8c925402b90f74566f71e64eea7bb9d83daac69cde71408ffd6c043be6a4991] actual hash: [e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855] status: [1;"Unsupported protocol"] So I assume the HTTPS is not supported. Now if I understand correctly the alternative is to download the modules manually in $HOME/ExternalData and point to that folder through the variable ExternalData_OBJECT_STORES. The question is what do I need to download, is that the only the two links above or there is more ? Is it maybe an option to change version of Cmake that can support that or/and how do I enable the support ? Any help is appreciated. Regards, Marco 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] >: Hello! OK, so it looks like you are using the current master branch of SimpleITK. I know this because you have the latest SimpleITK feature where CMake downloads the Superbuild dependencies with the CMake ?ExternalData? module. This enables some interesting options for your situation. You are on a cluster. On compute clusters, frequently the nodes don?t have access to the internet. So when cmake tries to download the URLS below it times out or errors. You can verify this with some command like ?wget https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. The alternative is that your version of CMake doesn?t support HTTPS. Yo can test this with the following script: https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake Frequently, there are nodes on a cluster which have access to the internet for situations like this. You may be able to just use one of them. With the new ExternalData download module you may be able to pre-download these dependencies on the log in node. If you set the environment variable ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache downloads to this directory. I assume your home directory is available on the log in nodes. You can configure the SuperBuild there and build just the ?SuperBuildSimpleITKSource? target. This will download the dependencies to the ExternaData directory. Then you can build in a cluster node, which should use this cache. Also note when testing is enabled for the actual SimpleITK sub-project, a bunch of testing data is downloaded too. You can disable testing to avoid this, download and un-tar a Data archive [1], or replace the above procedure for this subproject. HTH, Brad [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Source/ > On Aug 17, 2016, at 10:26 AM, marco giordano > wrote: > > Hi there, > > I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. > > I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this: > > -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- [download 100% complete] > -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- Fetching "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" > CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") > Call Stack (most recent call first): > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object) > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1 > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > Any help is welcome. > Regards > -- > Marco > _____________________________________ > 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 -- Marco Giordano SKYPE:marcogiord81 _____________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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.giord at gmail.com Thu Aug 18 12:04:47 2016 From: marco.giord at gmail.com (marco giordano) Date: Thu, 18 Aug 2016 18:04:47 +0200 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Thanks a lot for the help, I downloaded the Cmake binary and now it seems it is able to download, however the build process gets stuck at cloning ITK: -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua [ 18%] Completed 'Lua' [ 18%] Built target Lua [ 20%] Creating directories for 'ITK' [ 21%] Performing download step (git clone) for 'ITK' Cloning into 'ITK'... Install the project... -- Install configuration: "Release" -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua [ 18%] Completed 'Lua' [ 18%] Built target Lua [ 20%] Creating directories for 'ITK' [ 21%] Performing download step (git clone) for 'ITK' Cloning into 'ITK'... Maybe a wrong link somewhere ? Regards 2016-08-18 15:28 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov>: > And for the lazier there are now CMake binaries for Linux i386 and x86_64. > > https://cmake.org/download/ > > > On Aug 18, 2016, at 8:53 AM, D?enan Zuki? wrote: > > Hi Marco, > > as Matt said, you can build CMake from source and while configuring it > turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead > of the system one. > > Regards, > D?enan > > On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare > wrote: > >> A related problem, which I've never found a solution for, is that some >> cluster software (probably the curl library) is built without ssl support >> at a critical point. You may have the same issue. Maybe the configuration >> info for curl will tell you one way or another whether this is the case and >> you can request a reinstall. >> >> On Thu, Aug 18, 2016 at 7:37 PM, marco giordano >> wrote: >> >>> Hi there, >>> I checked the internet connection on the node and seems fine (I can >>> download with wget the https://midas3.kitware.com/midas/api/rest?method= >>> midas.bitstream.download&checksum=2e115fe26e435e33b0d5c >>> 022e4490567&algorithm=MD5?). >>> >>> I run the script SSLTest.cmake >>> >>> but it fails (it downloads a LICENSE file but it is empty): >>> CMake Error at SSLTest.cmake:5 (file): >>> file DOWNLOAD HASH mismatch >>> >>> for file: [/home/mgiordano/code/SimpleITK/LICENSE] >>> expected hash: [f8c925402b90f74566f71e64eea7b >>> b9d83daac69cde71408ffd6c043be6a4991] >>> actual hash: [e3b0c44298fc1c149afbf4c8996fb >>> 92427ae41e4649b934ca495991b7852b855] >>> status: [1;"Unsupported protocol"] >>> >>> So I assume the HTTPS is not supported. Now if I understand correctly >>> the alternative is to download the modules manually in $HOME/ExternalData >>> and point to that folder through the variable ExternalData_OBJECT_STORES. >>> The question is what do I need to download, is that the only the two links >>> above or there is more ? Is it maybe an option to change version of Cmake >>> that can support that or/and how do I enable the support ? >>> >>> Any help is appreciated. >>> Regards, >>> Marco >>> >>> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < >>> blowekamp at mail.nih.gov>: >>> >>>> Hello! >>>> >>>> OK, so it looks like you are using the current master branch of >>>> SimpleITK. I know this because you have the latest SimpleITK feature where >>>> CMake downloads the Superbuild dependencies with the CMake ?ExternalData? >>>> module. This enables some interesting options for your situation. >>>> >>>> You are on a cluster. On compute clusters, frequently the nodes don?t >>>> have access to the internet. So when cmake tries to download the URLS below >>>> it times out or errors. You can verify this with some command like ?wget >>>> https://midas3.kitware.com/midas/api/rest?method= >>>> midas.bitstream.download&checksum=2e115fe26e435e33b0d5c >>>> 022e4490567&algorithm=MD5?. The alternative is that your version of >>>> CMake doesn?t support HTTPS. Yo can test this with the following script: >>>> https://github.com/conda-forge/cmake-feedstock/ >>>> blob/master/recipe/SSLTest.cmake >>>> >>>> Frequently, there are nodes on a cluster which have access to the >>>> internet for situations like this. You may be able to just use one of them. >>>> >>>> With the new ExternalData download module you may be able to >>>> pre-download these dependencies on the log in node. If you set the >>>> environment variable ExternalData_OBJECT_STORES to say >>>> ?${HOME}/.ExternalData?, it will cache downloads to this directory. I >>>> assume your home directory is available on the log in nodes. You can >>>> configure the SuperBuild there and build just the >>>> ?SuperBuildSimpleITKSource? target. This will download the dependencies to >>>> the ExternaData directory. Then you can build in a cluster node, which >>>> should use this cache. >>>> >>>> Also note when testing is enabled for the actual SimpleITK sub-project, >>>> a bunch of testing data is downloaded too. You can disable testing to avoid >>>> this, download and un-tar a Data archive [1], or replace the above >>>> procedure for this subproject. >>>> >>>> HTH, >>>> Brad >>>> >>>> [1] https://sourceforge.net/projects/simpleitk/files/ >>>> SimpleITK/0.10.0/Source/ >>>> >>>> >>>> > On Aug 17, 2016, at 10:26 AM, marco giordano >>>> wrote: >>>> > >>>> > Hi there, >>>> > >>>> > I just downloaded SimpleTK and I tried to build it on a linux cluster >>>> (running Scientific Linux release 6.5- Carbon) using the superbuild. >>>> > >>>> > I use cmake 3.3.1. The Generation of build files is fine, then when I >>>> try to build i get this: >>>> > >>>> > -- Fetching "http://midas3.kitware.com/mid >>>> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >>>> 26e435e33b0d5c022e4490567&algorithm=MD5" >>>> > -- [download 100% complete] >>>> > -- Fetching "https://midas3.kitware.com/mi >>>> das/api/rest?method=midas.bitstream.download&checksum=2e115f >>>> e26e435e33b0d5c022e4490567&algorithm=MD5" >>>> > -- Fetching "https://itk.org/files/Externa >>>> lData/MD5/2e115fe26e435e33b0d5c022e4490567" >>>> > CMake Error at /cm/shared/apps/cmake/3.3.1/in >>>> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): >>>> > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: >>>> > >>>> > http://midas3.kitware.com/midas/api/rest?method=midas.bitst >>>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported >>>> protocol") >>>> > https://midas3.kitware.com/midas/api/rest?method=midas.bits >>>> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported >>>> protocol") >>>> > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5 >>>> c022e4490567 ("Unsupported protocol") >>>> > Call Stack (most recent call first): >>>> > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 >>>> (_ExternalData_download_object) >>>> > >>>> > >>>> > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] >>>> Error 1 >>>> > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] >>>> Error 2 >>>> > >>>> > Any help is welcome. >>>> > Regards >>>> > -- >>>> > Marco >>>> > _____________________________________ >>>> > 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 >>>> >>>> >>> >>> >>> -- >>> Marco Giordano >>> SKYPE:marcogiord81 >>> >>> _____________________________________ >>> 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 > > > > _____________________________________ > 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 > > -- Marco Giordano SKYPE:marcogiord81 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 blowekamp at mail.nih.gov Thu Aug 18 12:13:56 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 18 Aug 2016 16:13:56 +0000 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Hi! The lack of error message is not helpful to assist with debugging. You must try to reproduce the problem on the node then. Try running ?git clone https://itk.org/ITK.git? and see if it produces more output. The probable problems are there is network restrictions on your cluster node, or that your git version is too old and does not support the https protocol. You could try changing the CMake variable SITK_GIT_PROTOCOL from ?https? to ?git? [1]. Currently there is not ?ExternalData? cache work around for this. HTH, Brad [1] https://github.com/SimpleITK/SimpleITK/blob/master/SuperBuild/External_ITK.cmake#L36 On Aug 18, 2016, at 12:04 PM, marco giordano > wrote: Thanks a lot for the help, I downloaded the Cmake binary and now it seems it is able to download, however the build process gets stuck at cloning ITK: -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua [ 18%] Completed 'Lua' [ 18%] Built target Lua [ 20%] Creating directories for 'ITK' [ 21%] Performing download step (git clone) for 'ITK' Cloning into 'ITK'... Install the project... -- Install configuration: "Release" -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua [ 18%] Completed 'Lua' [ 18%] Built target Lua [ 20%] Creating directories for 'ITK' [ 21%] Performing download step (git clone) for 'ITK' Cloning into 'ITK'... Maybe a wrong link somewhere ? Regards 2016-08-18 15:28 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] >: And for the lazier there are now CMake binaries for Linux i386 and x86_64. https://cmake.org/download/ On Aug 18, 2016, at 8:53 AM, D?enan Zuki? > wrote: Hi Marco, as Matt said, you can build CMake from source and while configuring it turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead of the system one. Regards, D?enan On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare > wrote: A related problem, which I've never found a solution for, is that some cluster software (probably the curl library) is built without ssl support at a critical point. You may have the same issue. Maybe the configuration info for curl will tell you one way or another whether this is the case and you can request a reinstall. On Thu, Aug 18, 2016 at 7:37 PM, marco giordano > wrote: Hi there, I checked the internet connection on the node and seems fine (I can download with wget the https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?). I run the script SSLTest.cmake but it fails (it downloads a LICENSE file but it is empty): CMake Error at SSLTest.cmake:5 (file): file DOWNLOAD HASH mismatch for file: [/home/mgiordano/code/SimpleITK/LICENSE] expected hash: [f8c925402b90f74566f71e64eea7bb9d83daac69cde71408ffd6c043be6a4991] actual hash: [e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855] status: [1;"Unsupported protocol"] So I assume the HTTPS is not supported. Now if I understand correctly the alternative is to download the modules manually in $HOME/ExternalData and point to that folder through the variable ExternalData_OBJECT_STORES. The question is what do I need to download, is that the only the two links above or there is more ? Is it maybe an option to change version of Cmake that can support that or/and how do I enable the support ? Any help is appreciated. Regards, Marco 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] >: Hello! OK, so it looks like you are using the current master branch of SimpleITK. I know this because you have the latest SimpleITK feature where CMake downloads the Superbuild dependencies with the CMake ?ExternalData? module. This enables some interesting options for your situation. You are on a cluster. On compute clusters, frequently the nodes don?t have access to the internet. So when cmake tries to download the URLS below it times out or errors. You can verify this with some command like ?wget https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?. The alternative is that your version of CMake doesn?t support HTTPS. Yo can test this with the following script: https://github.com/conda-forge/cmake-feedstock/blob/master/recipe/SSLTest.cmake Frequently, there are nodes on a cluster which have access to the internet for situations like this. You may be able to just use one of them. With the new ExternalData download module you may be able to pre-download these dependencies on the log in node. If you set the environment variable ExternalData_OBJECT_STORES to say ?${HOME}/.ExternalData?, it will cache downloads to this directory. I assume your home directory is available on the log in nodes. You can configure the SuperBuild there and build just the ?SuperBuildSimpleITKSource? target. This will download the dependencies to the ExternaData directory. Then you can build in a cluster node, which should use this cache. Also note when testing is enabled for the actual SimpleITK sub-project, a bunch of testing data is downloaded too. You can disable testing to avoid this, download and un-tar a Data archive [1], or replace the above procedure for this subproject. HTH, Brad [1] https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/Source/ > On Aug 17, 2016, at 10:26 AM, marco giordano > wrote: > > Hi there, > > I just downloaded SimpleTK and I tried to build it on a linux cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. > > I use cmake 3.3.1. The Generation of build files is fine, then when I try to build i get this: > > -- Fetching "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- [download 100% complete] > -- Fetching "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5" > -- Fetching "https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567" > CMake Error at /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: > > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5c022e4490567 ("Unsupported protocol") > Call Stack (most recent call first): > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 (_ExternalData_download_object) > > > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] Error 1 > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] Error 2 > > Any help is welcome. > Regards > -- > Marco > _____________________________________ > 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 -- Marco Giordano SKYPE:marcogiord81 _____________________________________ 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 _____________________________________ 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 -- Marco Giordano SKYPE:marcogiord81 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 xzhao21 at lsu.edu Thu Aug 18 15:08:18 2016 From: xzhao21 at lsu.edu (Xiaodong Zhao) Date: Thu, 18 Aug 2016 19:08:18 +0000 Subject: [ITK] (beginner question) How to get transform matrix then apply it to another volume Message-ID: Hi, I used 2 MR volumes as inputs for ImageRegistration20.cxx, and got them aligned with each other. Now I have another CT volume. My questions is how do I get the transformation matrix from the affine transform in ImageRegistration20.cxx then apply it on the CT volume? Thanks in advance! Neo From dzenanz at gmail.com Fri Aug 19 08:51:32 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 19 Aug 2016 08:51:32 -0400 Subject: [ITK] (beginner question) How to get transform matrix then apply it to another volume In-Reply-To: References: Message-ID: Hi Neo, you need to apply resampling filter . You can look at examples linked in the documentation. Regards, D?enan On Thu, Aug 18, 2016 at 3:08 PM, Xiaodong Zhao wrote: > Hi, > > I used 2 MR volumes as inputs for ImageRegistration20.cxx, and got them > aligned with each other. Now I have another CT volume. My questions is how > do I get the transformation matrix from the affine transform in > ImageRegistration20.cxx then apply it on the CT volume? > > Thanks in advance! > Neo > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at insightsoftwareconsortium.org Fri Aug 19 09:51:30 2016 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Fri, 19 Aug 2016 09:51:30 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Cubic and Hermite splines for VTK Message-ID: <20160819135131.04CFE3D6208D@insight-journal.org> Hello, A new submission has been added to the MIDAS Journal. Title: Cubic and Hermite splines for VTK Authors: Kovacs N., Peters T., Chen E. Abstract: A cubic spline is a spline where each curve is defined by a third-order polynomial, while a Hermite spline has each polynomial specified in Hermite form, being computed using tangent information as well as the position of the points. We propose two new classes for VTK, vtkCubicSpline and vtkHermiteSpline, which compute interpolating splines using a Cubic and a Hermite Spline Interpolation function, respectively. We also propose two new auxiliary classes, vtkParametricCubicSpline and vtkParametricHermiteSpline, that create parametric functions for the 1D interpolating aforementioned splines. Download and review this publication at: http://hdl.handle.net/10380/3561 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/ . _____________________________________ 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 dzenanz at gmail.com Sat Aug 20 08:11:46 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sat, 20 Aug 2016 08:11:46 -0400 Subject: [ITK] (beginner question) How to get transform matrix then apply it to another volume In-Reply-To: <4B2A0549-3D6C-4E92-9BB9-AE81FFD7A181@lsu.edu> References: <4B2A0549-3D6C-4E92-9BB9-AE81FFD7A181@lsu.edu> Message-ID: Hi Neo, it sounds like you did not change the OutputPixelType from unsigned char to short, which is required to represent the entire range of CT numbers (-1000 to +3000). Regards, D?enan On Sat, Aug 20, 2016 at 12:37 AM, Xiaodong Zhao wrote: > Hi Dzenan, > > Thanks for your reply! > > I tried to edit the example ImageRegistration20.cxx a bit. Basically I > just input the the fixed MR, the moving MR, and the CT that?s > pre-registered with the moving MR, and after the affine transformation is > done b/w the 2 MR volumes, I just applied the same transformation matrix to > the CT, or at least that?s what i was trying to do(i just copied the > resampling part and changed some variables)... The MR looks good, but I got > all these streaking artifacts from the CT, and the CT numbers seems to be > rescaled to from 0 to around 250, which happens to be about the same range > of the difference image(the min and max of the IntensityRescaler in line > 451). I attached a screenshot of one CT slice, and the code(excuse my > POOOOOR programming skills!). Did I use a wrong resampling filter or?? > > Thanks again, > Neo > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeannasheen at gmail.com Sat Aug 20 17:06:45 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Sat, 20 Aug 2016 14:06:45 -0700 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Hi D?enan, Thanks for the suggestion. The multiscale filter gives much better results, I have attached the output to this email. I was wondering if there were any other settings I could change besides the sigma maximum and minimum which would be able to remove the last of the blobs. Right now my sigma maximum is 2. Thanks, Jeanna On Thu, Aug 11, 2016 at 4:51 AM, D?enan Zuki? wrote: > Hi Jeanna, > > since this is a 2D image, you may pay some extra computation to get better > results. Try using multi-scale > > approach, and then filter out smaller vessels. > > Regards > > On Wed, Aug 10, 2016 at 9:30 PM, Jeanna S. wrote: > >> Hi D?enan, >> >> I actually found that I had to put objectnessFilter->SetScaleObje >> ctnessMeasure(false);. I already had objectnessFilter->SetBrightObject(false); >> and objectnessFilter->SetObjectDimension(1);. Now the output, which >> I've attached, is much better, though it still shows some of the blobs. >> Thanks for all your help. >> >> Jeanna >> >> On Wed, Aug 10, 2016 at 4:59 AM, D?enan Zuki? wrote: >> >>> Hi Jeanna, >>> >>> by taking a look at the output, you need objectnessFilter->SetBrightObj >>> ect(false); and a larger size of objectnessFilter->SetObjectDimension(); >>> >>> HTH, >>> D?enan >>> >>> On Wed, Aug 10, 2016 at 12:01 AM, Jeanna S. >>> wrote: >>> >>>> Thanks for letting me know. I've changed the output image type to float >>>> and now it no longer shows up as just black. I've attached my output image >>>> (the image on the left is the input image; the image on the right is the >>>> output image). However, the filter seems not to detect blood vessels like I >>>> hoped, even after testing various values of Alpha, Beta, and Gamma. I was >>>> wondering if anybody has suggestions on how to improve the vessel detection? >>>> >>>> Thanks, >>>> Jeanna >>>> >>>> On Tue, Aug 9, 2016 at 6:29 AM, D?enan Zuki? wrote: >>>> >>>>> Hi Jeanna, >>>>> >>>>> output of this filter is in [0,1] range, and if your output image type >>>>> is not float then you will get an all-black image. Here is an example >>>>> invocation: >>>>> >>>>> typedef itk::HessianToObjectnessMeasureImageFilter< >>>>> HessianImageType, FloatImageType > ObjectnessFilterType; >>>>> ObjectnessFilterType::Pointer objectnessFilter = >>>>> ObjectnessFilterType::New(); >>>>> objectnessFilter->SetBrightObject(true); >>>>> objectnessFilter->SetScaleObjectnessMeasure(false); >>>>> objectnessFilter->SetObjectDimension(2.5); >>>>> objectnessFilter->SetAlpha(0.5); >>>>> objectnessFilter->SetBeta(1.0); >>>>> objectnessFilter->SetGamma(5.0); >>>>> objectnessFilter->SetInput(hc->GetOutput()); >>>>> objectnessFilter->Update(); >>>>> FloatImageType::Pointer objectness = objectnessFilter->GetOutput(); >>>>> >>>>> On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. >>>>> wrote: >>>>> >>>>>> Actually, I found a way to display the images to the screen. However, I >>>>>> am still not quite sure how to detect the blood vessels in my image. When I >>>>>> apply the itkHessianToObjectnessMeasureImageFilter on my image, it >>>>>> just turns out black. I was wondering if this is because there is not >>>>>> enough contrast between the vessels and the background. If so, is there any >>>>>> setting or threshold on the filter I can change so that it can detect the >>>>>> blood vessels? >>>>>> >>>>>> Thanks, >>>>>> Jeanna >>>>>> >>>>>> On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. >>>>>> wrote: >>>>>> >>>>>>> Hi Timothee, >>>>>>> >>>>>>> I'm using the itk:HessianToObjectnessMeasureImageFilter that you >>>>>>> suggested. I was wondering if there is any way for me to view the image on >>>>>>> the screen after it has been run through the filter, and if you have any >>>>>>> examples of the filter working on an image. >>>>>>> >>>>>>> Thanks, >>>>>>> Jeanna >>>>>>> >>>>>>> On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Timothee, >>>>>>>> >>>>>>>> Thank you for replying. I will look into these methods. >>>>>>>> >>>>>>>> Jeanna >>>>>>>> >>>>>>>> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < >>>>>>>> tevain at telecom-paristech.fr> wrote: >>>>>>>> >>>>>>>>> Hello Jeanna, >>>>>>>>> >>>>>>>>> I think this will be difficult just with the LabelMap framework. >>>>>>>>> Usually to filter vessels you rely on some measures based on their >>>>>>>>> shape, but in the ShapeLabelObject, the elongation measure is "the ratio of >>>>>>>>> the longest physical size of the region [i.e. the bounding box] on one >>>>>>>>> dimension and its smallest physical size". This is a quite coarse measure, >>>>>>>>> sensitive to rotation, and I doubt it will be useful in your case. >>>>>>>>> Aside from the attribute problem, you also have to detect the >>>>>>>>> vessels prior to filtering them (i.e. getting a binary or a label image of >>>>>>>>> vessels), and the LabelMap framework doesn't do that. >>>>>>>>> >>>>>>>>> I would suggest taking a look at these other methods: >>>>>>>>> -Frangi's vesselness (implemented in itk through these filter : >>>>>>>>> itkHessianToObjectnessMeasureImageFilter or >>>>>>>>> itkHessian3DToVesselnessMeasureImageFilter) >>>>>>>>> -Ranking Orientation Responses of Path Openings, aka RORPO ( >>>>>>>>> http://path-openings.github.io/RORPO/) >>>>>>>>> -Fast Marching (itkFastMarchingImageFilter) >>>>>>>>> >>>>>>>>> HTH, >>>>>>>>> >>>>>>>>> Tim >>>>>>>>> >>>>>>>>> ----- Mail original ----- >>>>>>>>> De: "Jeanna S." >>>>>>>>> ?: community at itk.org >>>>>>>>> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >>>>>>>>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >>>>>>>>> >>>>>>>>> Hello, >>>>>>>>> >>>>>>>>> I am trying to process the attached image using the >>>>>>>>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >>>>>>>>> retina, and I want to use the image filter to remove the blood vessels from >>>>>>>>> the picture (the blood vessels are the long, skinny, branching lines). I >>>>>>>>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >>>>>>>>> ) would be able to do this with a little modification, and if so, which >>>>>>>>> attribute would be the most useful to identify and remove the blood vessels. >>>>>>>>> >>>>>>>>> Thanks in advance. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Community mailing list >>>>>>>>> Community at itk.org >>>>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> when the rich wage war, it's the poor who die >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> when the rich wage war, it's the poor who die >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> when the rich wage war, it's the poor who die >>>>>> >>>>>> _______________________________________________ >>>>>> Community mailing list >>>>>> Community at itk.org >>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> when the rich wage war, it's the poor who die >>>> >>> >>> >> >> >> -- >> when the rich wage war, it's the poor who die >> > > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: multiscale.jpg Type: image/jpeg Size: 173680 bytes Desc: not available URL: From dzenanz at gmail.com Sat Aug 20 17:41:34 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sat, 20 Aug 2016 17:41:34 -0400 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Hi Jeanna, you can do a few things. The easiest would be to record chromaticity for each pixel when converting to grayscale, and then filter out the yellowish pixels with high intensity after objectness filter. You can also do a non-standard conversion from RGB to grayscale, which emphasizes the red blood vessels already there. The easiest kind would be to just extract the red channel instead of the standard RGB->gray conversion. Another approach, which reduces de-empahasizes pixels which are far from red is possible. Probably the hardest, but complimentary to the above two approaches is detecting the yellow spot, and starting from there trace the blood vessels (something similar to Canny filter which is also implemented in ITK). You can use the criterion that the vessels will only get thinner. Somewhat similar is to try the objectness filter with settings for detecting blobs - and subtract those from your vessel-enhancing filter output. Regards, D?enan On Sat, Aug 20, 2016 at 5:06 PM, Jeanna S. wrote: > Hi D?enan, > > Thanks for the suggestion. The multiscale filter gives much better > results, I have attached the output to this email. I was wondering if there > were any other settings I could change besides the sigma maximum and > minimum which would be able to remove the last of the blobs. Right now my > sigma maximum is 2. > > Thanks, > Jeanna > > On Thu, Aug 11, 2016 at 4:51 AM, D?enan Zuki? wrote: > >> Hi Jeanna, >> >> since this is a 2D image, you may pay some extra computation to get >> better results. Try using multi-scale >> >> approach, and then filter out smaller vessels. >> >> Regards >> >> On Wed, Aug 10, 2016 at 9:30 PM, Jeanna S. wrote: >> >>> Hi D?enan, >>> >>> I actually found that I had to put objectnessFilter->SetScaleObje >>> ctnessMeasure(false);. I already had objectnessFilter->SetBrightObject(false); >>> and objectnessFilter->SetObjectDimension(1);. Now the output, which >>> I've attached, is much better, though it still shows some of the blobs. >>> Thanks for all your help. >>> >>> Jeanna >>> >>> On Wed, Aug 10, 2016 at 4:59 AM, D?enan Zuki? wrote: >>> >>>> Hi Jeanna, >>>> >>>> by taking a look at the output, you need objectnessFilter->SetBrightObj >>>> ect(false); and a larger size of objectnessFilter->SetObjectDim >>>> ension(); >>>> >>>> HTH, >>>> D?enan >>>> >>>> On Wed, Aug 10, 2016 at 12:01 AM, Jeanna S. >>>> wrote: >>>> >>>>> Thanks for letting me know. I've changed the output image type to >>>>> float and now it no longer shows up as just black. I've attached my output >>>>> image (the image on the left is the input image; the image on the right is >>>>> the output image). However, the filter seems not to detect blood vessels >>>>> like I hoped, even after testing various values of Alpha, Beta, and Gamma. >>>>> I was wondering if anybody has suggestions on how to improve the vessel >>>>> detection? >>>>> >>>>> Thanks, >>>>> Jeanna >>>>> >>>>> On Tue, Aug 9, 2016 at 6:29 AM, D?enan Zuki? >>>>> wrote: >>>>> >>>>>> Hi Jeanna, >>>>>> >>>>>> output of this filter is in [0,1] range, and if your output image >>>>>> type is not float then you will get an all-black image. Here is an example >>>>>> invocation: >>>>>> >>>>>> typedef itk::HessianToObjectnessMeasureImageFilter< >>>>>> HessianImageType, FloatImageType > ObjectnessFilterType; >>>>>> ObjectnessFilterType::Pointer objectnessFilter = >>>>>> ObjectnessFilterType::New(); >>>>>> objectnessFilter->SetBrightObject(true); >>>>>> objectnessFilter->SetScaleObjectnessMeasure(false); >>>>>> objectnessFilter->SetObjectDimension(2.5); >>>>>> objectnessFilter->SetAlpha(0.5); >>>>>> objectnessFilter->SetBeta(1.0); >>>>>> objectnessFilter->SetGamma(5.0); >>>>>> objectnessFilter->SetInput(hc->GetOutput()); >>>>>> objectnessFilter->Update(); >>>>>> FloatImageType::Pointer objectness = >>>>>> objectnessFilter->GetOutput(); >>>>>> >>>>>> On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. >>>>>> wrote: >>>>>> >>>>>>> Actually, I found a way to display the images to the screen. >>>>>>> However, I am still not quite sure how to detect the blood vessels >>>>>>> in my image. When I apply the itkHessianToObjectnessMeasureImageFilter >>>>>>> on my image, it just turns out black. I was wondering if this is because >>>>>>> there is not enough contrast between the vessels and the background. If so, >>>>>>> is there any setting or threshold on the filter I can change so that it can >>>>>>> detect the blood vessels? >>>>>>> >>>>>>> Thanks, >>>>>>> Jeanna >>>>>>> >>>>>>> On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Timothee, >>>>>>>> >>>>>>>> I'm using the itk:HessianToObjectnessMeasureImageFilter that you >>>>>>>> suggested. I was wondering if there is any way for me to view the image on >>>>>>>> the screen after it has been run through the filter, and if you have any >>>>>>>> examples of the filter working on an image. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Jeanna >>>>>>>> >>>>>>>> On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Timothee, >>>>>>>>> >>>>>>>>> Thank you for replying. I will look into these methods. >>>>>>>>> >>>>>>>>> Jeanna >>>>>>>>> >>>>>>>>> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < >>>>>>>>> tevain at telecom-paristech.fr> wrote: >>>>>>>>> >>>>>>>>>> Hello Jeanna, >>>>>>>>>> >>>>>>>>>> I think this will be difficult just with the LabelMap framework. >>>>>>>>>> Usually to filter vessels you rely on some measures based on >>>>>>>>>> their shape, but in the ShapeLabelObject, the elongation measure is "the >>>>>>>>>> ratio of the longest physical size of the region [i.e. the bounding box] on >>>>>>>>>> one dimension and its smallest physical size". This is a quite coarse >>>>>>>>>> measure, sensitive to rotation, and I doubt it will be useful in your case. >>>>>>>>>> Aside from the attribute problem, you also have to detect the >>>>>>>>>> vessels prior to filtering them (i.e. getting a binary or a label image of >>>>>>>>>> vessels), and the LabelMap framework doesn't do that. >>>>>>>>>> >>>>>>>>>> I would suggest taking a look at these other methods: >>>>>>>>>> -Frangi's vesselness (implemented in itk through these filter : >>>>>>>>>> itkHessianToObjectnessMeasureImageFilter or >>>>>>>>>> itkHessian3DToVesselnessMeasureImageFilter) >>>>>>>>>> -Ranking Orientation Responses of Path Openings, aka RORPO ( >>>>>>>>>> http://path-openings.github.io/RORPO/) >>>>>>>>>> -Fast Marching (itkFastMarchingImageFilter) >>>>>>>>>> >>>>>>>>>> HTH, >>>>>>>>>> >>>>>>>>>> Tim >>>>>>>>>> >>>>>>>>>> ----- Mail original ----- >>>>>>>>>> De: "Jeanna S." >>>>>>>>>> ?: community at itk.org >>>>>>>>>> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >>>>>>>>>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >>>>>>>>>> >>>>>>>>>> Hello, >>>>>>>>>> >>>>>>>>>> I am trying to process the attached image using the >>>>>>>>>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >>>>>>>>>> retina, and I want to use the image filter to remove the blood vessels from >>>>>>>>>> the picture (the blood vessels are the long, skinny, branching lines). I >>>>>>>>>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >>>>>>>>>> ) would be able to do this with a little modification, and if so, which >>>>>>>>>> attribute would be the most useful to identify and remove the blood vessels. >>>>>>>>>> >>>>>>>>>> Thanks in advance. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Community mailing list >>>>>>>>>> Community at itk.org >>>>>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> when the rich wage war, it's the poor who die >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> when the rich wage war, it's the poor who die >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> when the rich wage war, it's the poor who die >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Community mailing list >>>>>>> Community at itk.org >>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> when the rich wage war, it's the poor who die >>>>> >>>> >>>> >>> >>> >>> -- >>> when the rich wage war, it's the poor who die >>> >> >> > > > -- > when the rich wage war, it's the poor who die > -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at insightsoftwareconsortium.org Mon Aug 22 03:11:36 2016 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Mon, 22 Aug 2016 03:11:36 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: ND morphological contour interpolation Message-ID: <20160822071136.020FE3D620D3@insight-journal.org> Hello, A new submission has been added to the Insight Journal. Title: ND morphological contour interpolation Authors: Zuki?? D., Vicory J., McCormick M., Wisse L., Gerig G., Yushkevich P., Aylward S. Abstract: This document describes a new class, itk::MorphologicalContourInterpolator, which implements a method proposed by Albu et al. in 2008. Interpolation is done by first determining correspondence between shapes on adjacent segmented slices by detecting overlaps, then aligning the corresponding shapes, generating transition sequence of one-pixel dilations and taking the median as result. Recursion is employed if the original segmented slices are separated by more than one empty slice. This class is n-dimensional, and supports inputs of 3 or more dimensions. `Slices' are n-1-dimensional, and can be both automatically detected and manually set. The class is efficient in both memory used and execution time. It requires little memory in addition to allocation of input and output images. The implementation is multi-threaded, and processing one of the test inputs takes around 1-2 seconds on a quad-core processor. The class is tested to operate on both itk::Image and itk::RLEImage. Since all the processing is done on extracted slices, usage of itk::RLEImage for input and/or output affects performance to a limited degree. This class is implemented to ease manual segmentation in ITK-SNAP (www.itksnap.org). The class, along with test data and automated regression tests is packaged as an ITK remote module https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation. Download and review this publication at: http://hdl.handle.net/10380/3563 Generated by the Insight Journal You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://www.insight-journal.org/ . -------------- next part -------------- _____________________________________ 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.giord at gmail.com Mon Aug 22 04:53:04 2016 From: marco.giord at gmail.com (marco giordano) Date: Mon, 22 Aug 2016 10:53:04 +0200 Subject: [ITK] [ITK-users] Error when Building SimpleITK with SuperBuild In-Reply-To: References: Message-ID: Finally I managed to build SimpleITK on the cluster node. Despite the suggestions I could not manage to clone ITK through the build process (still not sure why, maybe the git version 1.7.7.3?) but I could clone it separately and then set the ITK_REPOSITORY variable to the repository and it worked. Thanks a lot. regards 2016-08-18 18:13 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov>: > Hi! > > The lack of error message is not helpful to assist with debugging. You > must try to reproduce the problem on the node then. > > Try running ?git clone https://itk.org/ITK.git? and see if it produces > more output. > > The probable problems are there is network restrictions on your cluster > node, or that your git version is too old and does not support the https > protocol. > > You could try changing the CMake variable SITK_GIT_PROTOCOL from ?https? > to ?git? [1]. Currently there is not ?ExternalData? cache work around for > this. > > HTH, > Brad > > [1] https://github.com/SimpleITK/SimpleITK/blob/master/ > SuperBuild/External_ITK.cmake#L36 > > On Aug 18, 2016, at 12:04 PM, marco giordano > wrote: > > Thanks a lot for the help, > I downloaded the Cmake binary and now it seems it is able to download, > however the build process gets stuck at cloning ITK: > > -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua > [ 18%] Completed 'Lua' > [ 18%] Built target Lua > [ 20%] Creating directories for 'ITK' > [ 21%] Performing download step (git clone) for 'ITK' > Cloning into 'ITK'... > Install the project... > -- Install configuration: "Release" > -- Installing: /home/mgiordano/code/SimpleITK-build/Lua/bin/lua > [ 18%] Completed 'Lua' > [ 18%] Built target Lua > [ 20%] Creating directories for 'ITK' > [ 21%] Performing download step (git clone) for 'ITK' > Cloning into 'ITK'... > > Maybe a wrong link somewhere ? > Regards > > 2016-08-18 15:28 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < > blowekamp at mail.nih.gov>: > >> And for the lazier there are now CMake binaries for Linux i386 and >> x86_64. >> >> https://cmake.org/download/ >> >> >> On Aug 18, 2016, at 8:53 AM, D?enan Zuki? wrote: >> >> Hi Marco, >> >> as Matt said, you can build CMake from source and while configuring it >> turn CMAKE_USE_OPENSSL on. Then use it or you can even drop it in instead >> of the system one. >> >> Regards, >> D?enan >> >> On Thu, Aug 18, 2016 at 6:14 AM, Richard Beare >> wrote: >> >>> A related problem, which I've never found a solution for, is that some >>> cluster software (probably the curl library) is built without ssl support >>> at a critical point. You may have the same issue. Maybe the configuration >>> info for curl will tell you one way or another whether this is the case and >>> you can request a reinstall. >>> >>> On Thu, Aug 18, 2016 at 7:37 PM, marco giordano >>> wrote: >>> >>>> Hi there, >>>> I checked the internet connection on the node and seems fine (I can >>>> download with wget the https://midas3.kitware.com >>>> /midas/api/rest?method=midas.bitstream.download&checksum= >>>> 2e115fe26e435e33b0d5c022e4490567&algorithm=MD5?). >>>> >>>> I run the script SSLTest.cmake >>>> >>>> but it fails (it downloads a LICENSE file but it is empty): >>>> CMake Error at SSLTest.cmake:5 (file): >>>> file DOWNLOAD HASH mismatch >>>> >>>> for file: [/home/mgiordano/code/SimpleITK/LICENSE] >>>> expected hash: [f8c925402b90f74566f71e64eea7b >>>> b9d83daac69cde71408ffd6c043be6a4991] >>>> actual hash: [e3b0c44298fc1c149afbf4c8996fb >>>> 92427ae41e4649b934ca495991b7852b855] >>>> status: [1;"Unsupported protocol"] >>>> >>>> So I assume the HTTPS is not supported. Now if I understand correctly >>>> the alternative is to download the modules manually in $HOME/ExternalData >>>> and point to that folder through the variable ExternalData_OBJECT_STORES. >>>> The question is what do I need to download, is that the only the two links >>>> above or there is more ? Is it maybe an option to change version of Cmake >>>> that can support that or/and how do I enable the support ? >>>> >>>> Any help is appreciated. >>>> Regards, >>>> Marco >>>> >>>> 2016-08-17 16:51 GMT+02:00 Lowekamp, Bradley (NIH/NLM/LHC) [C] < >>>> blowekamp at mail.nih.gov>: >>>> >>>>> Hello! >>>>> >>>>> OK, so it looks like you are using the current master branch of >>>>> SimpleITK. I know this because you have the latest SimpleITK feature where >>>>> CMake downloads the Superbuild dependencies with the CMake ?ExternalData? >>>>> module. This enables some interesting options for your situation. >>>>> >>>>> You are on a cluster. On compute clusters, frequently the nodes don?t >>>>> have access to the internet. So when cmake tries to download the URLS below >>>>> it times out or errors. You can verify this with some command like ?wget >>>>> https://midas3.kitware.com/midas/api/rest?method=midas >>>>> .bitstream.download&checksum=2e115fe26e435e33b0d5c022e44905 >>>>> 67&algorithm=MD5?. The alternative is that your version of CMake >>>>> doesn?t support HTTPS. Yo can test this with the following script: >>>>> https://github.com/conda-forge/cmake-feedstock/blob/ >>>>> master/recipe/SSLTest.cmake >>>>> >>>>> Frequently, there are nodes on a cluster which have access to the >>>>> internet for situations like this. You may be able to just use one of them. >>>>> >>>>> With the new ExternalData download module you may be able to >>>>> pre-download these dependencies on the log in node. If you set the >>>>> environment variable ExternalData_OBJECT_STORES to say >>>>> ?${HOME}/.ExternalData?, it will cache downloads to this directory. I >>>>> assume your home directory is available on the log in nodes. You can >>>>> configure the SuperBuild there and build just the >>>>> ?SuperBuildSimpleITKSource? target. This will download the dependencies to >>>>> the ExternaData directory. Then you can build in a cluster node, which >>>>> should use this cache. >>>>> >>>>> Also note when testing is enabled for the actual SimpleITK >>>>> sub-project, a bunch of testing data is downloaded too. You can disable >>>>> testing to avoid this, download and un-tar a Data archive [1], or replace >>>>> the above procedure for this subproject. >>>>> >>>>> HTH, >>>>> Brad >>>>> >>>>> [1] https://sourceforge.net/projects/simpleitk/files/SimpleI >>>>> TK/0.10.0/Source/ >>>>> >>>>> >>>>> > On Aug 17, 2016, at 10:26 AM, marco giordano >>>>> wrote: >>>>> > >>>>> > Hi there, >>>>> > >>>>> > I just downloaded SimpleTK and I tried to build it on a linux >>>>> cluster (running Scientific Linux release 6.5- Carbon) using the superbuild. >>>>> > >>>>> > I use cmake 3.3.1. The Generation of build files is fine, then when >>>>> I try to build i get this: >>>>> > >>>>> > -- Fetching "http://midas3.kitware.com/mid >>>>> as/api/rest?method=midas.bitstream.download&checksum=2e115fe >>>>> 26e435e33b0d5c022e4490567&algorithm=MD5" >>>>> > -- [download 100% complete] >>>>> > -- Fetching "https://midas3.kitware.com/mi >>>>> das/api/rest?method=midas.bitstream.download&checksum=2e115f >>>>> e26e435e33b0d5c022e4490567&algorithm=MD5" >>>>> > -- Fetching "https://itk.org/files/Externa >>>>> lData/MD5/2e115fe26e435e33b0d5c022e4490567" >>>>> > CMake Error at /cm/shared/apps/cmake/3.3.1/in >>>>> stall/share/cmake-3.3/Modules/ExternalData.cmake:1012 (message): >>>>> > Object MD5=2e115fe26e435e33b0d5c022e4490567 not found at: >>>>> > >>>>> > http://midas3.kitware.com/midas/api/rest?method=midas.bitst >>>>> ream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 ("Unsupported >>>>> protocol") >>>>> > https://midas3.kitware.com/midas/api/rest?method=midas.bits >>>>> tream.download&checksum=2e115fe26e435e33b0d5c022e4490567&algorithm=MD5 >>>>> ("Unsupported protocol") >>>>> > https://itk.org/files/ExternalData/MD5/2e115fe26e435e33b0d5 >>>>> c022e4490567 ("Unsupported protocol") >>>>> > Call Stack (most recent call first): >>>>> > /cm/shared/apps/cmake/3.3.1/install/share/cmake-3.3/Modules/ExternalData.cmake:1034 >>>>> (_ExternalData_download_object) >>>>> > >>>>> > >>>>> > make[2]: *** [ExternalData/.ExternalSource/lua-5.1.5.tar.gz.md5-stamp] >>>>> Error 1 >>>>> > make[1]: *** [CMakeFiles/SuperBuildSimpleITKSourceReal.dir/all] >>>>> Error 2 >>>>> > >>>>> > Any help is welcome. >>>>> > Regards >>>>> > -- >>>>> > Marco >>>>> > _____________________________________ >>>>> > 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 >>>>> >>>>> >>>> >>>> >>>> -- >>>> Marco Giordano >>>> SKYPE:marcogiord81 >>>> >>>> _____________________________________ >>>> 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 >> >> >> >> _____________________________________ >> 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 >> >> > > > -- > Marco Giordano > SKYPE:marcogiord81 > > > -- Marco Giordano SKYPE:marcogiord81 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 dzenanz at gmail.com Mon Aug 22 09:33:03 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 22 Aug 2016 09:33:03 -0400 Subject: [ITK] [ITK-users] RLEImage Message-ID: Hi everybody, an article was recently published in Insight ?Journal, but for some reason was not automatically announce to this list. The title is "RLEImage: run-length encoded memory compression scheme for an itk::Image" and can be accessed here: http://www.insight-journal.org/browse/publication/978 Regards, D?enan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 Aug 22 12:57:36 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 Aug 2016 12:57:36 -0400 Subject: [ITK] [ITK-dev] Midas mirror script In-Reply-To: <2C043DCE-BEA2-44CC-AAD5-96B75EDF2A16@mail.nih.gov> References: <2C043DCE-BEA2-44CC-AAD5-96B75EDF2A16@mail.nih.gov> Message-ID: Hi Brad, I am not aware of a script to download / mirror a directory on midas3.kitware.com. However, last week we performed a one-time mirror of the ITK Community on midas3.kitware.com (including all the SimpleITK data), to the Girder instance on data.kitware.com: https://data.kitware.com/#collection/57b5c9e58d777f126827f5a1/folder/57b5dd988d777f10f2695f32 There is a command line and Python client that can be used to locally mirror the data: http://girder.readthedocs.io/en/latest/python-client.html A patch is in progress to add testing data support to the ExternalData CMake module: http://review.source.kitware.com/#/c/21468/ An important difference to note between Girder and Midas is that Girder does not support different revisions for the same file. HTH, Matt On Wed, Aug 10, 2016 at 1:14 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Hello, > > I am looking to mirror the SimpleITK directory of the midas3.kitware.com > MIDAS server. Are there any scripts around to aid in this? > > Thanks, > Brad > > _______________________________________________ > 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://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-developers > _______________________________________________ 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://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-developers From aharr8 at uwo.ca Mon Aug 22 15:25:56 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Mon, 22 Aug 2016 15:25:56 -0400 Subject: [ITK] [ITK-users] CorrelationImageToImageMetricv4 returns 0 from GetValue() Message-ID: Hello all, I am having a devil of a time setting up the CorrelationImageToImageMetricv4 and getting a result that makes sense. I have written an observer that outputs to a text file the iteration number, correlation value, and current position. I have generated a virtual phantom image of a white cube on a black background, and when I put the same image through for fixed and moving images, I get [0,0,0,0,0,0], meaning that no rotation or translation is required for the images to be aligned. This is the correct versor and vector transform, and if I apply a translation the correct distance values are returned to have the images align, however the metric value returned is also 0 and a perfect registration like this should yield a metric of -1 according to the documentation. Additionally, it doesn?t seem to be analyzing rotation properly, as when I introduce a rotation around any axis the metric returns a translation on the other two axes but the rotation versor remains at zero. I?m attaching my code as well, it?s possible I?ve not set some parameters up properly: -- 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: Correlator3D.cpp Type: text/x-c++src Size: 16036 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Correlator3D.h Type: text/x-chdr Size: 4336 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ 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 blowekamp at mail.nih.gov Mon Aug 22 15:49:22 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Mon, 22 Aug 2016 19:49:22 +0000 Subject: [ITK] [ITK-dev] CircleCi for ITK? Message-ID: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> Hello, I have gotten CircleCi to compile and test SimpleITK[1]. Occasionally it runs into some memory problems linking, but I was able to over come the time constraint by compiling the library and tests by utilizing distcc with multiple containers, then dividing the testing across the containers. Based on that work, I was able to do a similar thing for ITK and created a pull request on github with the current status[2]. I would like to discontinue the current ITK continuous builds. The current continuous build should be able to be replaced with the some of the Continuous Integration services available online in a modern on demand basis. The next step would be to update the script to report to CDash correctly. I would also note that this may be a better way to test many External/Remote ITK modules as it would avoid the maintaince of multiple docker images. Brad [1] https://circleci.com/gh/SimpleITK/SimpleITK [2] https://github.com/InsightSoftwareConsortium/ITK/pull/14 _______________________________________________ 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://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-developers From bill.lorensen at gmail.com Mon Aug 22 16:11:51 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 22 Aug 2016 16:11:51 -0400 Subject: [ITK] [ITK-dev] CircleCi for ITK? In-Reply-To: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> References: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> Message-ID: Certainly needs integration into ctest. I find the current reporting to be confusing. On Mon, Aug 22, 2016 at 3:49 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Hello, > > I have gotten CircleCi to compile and test SimpleITK[1]. Occasionally it runs into some memory problems linking, but I was able to over come the time constraint by compiling the library and tests by utilizing distcc with multiple containers, then dividing the testing across the containers. > > Based on that work, I was able to do a similar thing for ITK and created a pull request on github with the current status[2]. > > I would like to discontinue the current ITK continuous builds. The current continuous build should be able to be replaced with the some of the Continuous Integration services available online in a modern on demand basis. The next step would be to update the script to report to CDash correctly. > > I would also note that this may be a better way to test many External/Remote ITK modules as it would avoid the maintaince of multiple docker images. > > Brad > > [1] https://circleci.com/gh/SimpleITK/SimpleITK > [2] https://github.com/InsightSoftwareConsortium/ITK/pull/14 > _______________________________________________ > 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://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-developers > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -- 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://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-developers From matt.mccormick at kitware.com Mon Aug 22 16:16:58 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 Aug 2016 16:16:58 -0400 Subject: [ITK] [ITK-dev] CircleCi for ITK? In-Reply-To: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> References: <34056D70-5580-461B-9890-B065B2ADA738@mail.nih.gov> Message-ID: Thanks for looking into this, Brad. The CircleCI service has been enabled for the ITK repository: https://circleci.com/gh/InsightSoftwareConsortium/ITK It would be great to have Continuous builds via this service. Of course, we still need the current Gerrit/Jenkins system for code review, Windows builds, and CDash integration. Thanks, Matt On Mon, Aug 22, 2016 at 3:49 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Hello, > > I have gotten CircleCi to compile and test SimpleITK[1]. Occasionally it runs into some memory problems linking, but I was able to over come the time constraint by compiling the library and tests by utilizing distcc with multiple containers, then dividing the testing across the containers. > > Based on that work, I was able to do a similar thing for ITK and created a pull request on github with the current status[2]. > > I would like to discontinue the current ITK continuous builds. The current continuous build should be able to be replaced with the some of the Continuous Integration services available online in a modern on demand basis. The next step would be to update the script to report to CDash correctly. > > I would also note that this may be a better way to test many External/Remote ITK modules as it would avoid the maintaince of multiple docker images. > > Brad > > [1] https://circleci.com/gh/SimpleITK/SimpleITK > [2] https://github.com/InsightSoftwareConsortium/ITK/pull/14 > _______________________________________________ > 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://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-developers _______________________________________________ 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://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-developers From dzenanz at gmail.com Tue Aug 23 09:53:45 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 23 Aug 2016 09:53:45 -0400 Subject: [ITK] [ITK-users] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: Hi Andrew, you are doing so many things in a nonstandard way, starting with passing around pointers to buffers and metadata as plain parameters, instead of just once converting to itk::Image and then using itk::Image::Pointer to pass the images around. Your approach is more prone to errors. Can you provide the inputs and the main function which invokes this class to have a runnable example? I will try to find the problem. Regards, D?enan On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: > Hello all, > I am having a devil of a time setting up the CorrelationImageToImageMetricv4 > and getting a result that makes sense. I have written an observer that > outputs to a text file the iteration number, correlation value, and current > position. I have generated a virtual phantom image of a white cube on a > black background, and when I put the same image through for fixed and > moving images, I get [0,0,0,0,0,0], meaning that no rotation or translation > is required for the images to be aligned. This is the correct versor and > vector transform, and if I apply a translation the correct distance values > are returned to have the images align, however the metric value returned is > also 0 and a perfect registration like this should yield a metric of -1 > according to the documentation. Additionally, it doesn?t seem to be > analyzing rotation properly, as when I introduce a rotation around any axis > the metric returns a translation on the other two axes but the rotation > versor remains at zero. > > I?m attaching my code as well, it?s possible I?ve not set some parameters > up properly: > > > -- > > 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: -------------- next part -------------- _____________________________________ 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 k.marstal at erasmusmc.nl Tue Aug 23 12:04:43 2016 From: k.marstal at erasmusmc.nl (K.K. Marstal) Date: Tue, 23 Aug 2016 16:04:43 +0000 Subject: [ITK] [ITK-dev] BUG: Undefined symbol ImageBase::ImageDimension with clang compiler Message-ID: <1868B119ADBA1240A7DB9DF965237231D98B9A72@EXCH-HE03.erasmusmc.nl> Hello, As discussed in this gerrit ticket http://review.source.kitware.com/#/c/20900 the recent change to itkGetStaticConstMacro hides the ImageBase::ImageDimension symbol for linking in some cases. While the problem seemed to have been solved in that particular case, I am getting the same error compiling SimpleITK and linking against the Python wrapper on Mac OS X with GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5) compiler. The issue is fixed if I change line 780 of itkMacro.h "itkStaticConstMacro(name,type,value) static ITK_CONSTEXPR type name = value" back the version of itk 4.8.2, namely "#define itkStaticConstMacro(name, type, value) enum { name = value }". To clarify, the problem seem to be with ITK, not with SimpleITK. Kind Regards, Kasper Marstal -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From kolin9105 at gmail.com Tue Aug 23 14:50:57 2016 From: kolin9105 at gmail.com (meikolin saimara) Date: Wed, 24 Aug 2016 01:50:57 +0700 Subject: [ITK] [ITK-users] (no subject) Message-ID: hello every one... how I can found sp x and sp y of my image with itk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 blowekamp at mail.nih.gov Tue Aug 23 15:10:09 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 23 Aug 2016 19:10:09 +0000 Subject: [ITK] [ITK-dev] BUG: Undefined symbol ImageBase::ImageDimension with clang compiler In-Reply-To: <1868B119ADBA1240A7DB9DF965237231D98B9A72@EXCH-HE03.erasmusmc.nl> References: <1868B119ADBA1240A7DB9DF965237231D98B9A72@EXCH-HE03.erasmusmc.nl> Message-ID: <5CE651EE-994F-42A2-936F-71D71BA748EF@mail.nih.gov> Hello, Do you have a specific version of SimpleITK and ITK and Xcode which cause this problem? The current SimpleITK master with Xcode 7.3 seems ok to me. Brad On Aug 23, 2016, at 12:04 PM, K.K. Marstal > wrote: Hello, As discussed in this gerrit ticket http://review.source.kitware.com/#/c/20900 the recent change to itkGetStaticConstMacro hides the ImageBase::ImageDimension symbol for linking in some cases. While the problem seemed to have been solved in that particular case, I am getting the same error compiling SimpleITK and linking against the Python wrapper on Mac OS X with GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5) compiler. The issue is fixed if I change line 780 of itkMacro.h "itkStaticConstMacro(name,type,value) static ITK_CONSTEXPR type name = value" back the version of itk 4.8.2, namely "#define itkStaticConstMacro(name, type, value) enum { name = value }". To clarify, the problem seem to be with ITK, not with SimpleITK. Kind Regards, Kasper Marstal _______________________________________________ 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://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-developers _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From andinet.enqu at kitware.com Tue Aug 23 20:15:34 2016 From: andinet.enqu at kitware.com (Andinet Enquobahrie) Date: Tue, 23 Aug 2016 20:15:34 -0400 Subject: [ITK] [ITK-users] ANN:Kitware is hiring software developers for ITK and 3D Slicer Message-ID: Apologies for duplicate postings. =================== Hi folks, Kitware is seeking to hire highly skilled software developers to assist us in creating high quality software by utilizing and extending ITK and 3D Slicer for our research and commercial collaborations. If you are interested in this opportunity, please consider applying. Software Developer for ITK and Slicer http://tinyurl.com/h3e6ukh Another opportunity in the Medical Computing group: Research and Development Involving Machine Learning and Medical Image Analysis http://tinyurl.com/hy58kq8 For other job openings including internships at Kitware, please check http://jobs.kitware.com/opportunities.html -- Andinet Enquobahrie, Ph.D., MBA Assistant Director of Medical Computing Kitware, Inc. http://www.kitware.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 andinet.enqu at kitware.com Tue Aug 23 20:15:34 2016 From: andinet.enqu at kitware.com (Andinet Enquobahrie) Date: Tue, 23 Aug 2016 20:15:34 -0400 Subject: [ITK] [ITK-dev] ANN:Kitware is hiring software developers for ITK and 3D Slicer Message-ID: Apologies for duplicate postings. =================== Hi folks, Kitware is seeking to hire highly skilled software developers to assist us in creating high quality software by utilizing and extending ITK and 3D Slicer for our research and commercial collaborations. If you are interested in this opportunity, please consider applying. Software Developer for ITK and Slicer http://tinyurl.com/h3e6ukh Another opportunity in the Medical Computing group: Research and Development Involving Machine Learning and Medical Image Analysis http://tinyurl.com/hy58kq8 For other job openings including internships at Kitware, please check http://jobs.kitware.com/opportunities.html -- Andinet Enquobahrie, Ph.D., MBA Assistant Director of Medical Computing Kitware, Inc. http://www.kitware.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From zhuangming.shen at sphic.org.cn Tue Aug 23 21:53:03 2016 From: zhuangming.shen at sphic.org.cn (=?utf-8?B?5rKI5bqE5piO?=) Date: Wed, 24 Aug 2016 01:53:03 +0000 Subject: [ITK] [ITK-users] How to use itk::LandmarkBasedTransformInitializer for python supported ITK? Message-ID: <1472003582182.51985@sphic.org.cn> Hi all, I'd like to do landmark based image registration using python supported ITK. I referred to this example (https://itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer) and want to modify the code to python. In this example, itk::LandmarkBasedTransformInitializer can be wrapped to python. But how to SetFixedLandmarks/SetMovingLandmarks? using python? Because the input of SetFixedLandmarks/SetMovingLandmarks? is fixedLandmarks/movingLandmarks, whose actual type is std::vector. Could anyone give me a short example on how to write it? Thanks in advance. Regards, Zhuangming Shen -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 cory.quammen at kitware.com Tue Aug 23 22:44:05 2016 From: cory.quammen at kitware.com (Cory Quammen) Date: Tue, 23 Aug 2016 22:44:05 -0400 Subject: [ITK] Problems compiling Python wrappings in current ITK master Message-ID: Hi all, I am attempting to compile ITK with Python wrappings on. I had this working for ITK 4.9RC1, but current ITK master isn't so happy. When I compile target ITKCommonCastXML, I get the following errors: /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:40:50: error: expected expression typedef itk::VectorContainer< unsigned long, > itkVectorContainerUL; ^ /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:41:50: error: expected expression typedef itk::VectorContainer< unsigned long, >::Pointer itkVectorContainerUL_Pointer; ^ /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:41:53: error: definition or redeclaration of 'Pointer' cannot name the global scope typedef itk::VectorContainer< unsigned long, >::Pointer itkVectorContainerUL_Pointer; ~~^ /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:41:53: error: typedef declarator cannot be qualified typedef itk::VectorContainer< unsigned long, >::Pointer itkVectorContainerUL_Pointer; ~~^ /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:41:60: error: expected ';' after top level declarator typedef itk::VectorContainer< unsigned long, >::Pointer itkVectorContainerUL_Pointer; ^ ; /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:49:50: error: expected expression typedef itk::VectorContainer< unsigned long, > itkVectorContainerUL; ^ /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:50:50: error: expected expression typedef itk::VectorContainer< unsigned long, >::Pointer itkVectorContainerUL_Pointer; ^ /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:50:53: error: definition or redeclaration of 'Pointer' cannot name the global scope typedef itk::VectorContainer< unsigned long, >::Pointer itkVectorContainerUL_Pointer; ~~^ /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:50:53: error: typedef declarator cannot be qualified typedef itk::VectorContainer< unsigned long, >::Pointer itkVectorContainerUL_Pointer; ~~^ /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:50:60: error: expected ';' after top level declarator typedef itk::VectorContainer< unsigned long, >::Pointer itkVectorContainerUL_Pointer; And so on. I also get similar errors for /Users/cory.quammen/bin/itk-default/Wrapping/itkMapContainer.cxx:27:47: error: expected expression typedef itk::MapContainer< unsigned long, > itkMapContainerUL; It seems as though the second template parameter for the UL wrapped type is being left out. Does anyone know what might be going on? Thanks! Cory -- Cory Quammen R&D Engineer Kitware, Inc. From matt.mccormick at kitware.com Wed Aug 24 00:02:03 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Aug 2016 00:02:03 -0400 Subject: [ITK] [ITK-users] How to use itk::LandmarkBasedTransformInitializer for python supported ITK? In-Reply-To: <1472003582182.51985@sphic.org.cn> References: <1472003582182.51985@sphic.org.cn> Message-ID: Hi, I added a Python version of the example to the wiki page, although it required a few fixes to the wrapping. This patch fixes wrapping of the LandmarkTransformInitializer class for 2D Transform's: http://review.source.kitware.com/#/c/21481/ and this patch adds wrapping for std::vector< itk::Point > so the landmarks can be added. http://review.source.kitware.com/#/c/21480/ Please review the patches. Thanks, Matt On Tue, Aug 23, 2016 at 9:53 PM, ??? wrote: > Hi all, > > > I'd like to do landmark based image registration using python supported ITK. > I referred to this example > (https://itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer) > and want to modify the code to python. In this example, > itk::LandmarkBasedTransformInitializer can be wrapped to python. But how to > SetFixedLandmarks/SetMovingLandmarks using python? Because the input of > SetFixedLandmarks/SetMovingLandmarks is fixedLandmarks/movingLandmarks, > whose actual type is std::vector. Could anyone give me a short example on > how to write it? Thanks in advance. > > > > Regards, > > > Zhuangming Shen > > > _____________________________________ > 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 zhuangming.shen at sphic.org.cn Wed Aug 24 00:51:32 2016 From: zhuangming.shen at sphic.org.cn (=?gb2312?B?yfLXr8P3?=) Date: Wed, 24 Aug 2016 04:51:32 +0000 Subject: [ITK] [ITK-users] How to use itk::LandmarkBasedTransformInitializer for python supported ITK? In-Reply-To: References: <1472003582182.51985@sphic.org.cn>, Message-ID: <1472014291321.59445@sphic.org.cn> Thank you so much. ________________________________________ From: Matt McCormick Sent: Wednesday, August 24, 2016 12:02 PM To: ??? Cc: insight-users at itk.org Subject: Re: [ITK-users] How to use itk::LandmarkBasedTransformInitializer for python supported ITK? Hi, I added a Python version of the example to the wiki page, although it required a few fixes to the wrapping. This patch fixes wrapping of the LandmarkTransformInitializer class for 2D Transform's: http://review.source.kitware.com/#/c/21481/ and this patch adds wrapping for std::vector< itk::Point > so the landmarks can be added. http://review.source.kitware.com/#/c/21480/ Please review the patches. Thanks, Matt On Tue, Aug 23, 2016 at 9:53 PM, ??? wrote: > Hi all, > > > I'd like to do landmark based image registration using python supported ITK. > I referred to this example > (https://itk.org/Wiki/ITK/Examples/Registration/LandmarkBasedTransformInitializer) > and want to modify the code to python. In this example, > itk::LandmarkBasedTransformInitializer can be wrapped to python. But how to > SetFixedLandmarks/SetMovingLandmarks using python? Because the input of > SetFixedLandmarks/SetMovingLandmarks is fixedLandmarks/movingLandmarks, > whose actual type is std::vector. Could anyone give me a short example on > how to write it? Thanks in advance. > > > > Regards, > > > Zhuangming Shen > > > _____________________________________ > 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 jhlegarreta at vicomtech.org Wed Aug 24 03:12:47 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Wed, 24 Aug 2016 09:12:47 +0200 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi, section 4.1.4 in the ITK software guide [1] may be of help. In essence, image->GetSpacing(); will give you the image spacing. HTH, JON HAITZ [1] https://itk.org/ItkSoftwareGuide.pdf -- On 23 August 2016 at 20:50, meikolin saimara wrote: > hello every one... > how I can found sp x and sp y of my image with itk > > _____________________________________ > 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 -------------- _____________________________________ 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 k.marstal at erasmusmc.nl Wed Aug 24 06:26:25 2016 From: k.marstal at erasmusmc.nl (K.K. Marstal) Date: Wed, 24 Aug 2016 10:26:25 +0000 Subject: [ITK] [ITK-dev] BUG: Undefined symbol ImageBase::ImageDimension with clang compiler In-Reply-To: <5CE651EE-994F-42A2-936F-71D71BA748EF@mail.nih.gov> References: <1868B119ADBA1240A7DB9DF965237231D98B9A72@EXCH-HE03.erasmusmc.nl>, <5CE651EE-994F-42A2-936F-71D71BA748EF@mail.nih.gov> Message-ID: <1868B119ADBA1240A7DB9DF965237231D98B9A97@EXCH-HE03.erasmusmc.nl> I am using xcode 7.3.1, ITK v4.10, and SimpleITK v0.10.0. I should clarify that SimpleITK itself compiles and links allright, but the error happens when linking against my own extensions to SimpleITK (https://github.com/kaspermarstal/SimpleElastix). The way itkStaticConstMacro and the ImageDimension is used here here https://github.com/kaspermarstal/elastix/blob/641c83af7f97dfe2397e26e832cdda76e166fd14/src/Core/Main/elxElastixFilter.h#L80-L81 seems to hide the ImageDimension symbol during linking, much in the same way as in the referenced gerrit discussion. There are workarounds of course, just thought you should know. Kasper ________________________________ From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [blowekamp at mail.nih.gov] Sent: Tuesday, August 23, 2016 9:10 PM To: K.K. Marstal Cc: insight-developers at itk.org Subject: Re: [ITK] [ITK-dev] BUG: Undefined symbol ImageBase::ImageDimension with clang compiler Hello, Do you have a specific version of SimpleITK and ITK and Xcode which cause this problem? The current SimpleITK master with Xcode 7.3 seems ok to me. Brad On Aug 23, 2016, at 12:04 PM, K.K. Marstal > wrote: Hello, As discussed in this gerrit ticket http://review.source.kitware.com/#/c/20900 the recent change to itkGetStaticConstMacro hides the ImageBase::ImageDimension symbol for linking in some cases. While the problem seemed to have been solved in that particular case, I am getting the same error compiling SimpleITK and linking against the Python wrapper on Mac OS X with GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5) compiler. The issue is fixed if I change line 780 of itkMacro.h "itkStaticConstMacro(name,type,value) static ITK_CONSTEXPR type name = value" back the version of itk 4.8.2, namely "#define itkStaticConstMacro(name, type, value) enum { name = value }". To clarify, the problem seem to be with ITK, not with SimpleITK. Kind Regards, Kasper Marstal _______________________________________________ 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://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-developers _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From matt.mccormick at kitware.com Wed Aug 24 08:22:08 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 24 Aug 2016 08:22:08 -0400 Subject: [ITK] Problems compiling Python wrappings in current ITK master In-Reply-To: References: Message-ID: Hi Cory, Are there non-default CMake options for the build? Thanks, Matt On Tue, Aug 23, 2016 at 10:44 PM, Cory Quammen wrote: > Hi all, > > I am attempting to compile ITK with Python wrappings on. I had this > working for ITK 4.9RC1, but current ITK master isn't so happy. > > When I compile target ITKCommonCastXML, I get the following errors: > > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:40:50: > error: expected expression > typedef itk::VectorContainer< unsigned long, > itkVectorContainerUL; > ^ > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:41:50: > error: expected expression > typedef itk::VectorContainer< unsigned long, >::Pointer > itkVectorContainerUL_Pointer; > ^ > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:41:53: > error: definition or redeclaration of 'Pointer' cannot name the global > scope > typedef itk::VectorContainer< unsigned long, >::Pointer > itkVectorContainerUL_Pointer; > ~~^ > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:41:53: > error: typedef declarator cannot be qualified > typedef itk::VectorContainer< unsigned long, >::Pointer > itkVectorContainerUL_Pointer; > ~~^ > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:41:60: > error: expected ';' after top level declarator > typedef itk::VectorContainer< unsigned long, >::Pointer > itkVectorContainerUL_Pointer; > ^ > ; > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:49:50: > error: expected expression > typedef itk::VectorContainer< unsigned long, > itkVectorContainerUL; > ^ > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:50:50: > error: expected expression > typedef itk::VectorContainer< unsigned long, >::Pointer > itkVectorContainerUL_Pointer; > ^ > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:50:53: > error: definition or redeclaration of 'Pointer' cannot name the global > scope > typedef itk::VectorContainer< unsigned long, >::Pointer > itkVectorContainerUL_Pointer; > ~~^ > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:50:53: > error: typedef declarator cannot be qualified > typedef itk::VectorContainer< unsigned long, >::Pointer > itkVectorContainerUL_Pointer; > ~~^ > /Users/cory.quammen/bin/itk-default/Wrapping/itkVectorContainer.cxx:50:60: > error: expected ';' after top level declarator > typedef itk::VectorContainer< unsigned long, >::Pointer > itkVectorContainerUL_Pointer; > > And so on. I also get similar errors for > > /Users/cory.quammen/bin/itk-default/Wrapping/itkMapContainer.cxx:27:47: > error: expected expression > typedef itk::MapContainer< unsigned long, > itkMapContainerUL; > > It seems as though the second template parameter for the UL wrapped > type is being left out. > > Does anyone know what might be going on? > > Thanks! > Cory > > -- > Cory Quammen > R&D Engineer > Kitware, Inc. > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From aharr8 at uwo.ca Wed Aug 24 11:13:13 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Wed, 24 Aug 2016 11:13:13 -0400 Subject: [ITK] [ITK-users] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: Thanks for getting back to me. I know the approach isn?t ideal, I?m building my class on top of an existing project, so that?s the reason for using the primative types. I?m going to write a main function as well as sending you a data set so that you can skip figuring out how to get data in to the class and can focus directly on the problem, should have both the program and data to you by the end of the day. Thanks again. -- 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 Tue, Aug 23, 2016 at 9:53 AM, D?enan Zuki? wrote: > Hi Andrew, > > you are doing so many things in a nonstandard way, starting with passing > around pointers to buffers and metadata as plain parameters, instead of > just once converting to itk::Image and then using itk::Image::Pointer to > pass the images around. Your approach is more prone to errors. > > Can you provide the inputs and the main function which invokes this class > to have a runnable example? I will try to find the problem. > > Regards, > D?enan > > On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: > >> Hello all, >> I am having a devil of a time setting up the >> CorrelationImageToImageMetricv4 and getting a result that makes sense. >> I have written an observer that outputs to a text file the iteration >> number, correlation value, and current position. I have generated a >> virtual phantom image of a white cube on a black background, and when I put >> the same image through for fixed and moving images, I get [0,0,0,0,0,0], >> meaning that no rotation or translation is required for the images to be >> aligned. This is the correct versor and vector transform, and if I apply a >> translation the correct distance values are returned to have the images >> align, however the metric value returned is also 0 and a perfect >> registration like this should yield a metric of -1 according to the >> documentation. Additionally, it doesn?t seem to be analyzing rotation >> properly, as when I introduce a rotation around any axis the metric returns >> a translation on the other two axes but the rotation versor remains at zero. >> >> I?m attaching my code as well, it?s possible I?ve not set some parameters >> up properly: >> >> >> -- >> >> 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: -------------- next part -------------- _____________________________________ 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 sepideh.movaghati at gmail.com Wed Aug 24 13:52:21 2016 From: sepideh.movaghati at gmail.com (Sepide Movaghati) Date: Wed, 24 Aug 2016 13:52:21 -0400 Subject: [ITK] [ITK-users] Problem Using ScaleEstimator in V4 Registration Message-ID: Hi, I found a problem while I was using ScaleEstimator in v4 registration: In itkRegistrationParametersScaleEstimator class there are two functions SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the sampling strategy is chosen based on the Transformation type. For example if the transformation is of type displacement field or BSpline, it uses all of the samples. If transformation is any regular affine or rigid transformation (child of class MatrixOffsetTransformBase) it performs corner sampling. However, if the transformation is none of the known ones, it uses Random Sampling. Here is the problem: in itkImageRegistrationMethodv4.hxx the Metric transformation is set using ->SetMovingTransform() and it is always a CompositeTransform! Therefore, ScaleEstimator cannot detect the transformation type and it always fall into "else" which is using Random Sampling! It does not matter if you do a multilevel registration or not. The transformation is always of type CompositeTransform even if you do just a one level rigid transform! I would appreciate if you let me know if I was correct about this issue and whether we can consider this a bug and hope to get it fixed for the upcoming versions. Thanks a lot for your consideration in advance, Sepide _____________________________________ 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 cory.quammen at kitware.com Wed Aug 24 14:41:31 2016 From: cory.quammen at kitware.com (Cory Quammen) Date: Wed, 24 Aug 2016 14:41:31 -0400 Subject: [ITK] Problems compiling Python wrappings in current ITK master In-Reply-To: References: Message-ID: Thanks for responding, Matt. More details on posted on this tomviz pull request: https://github.com/OpenChemistry/tomviz/pull/567 Thanks, Cory On Wed, Aug 24, 2016 at 8:22 AM, Matt McCormick wrote: > Hi Cory, > > Are there non-default CMake options for the build? > > Thanks, > Matt > > On Tue, Aug 23, 2016 at 10:44 PM, Cory Quammen > wrote: > > Hi all, > > > > I am attempting to compile ITK with Python wrappings on. I had this > > working for ITK 4.9RC1, but current ITK master isn't so happy. > > > > When I compile target ITKCommonCastXML, I get the following errors: > > > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:40:50: > > error: expected expression > > typedef itk::VectorContainer< unsigned long, > itkVectorContainerUL; > > ^ > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:41:50: > > error: expected expression > > typedef itk::VectorContainer< unsigned long, >::Pointer > > itkVectorContainerUL_Pointer; > > ^ > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:41:53: > > error: definition or redeclaration of 'Pointer' cannot name the global > > scope > > typedef itk::VectorContainer< unsigned long, >::Pointer > > itkVectorContainerUL_Pointer; > > ~~^ > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:41:53: > > error: typedef declarator cannot be qualified > > typedef itk::VectorContainer< unsigned long, >::Pointer > > itkVectorContainerUL_Pointer; > > ~~^ > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:41:60: > > error: expected ';' after top level declarator > > typedef itk::VectorContainer< unsigned long, >::Pointer > > itkVectorContainerUL_Pointer; > > ^ > > ; > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:49:50: > > error: expected expression > > typedef itk::VectorContainer< unsigned long, > itkVectorContainerUL; > > ^ > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:50:50: > > error: expected expression > > typedef itk::VectorContainer< unsigned long, >::Pointer > > itkVectorContainerUL_Pointer; > > ^ > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:50:53: > > error: definition or redeclaration of 'Pointer' cannot name the global > > scope > > typedef itk::VectorContainer< unsigned long, >::Pointer > > itkVectorContainerUL_Pointer; > > ~~^ > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:50:53: > > error: typedef declarator cannot be qualified > > typedef itk::VectorContainer< unsigned long, >::Pointer > > itkVectorContainerUL_Pointer; > > ~~^ > > /Users/cory.quammen/bin/itk-default/Wrapping/ > itkVectorContainer.cxx:50:60: > > error: expected ';' after top level declarator > > typedef itk::VectorContainer< unsigned long, >::Pointer > > itkVectorContainerUL_Pointer; > > > > And so on. I also get similar errors for > > > > /Users/cory.quammen/bin/itk-default/Wrapping/itkMapContainer.cxx:27:47: > > error: expected expression > > typedef itk::MapContainer< unsigned long, > itkMapContainerUL; > > > > It seems as though the second template parameter for the UL wrapped > > type is being left out. > > > > Does anyone know what might be going on? > > > > Thanks! > > Cory > > > > -- > > Cory Quammen > > R&D Engineer > > Kitware, Inc. > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > -- Cory Quammen R&D Engineer Kitware, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Aug 24 14:45:00 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 24 Aug 2016 14:45:00 -0400 Subject: [ITK] [ITK-users] Problem Using ScaleEstimator in V4 Registration In-Reply-To: References: Message-ID: Hi Sepide, if I remember correctly, registration framework is advertised as using random sampling. And the function you mention is not used for sampling the registration metric, but rather for parameter scale estimation. So even if random sampling usage for scale estimation is unintentional, I don't believe it is a major problem. Perhaps someone who participated in writing the registration framework can chime in? Regards, D?enan On Wed, Aug 24, 2016 at 1:52 PM, Sepide Movaghati < sepideh.movaghati at gmail.com> wrote: > Hi, > > I found a problem while I was using ScaleEstimator in v4 registration: > > In itkRegistrationParametersScaleEstimator class there are two functions > SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the > sampling strategy is chosen based on the Transformation type. For example > if the transformation is of type displacement field or BSpline, it uses all > of the samples. If transformation is any regular affine or rigid > transformation (child of class MatrixOffsetTransformBase) it performs > corner sampling. However, if the transformation is none of the known ones, > it uses Random Sampling. > > Here is the problem: in itkImageRegistrationMethodv4.hxx the Metric > transformation is set using ->SetMovingTransform() and it is always a > CompositeTransform! Therefore, ScaleEstimator cannot detect the > transformation type and it always fall into "else" which is using Random > Sampling! It does not matter if you do a multilevel registration or not. > The transformation is always of type CompositeTransform even if you do just > a one level rigid transform! > > I would appreciate if you let me know if I was correct about this issue > and whether we can consider this a bug and hope to get it fixed for the > upcoming versions. > > Thanks a lot for your consideration in advance, > Sepide > _____________________________________ > 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 -------------- _____________________________________ 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 tevain at telecom-paristech.fr Thu Aug 25 04:59:24 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Thu, 25 Aug 2016 10:59:24 +0200 (CEST) Subject: [ITK] [ITK-users] ASM and AAM in ITK In-Reply-To: <1121240625.46335790.1472114394416.JavaMail.zimbra@enst.fr> Message-ID: <1090038339.46348680.1472115564462.JavaMail.zimbra@enst.fr> Hi everybody, I'm currently trying to build teeth models to guide segmentation in CBCT data. With the help of the ImagePCAShapeModelEstimator I was able to build an ASM model. But that's not enough and I would like to add the intensity information, thus building an appearance model. Since there isn't build-in solution, I have two questions: -Is anyone aware of a code project for AAM which could be used with itk? -In the perspective of coding my own method, I've taken a look to the ImagePCAShapeModelEstimator code. The way the PCA is performed puzzle me. The principal component are computed by combining the data matrix to the eigenvectors of the inner product matrix, not by taking the eigenvector of covariance matrix, for computational efficiency. I don't see the equivalence between these methods. Is there somewhere I could get information on this, a math sheet or something like that ? Tim _____________________________________ 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 Thu Aug 25 07:53:47 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Thu, 25 Aug 2016 07:53:47 -0400 Subject: [ITK] [ITK-users] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: It's taking me longer than I thought it would to put a main function together, so I thought I would get you some image data to look at. This is a virtual phantom I generated, a white cube on a black background. The second image is the same cube but rotated by 5 degrees in the X direction. The .nfo files contain information about the image size and spacing. Let me know if you find anything out, I'll keep working on getting you a simple main function in case you need it. Thanks again.? PhantomBox.nfo ?? PhantomBox.raw ?? PhantomBoxRotX2.nfo ?? PhantomBoxRotX2.raw ? -- 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 Tue, Aug 23, 2016 at 9:53 AM, D?enan Zuki? wrote: > Hi Andrew, > > you are doing so many things in a nonstandard way, starting with passing > around pointers to buffers and metadata as plain parameters, instead of > just once converting to itk::Image and then using itk::Image::Pointer to > pass the images around. Your approach is more prone to errors. > > Can you provide the inputs and the main function which invokes this class > to have a runnable example? I will try to find the problem. > > Regards, > D?enan > > On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: > >> Hello all, >> I am having a devil of a time setting up the >> CorrelationImageToImageMetricv4 and getting a result that makes sense. >> I have written an observer that outputs to a text file the iteration >> number, correlation value, and current position. I have generated a >> virtual phantom image of a white cube on a black background, and when I put >> the same image through for fixed and moving images, I get [0,0,0,0,0,0], >> meaning that no rotation or translation is required for the images to be >> aligned. This is the correct versor and vector transform, and if I apply a >> translation the correct distance values are returned to have the images >> align, however the metric value returned is also 0 and a perfect >> registration like this should yield a metric of -1 according to the >> documentation. Additionally, it doesn?t seem to be analyzing rotation >> properly, as when I introduce a rotation around any axis the metric returns >> a translation on the other two axes but the rotation versor remains at zero. >> >> I?m attaching my code as well, it?s possible I?ve not set some parameters >> up properly: >> >> >> -- >> >> 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: -------------- next part -------------- _____________________________________ 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 zivrafael.yaniv at nih.gov Thu Aug 25 09:25:06 2016 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Thu, 25 Aug 2016 13:25:06 +0000 Subject: [ITK] [ITK-users] ASM and AAM in ITK Message-ID: Hi Tim, Before you continue on this path I would recommend that you take a look at the Statismo project (http://www.si-cas.com/ncssm/software.htm) . It may be doing what you want, to quote from their github documentation "Although the main focus of statismo lies on shape modeling, it is designed such that it supports any kind of PCA based statistical model, including statistical deformation models and intensity models." It is built on top of ITK. hope this helps Ziv On 8/25/16, 4:59 AM, "Timothee Evain" wrote: >Hi everybody, > >I'm currently trying to build teeth models to guide segmentation in CBCT >data. > >With the help of the ImagePCAShapeModelEstimator I was able to build an >ASM model. But that's not enough and I would like to add the intensity >information, thus building an appearance model. >Since there isn't build-in solution, I have two questions: > >-Is anyone aware of a code project for AAM which could be used with itk? > >-In the perspective of coding my own method, I've taken a look to the >ImagePCAShapeModelEstimator code. The way the PCA is performed puzzle me. >The principal component are computed by combining the data matrix to the >eigenvectors of the inner product matrix, not by taking the eigenvector >of covariance matrix, for computational efficiency. I don't see the >equivalence between these methods. Is there somewhere I could get >information on this, a math sheet or something like that ? > >Tim >_____________________________________ >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 tevain at telecom-paristech.fr Thu Aug 25 11:59:24 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Thu, 25 Aug 2016 17:59:24 +0200 (CEST) Subject: [ITK] [ITK-users] ASM and AAM in ITK In-Reply-To: References: Message-ID: <1528465751.46616463.1472140764261.JavaMail.zimbra@enst.fr> Thanks a lot Ziv! I will take a look into that library. From a quick search, I'm not sure it will be able to model the intensity of the data, I will see. Anyway, this project is a quite interesting contribution to statistical modelling with it implementation-independant model approach, and deserve to be known. Thanks for the hint :) Tim ----- Mail original ----- De: "Ziv Rafael Yaniv (NIH/NLM/LHC) [C]" ?: "Timothee Evain" , "Insight Users" Envoy?: Jeudi 25 Ao?t 2016 15:25:06 Objet: Re: [ITK-users] ASM and AAM in ITK Hi Tim, Before you continue on this path I would recommend that you take a look at the Statismo project (http://www.si-cas.com/ncssm/software.htm) . It may be doing what you want, to quote from their github documentation "Although the main focus of statismo lies on shape modeling, it is designed such that it supports any kind of PCA based statistical model, including statistical deformation models and intensity models." It is built on top of ITK. hope this helps Ziv On 8/25/16, 4:59 AM, "Timothee Evain" wrote: >Hi everybody, > >I'm currently trying to build teeth models to guide segmentation in CBCT >data. > >With the help of the ImagePCAShapeModelEstimator I was able to build an >ASM model. But that's not enough and I would like to add the intensity >information, thus building an appearance model. >Since there isn't build-in solution, I have two questions: > >-Is anyone aware of a code project for AAM which could be used with itk? > >-In the perspective of coding my own method, I've taken a look to the >ImagePCAShapeModelEstimator code. The way the PCA is performed puzzle me. >The principal component are computed by combining the data matrix to the >eigenvectors of the inner product matrix, not by taking the eigenvector >of covariance matrix, for computational efficiency. I don't see the >equivalence between these methods. Is there somewhere I could get >information on this, a math sheet or something like that ? > >Tim >_____________________________________ >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 aharr8 at uwo.ca Fri Aug 26 15:14:41 2016 From: aharr8 at uwo.ca (Andrew Harris) Date: Fri, 26 Aug 2016 15:14:41 -0400 Subject: [ITK] [ITK-users] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: Sorry again for the delay, we determined the images we were creating were too big so we created a smaller phantom image, attached. In addition, there is a main() function in CorrelationTest.cpp that runs the correlation and outputs it to a file called observer.txt, and I have included the most up-to-date versions of my class and header files. The function is expecting the phantom to exist in a folder at c:/Scans/Phantom. Let me know if you need further info, and thanks again for your help.? SmallPhantomBox.raw ?? CorrelationTest.cpp ?? Correlator3D.cpp ?? Correlator3D.h ? -- 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 Tue, Aug 23, 2016 at 9:53 AM, D?enan Zuki? wrote: > Hi Andrew, > > you are doing so many things in a nonstandard way, starting with passing > around pointers to buffers and metadata as plain parameters, instead of > just once converting to itk::Image and then using itk::Image::Pointer to > pass the images around. Your approach is more prone to errors. > > Can you provide the inputs and the main function which invokes this class > to have a runnable example? I will try to find the problem. > > Regards, > D?enan > > On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: > >> Hello all, >> I am having a devil of a time setting up the >> CorrelationImageToImageMetricv4 and getting a result that makes sense. >> I have written an observer that outputs to a text file the iteration >> number, correlation value, and current position. I have generated a >> virtual phantom image of a white cube on a black background, and when I put >> the same image through for fixed and moving images, I get [0,0,0,0,0,0], >> meaning that no rotation or translation is required for the images to be >> aligned. This is the correct versor and vector transform, and if I apply a >> translation the correct distance values are returned to have the images >> align, however the metric value returned is also 0 and a perfect >> registration like this should yield a metric of -1 according to the >> documentation. Additionally, it doesn?t seem to be analyzing rotation >> properly, as when I introduce a rotation around any axis the metric returns >> a translation on the other two axes but the rotation versor remains at zero. >> >> I?m attaching my code as well, it?s possible I?ve not set some parameters >> up properly: >> >> >> -- >> >> 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: -------------- next part -------------- _____________________________________ 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 dzenanz at gmail.com Fri Aug 26 16:50:14 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 26 Aug 2016 16:50:14 -0400 Subject: [ITK] [ITK-users] CorrelationImageToImageMetricv4 returns 0 from GetValue() In-Reply-To: References: Message-ID: Hi Andrew, the problem was that you were setting the mask to just the white box. This caused the metric to only be evaluated on one pixel intensity, which is a degenerate case and is probably what caused the correlation to be 0. Without setting either mask, the registration does something - I did not examine whether the result is correct or even meaningful. The modified files are attached - you can do a diff to see the few differences. If you need the mask for a similar case in practice, you could use dilate filter to enlarge the mask by a few voxels. Regards, D?enan On Fri, Aug 26, 2016 at 3:14 PM, Andrew Harris wrote: > Sorry again for the delay, we determined the images we were creating were > too big so we created a smaller phantom image, attached. In addition, > there is a main() function in CorrelationTest.cpp that runs the correlation > and outputs it to a file called observer.txt, and I have included the most > up-to-date versions of my class and header files. The function is > expecting the phantom to exist in a folder at c:/Scans/Phantom. Let me > know if you need further info, and thanks again for your help.? > SmallPhantomBox.raw > > ?? > CorrelationTest.cpp > > ?? > Correlator3D.cpp > > ?? > Correlator3D.h > > ? > > -- > > 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 Tue, Aug 23, 2016 at 9:53 AM, D?enan Zuki? wrote: > >> Hi Andrew, >> >> you are doing so many things in a nonstandard way, starting with passing >> around pointers to buffers and metadata as plain parameters, instead of >> just once converting to itk::Image and then using itk::Image::Pointer to >> pass the images around. Your approach is more prone to errors. >> >> Can you provide the inputs and the main function which invokes this class >> to have a runnable example? I will try to find the problem. >> >> Regards, >> D?enan >> >> On Mon, Aug 22, 2016 at 3:25 PM, Andrew Harris wrote: >> >>> Hello all, >>> I am having a devil of a time setting up the >>> CorrelationImageToImageMetricv4 and getting a result that makes sense. >>> I have written an observer that outputs to a text file the iteration >>> number, correlation value, and current position. I have generated a >>> virtual phantom image of a white cube on a black background, and when I put >>> the same image through for fixed and moving images, I get [0,0,0,0,0,0], >>> meaning that no rotation or translation is required for the images to be >>> aligned. This is the correct versor and vector transform, and if I apply a >>> translation the correct distance values are returned to have the images >>> align, however the metric value returned is also 0 and a perfect >>> registration like this should yield a metric of -1 according to the >>> documentation. Additionally, it doesn?t seem to be analyzing rotation >>> properly, as when I introduce a rotation around any axis the metric returns >>> a translation on the other two axes but the rotation versor remains at zero. >>> >>> I?m attaching my code as well, it?s possible I?ve not set some >>> parameters up properly: >>> >>> >>> -- >>> >>> 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: -------------- next part -------------- Iteration: 0 Calculation: 1 Value = -0.714321 Position: [0, 0, 0, 0, 0, 0] Iteration: 0 Calculation: 2 Value = 0 Position: [-0.44869711458819234, -0.3193438163428909, 0.8322332598948731, -0.03702978345737059, 0.05202905520612079, 7.648517331413413e-11] Iteration: 0 Calculation: 3 Value = -0.259188 Position: [-0.05356018556689876, -0.03811950981379673, 0.09934222081152533, -0.004420180137104539, 0.00621061683061597, 9.129900644850814e-12] Iteration: 0 Calculation: 4 Value = -0.741777 Position: [-0.0018972980288040964, -0.0013503327156766355, 0.003519065472379799, -0.00015657897694571133, 0.0002200028051745136, 3.234145347576637e-13] Iteration: 0 Calculation: 5 Value = -0.741777 Position: [-0.0018972980288040964, -0.0013503327156766355, 0.003519065472379799, -0.00015657897694571133, 0.0002200028051745136, 3.234145347576637e-13] Iteration: 1 Calculation: 6 Value = -0.764069 Position: [-0.008864090218485405, -0.007374896592515705, 0.020338116205582384, -0.0006576375484633565, 0.0012860372951096447, 0.00022307664983305773] Iteration: 1 Calculation: 7 Value = -0.764069 Position: [-0.008864090218485405, -0.007374896592515705, 0.020338116205582384, -0.0006576375484633565, 0.0012860372951096447, 0.00022307664983305773] Iteration: 2 Calculation: 8 Value = -0.768639 Position: [-0.007362369143132123, -0.005453990604406128, 0.01819539033060534, -0.0003739565466923287, 0.0012063875812397637, 0.0002982793118707005] Iteration: 2 Calculation: 9 Value = -0.768639 Position: [-0.007362369143132123, -0.005453990604406128, 0.01819539033060534, -0.0003739565466923287, 0.0012063875812397637, 0.0002982793118707005] Iteration: 3 Calculation: 10 Value = -0.769345 Position: [-0.0063722110784427445, -0.004674860804162271, 0.01869368990204535, -0.0001296212038001693, 0.0012940408600778173, 0.0004709802964571845] Iteration: 3 Calculation: 11 Value = -0.769345 Position: [-0.0063722110784427445, -0.004674860804162271, 0.01869368990204535, -0.0001296212038001693, 0.0012940408600778173, 0.0004709802964571845] Iteration: 4 Calculation: 12 Value = -0.771464 Position: [0.007388884078228691, 0.008516254318087854, 0.0293297785177389, 0.003835853083661105, 0.00290783602505402, 0.0032057741175897177] Iteration: 4 Calculation: 13 Value = -0.771464 Position: [0.007388884078228691, 0.008516254318087854, 0.0293297785177389, 0.003835853083661105, 0.00290783602505402, 0.0032057741175897177] Iteration: 5 Calculation: 14 Value = -0.771616 Position: [0.03099193061558464, 0.032248721416564013, 0.05173840999553268, 0.011093456031267445, 0.006026166796194969, 0.008235101260558113] Iteration: 5 Calculation: 15 Value = -0.771616 Position: [0.03099193061558464, 0.032248721416564013, 0.05173840999553268, 0.011093456031267445, 0.006026166796194969, 0.008235101260558113] -------------- next part -------------- A non-text attachment was scrubbed... Name: tester.cpp Type: text/x-c++src Size: 1141 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Correlator3D.cpp Type: text/x-c++src Size: 18667 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Correlator3D.h Type: text/x-chdr Size: 4592 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rotatedImage.nrrd Type: application/octet-stream Size: 1366 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: fixedImage.nrrd Type: application/octet-stream Size: 1159 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ 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 tammy.diprima at stonybrook.edu Sat Aug 27 16:04:13 2016 From: tammy.diprima at stonybrook.edu (Tammy DiPrima) Date: Sat, 27 Aug 2016 16:04:13 -0400 Subject: [ITK] [ITK-users] max min image matrix Message-ID: Hello, Is StatisticsImageFilter->GetMaximum() and GetMinimum() the ITK functions that calculate the max/min values in the 2D image array? I?m running the example code from ITKWikiExamples , and the output is: Mean: 23.5875 Std.: 73.8819 Min: Max: ? I modified the code to write the image to file (attached). As far as I can tell, statisticsImageFilter->GetMinimum() should be 0 and statisticsImageFilter->GetMaximum() should be 255. Is GetMinimum() and GetMaximum() not the right functions? Thanks in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 3886 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ 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 chinander at gmail.com Sat Aug 27 16:33:16 2016 From: chinander at gmail.com (Mike Chinander) Date: Sat, 27 Aug 2016 15:33:16 -0500 Subject: [ITK] [ITK-users] max min image matrix In-Reply-To: References: Message-ID: Since the image type is unsigned char, cout is interpreting the values of GetMaximum() and GetMinimum as chars. Cast the result to int before sending to cout: std::cout << "Min: " << static_cast(statisticsImageFilter->GetMinimum()) << std::endl; std::cout << "Max: " << static_cast(statisticsImageFilter->GetMaximum()) << std::endl; On Sat, Aug 27, 2016 at 3:04 PM, Tammy DiPrima wrote: > Hello, > > Is StatisticsImageFilter->GetMaximum() and GetMinimum() the ITK functions > that calculate the max/min values in the 2D image array? > I?m running the example code from ITKWikiExamples > , > and the output is: > > Mean: 23.5875 > Std.: 73.8819 > Min: > Max: ? > > I modified the code to write the image to file (attached). As far as I > can tell, statisticsImageFilter->GetMinimum() should be 0 > and statisticsImageFilter->GetMaximum() should be 255. > > Is GetMinimum() and GetMaximum() not the right functions? > > Thanks in advance > > > _____________________________________ > 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: image.png Type: image/png Size: 3886 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ 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 jaroslawlobaza at gmail.com Sun Aug 28 05:23:36 2016 From: jaroslawlobaza at gmail.com (Krakers) Date: Sun, 28 Aug 2016 02:23:36 -0700 (MST) Subject: [ITK] [ITK-users] Reopening data after conversion vtk -> itk -> vtk Message-ID: <1472376216630-37443.post@n7.nabble.com> Hello wise itk users. Context of my situation is : - I use vtk for opening dicom image and convert it to ITK image, with VTKImageToImageFilter - process it with MedianImageFilter - convert back to VTK and save to a file. I encounter a problem with opening saved data after conversion. I don't get any specific error, maybe I should compile with debug options? I will be greatfull for every advice. -- View this message in context: http://itk-users.7.n7.nabble.com/Reopening-data-after-conversion-vtk-itk-vtk-tp37443.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 dzenanz at gmail.com Mon Aug 29 09:29:13 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 29 Aug 2016 09:29:13 -0400 Subject: [ITK] [ITK-users] Reopening data after conversion vtk -> itk -> vtk In-Reply-To: <1472376216630-37443.post@n7.nabble.com> References: <1472376216630-37443.post@n7.nabble.com> Message-ID: Hi Jaroslaw, what kind of problem do you encounter? Crash? Exception? What is the error message? Or maybe the image loads incorrectly? Why are you using VTK to load DICOM data? Using ITK only simplifies things. Regards, D?enan On Sun, Aug 28, 2016 at 5:23 AM, Krakers wrote: > Hello wise itk users. > > Context of my situation is : > - I use vtk for opening dicom image and convert it to ITK image, with > VTKImageToImageFilter > - process it with MedianImageFilter > - convert back to VTK and save to a file. > > I encounter a problem with opening saved data after conversion. > I don't get any specific error, maybe I should compile with debug options? > I will be greatfull for every advice. > > > > > > -- > View this message in context: http://itk-users.7.n7.nabble. > com/Reopening-data-after-conversion-vtk-itk-vtk-tp37443.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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ 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 sepideh.movaghati at gmail.com Mon Aug 29 12:23:37 2016 From: sepideh.movaghati at gmail.com (sepideh movaghati) Date: Mon, 29 Aug 2016 12:23:37 -0400 Subject: [ITK] [ITK-users] Problem Using ScaleEstimator in V4 Registration In-Reply-To: References: Message-ID: Hi D?enan, Thanks for your response. You are right. The functions I mentioned are setting the sampling strategy of the scale estimator not the registration metric. In my tests I made sure that I use a regular sampling for registration metric. The problem I mentioned is causing a non-deterministic behavior when changing the order of two completely unrelated registrations. I reposted the same issue in insight-developer mailing and there I explained this non-deterministic behavior in detail. Thanks a lot, Sepide On Wed, Aug 24, 2016 at 2:45 PM, D?enan Zuki? wrote: > Hi Sepide, > > if I remember correctly, registration framework is advertised as using > random sampling. And the function you mention is not used for sampling the > registration metric, but rather for parameter scale estimation. So even if > random sampling usage for scale estimation is unintentional, I don't > believe it is a major problem. Perhaps someone who participated in writing > the registration framework can chime in? > > Regards, > D?enan > > On Wed, Aug 24, 2016 at 1:52 PM, Sepide Movaghati < > sepideh.movaghati at gmail.com> wrote: > >> Hi, >> >> I found a problem while I was using ScaleEstimator in v4 registration: >> >> In itkRegistrationParametersScaleEstimator class there are two functions >> SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the >> sampling strategy is chosen based on the Transformation type. For example >> if the transformation is of type displacement field or BSpline, it uses all >> of the samples. If transformation is any regular affine or rigid >> transformation (child of class MatrixOffsetTransformBase) it performs >> corner sampling. However, if the transformation is none of the known ones, >> it uses Random Sampling. >> >> Here is the problem: in itkImageRegistrationMethodv4.hxx the Metric >> transformation is set using ->SetMovingTransform() and it is always a >> CompositeTransform! Therefore, ScaleEstimator cannot detect the >> transformation type and it always fall into "else" which is using Random >> Sampling! It does not matter if you do a multilevel registration or not. >> The transformation is always of type CompositeTransform even if you do just >> a one level rigid transform! >> >> I would appreciate if you let me know if I was correct about this issue >> and whether we can consider this a bug and hope to get it fixed for the >> upcoming versions. >> >> Thanks a lot for your consideration in advance, >> Sepide >> _____________________________________ >> 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 -------------- _____________________________________ 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 sepideh.movaghati at gmail.com Mon Aug 29 13:54:45 2016 From: sepideh.movaghati at gmail.com (sepideh movaghati) Date: Mon, 29 Aug 2016 13:54:45 -0400 Subject: [ITK] [ITK-dev] Source of Non-deterministic behavior of Registration v4 Message-ID: Hi, I posted the same issue on insight-users initially but then I thought it would be more relevant to developers mailing list. I was observing an unexpected non-deterministic behavior while changing the order of completely unrelated registrations. In the following example, my test revealed that transform and transform' are not identical: transform = Register(image1, image2); vs. transform-foo = Register(image-foo1, image-foo2); transform' = Register(image1, image2); I looked into the source of this non-deterministic behavior while making sure the metric sampling strategy has been set to Regular. Eventually I found the cause of the problem in itkRegistrationParametersScaleEstimator class. In this class there are two functions SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the sampling strategy is chosen based on the Transformation type. For example if the transformation is of type displacement field or BSpline, it uses all of the samples. If transformation is any regular affine or rigid transformation (child of class MatrixOffsetTransformBase) it performs corner sampling. However, if the transformation is none of the known ones, it uses Random Sampling. In my test I was using one level rigid transformation (v4). But here is were the problem happens: in itkImageRegistrationMethodv4.hxx the Metric transformation (MovingTransform) always set to a CompositeTransform! Therefore, ScaleEstimator cannot detect the transformation type and it always fall into "else" which is using Random Sampling! It does not matter if you do a multilevel registration or not. The transformation is always of type CompositeTransform. By changing the sampling strategy in ScaleEstimator class from Random to a regular sampling, the non-deterministic behavior is gone and transform and transform' in the above example become identical. I would appreciate if you let me know if I was correct about this issue and whether we can consider this a bug and hope to get it fixed for the upcoming versions. Thanks a lot for your consideration in advance, Sepide -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ 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://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-developers From blowekamp at mail.nih.gov Mon Aug 29 14:06:46 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Mon, 29 Aug 2016 18:06:46 +0000 Subject: [ITK] [ITK-dev] Source of Non-deterministic behavior of Registration v4 In-Reply-To: References: Message-ID: Hello, There should be a way to set the seed to a fixed value. Sorry I don?t have anything more specific, but grep through ITK for ?SetSeed? and there should be some tests or examples which do this. If you set a consistent seed before performing a registration ( inside your Register method ) it may solve your problem. HTH, Brad > On Aug 29, 2016, at 1:54 PM, sepideh movaghati wrote: > > Hi, > > I posted the same issue on insight-users initially but then I thought it would be more relevant to developers mailing list. > > I was observing an unexpected non-deterministic behavior while changing the order of completely unrelated registrations. In the following example, my test revealed that transform and transform' are not identical: > > transform = Register(image1, image2); > > vs. > > transform-foo = Register(image-foo1, image-foo2); > transform' = Register(image1, image2); > > > I looked into the source of this non-deterministic behavior while making sure the metric sampling strategy has been set to Regular. > Eventually I found the cause of the problem in itkRegistrationParametersScaleEstimator class. In this class there are two functions SetScaleSamplingStrategy and SetStepScaleSamplingStrategy. In both the sampling strategy is chosen based on the Transformation type. For example if the transformation is of type displacement field or BSpline, it uses all of the samples. If transformation is any regular affine or rigid transformation (child of class MatrixOffsetTransformBase) it performs corner sampling. However, if the transformation is none of the known ones, it uses Random Sampling. > > In my test I was using one level rigid transformation (v4). But here is were the problem happens: in itkImageRegistrationMethodv4.hxx the Metric transformation (MovingTransform) always set to a CompositeTransform! Therefore, ScaleEstimator cannot detect the transformation type and it always fall into "else" which is using Random Sampling! It does not matter if you do a multilevel registration or not. The transformation is always of type CompositeTransform. > > By changing the sampling strategy in ScaleEstimator class from Random to a regular sampling, the non-deterministic behavior is gone and transform and transform' in the above example become identical. > > I would appreciate if you let me know if I was correct about this issue and whether we can consider this a bug and hope to get it fixed for the upcoming versions. > > Thanks a lot for your consideration in advance, > Sepide > _______________________________________________ > 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://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-developers _______________________________________________ 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://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-developers From tammy.diprima at stonybrook.edu Tue Aug 30 12:25:22 2016 From: tammy.diprima at stonybrook.edu (Tammy Diprima) Date: Tue, 30 Aug 2016 12:25:22 -0400 Subject: [ITK] [ITK-users] built opencv bridge but can't find Message-ID: I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. I recompiled using make. In my C++ program I'm including the headers: #include *#include "itkOpenCVImageBridge.h"* But it's saying "cannot find itkOpenCVImageBridge.h" I put messaging output in my CMakeLists.txt: include_directories(${OpenCV_INCLUDE_DIRS}) MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) And the output shows that the directory is incorrect: *OpenCV_INCLUDE_DIRS* /usr/local/include/opencv*/usr/local/include* This might be what's causing the problem. I tried to do a set() but it didn't seem to fix it. Can somebody please advise? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From tammy.diprima at stonybrook.edu Tue Aug 30 12:35:34 2016 From: tammy.diprima at stonybrook.edu (Tammy Diprima) Date: Tue, 30 Aug 2016 12:35:34 -0400 Subject: [ITK] [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: OK I have an update. So, set() worked to reset the broken variable (workaround). And then I had to locate itkOpenCVImageBridge.* and copy the files to the location. That worked. But -- does anybody have an idea how I could have broken OpenCV_INCLUDE_DIRS in the first place? And also -- something tells me I shouldn't have had to copy the source files to the OpenCV_INCLUDE_DIRS. What did I do wrong? Thanks again. *30 August 2016 at 12:25:* > I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. > I recompiled using make. > > In my C++ program I'm including the headers: > #include > *#include "itkOpenCVImageBridge.h"* > > But it's saying "cannot find itkOpenCVImageBridge.h" > > I put messaging output in my CMakeLists.txt: > include_directories(${OpenCV_INCLUDE_DIRS}) > MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) > > And the output shows that the directory is incorrect: > *OpenCV_INCLUDE_DIRS* /usr/local/include/opencv*/usr/local/include* > > This might be what's causing the problem. I tried to do a set() but it > didn't seem to fix it. > > Can somebody please advise? > > Thanks. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Aug 30 13:28:38 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 Aug 2016 13:28:38 -0400 Subject: [ITK] [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: Hi Tammy, Your project's CMakeLists.txt needs: find_package(ITK) include(${ITK_USE_FILE}) The "include(${ITK_USE_FILE})" command calls "include_directories" with the directories containing itkOpenCVImageBridge.h. HTH, Matt On Tue, Aug 30, 2016 at 12:35 PM, Tammy Diprima wrote: > OK I have an update. So, set() worked to reset the broken variable > (workaround). And then I had to locate itkOpenCVImageBridge.* and copy the > files to the location. > > That worked. > > But -- does anybody have an idea how I could have broken OpenCV_INCLUDE_DIRS > in the first place? > And also -- something tells me I shouldn't have had to copy the source files > to the OpenCV_INCLUDE_DIRS. What did I do wrong? > > Thanks again. > > > > 30 August 2016 at 12:25: > >> I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. >> I recompiled using make. >> >> In my C++ program I'm including the headers: >> #include >> #include "itkOpenCVImageBridge.h" >> >> But it's saying "cannot find itkOpenCVImageBridge.h" >> >> I put messaging output in my CMakeLists.txt: >> include_directories(${OpenCV_INCLUDE_DIRS}) >> MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) >> >> And the output shows that the directory is incorrect: >> OpenCV_INCLUDE_DIRS /usr/local/include/opencv/usr/local/include >> >> This might be what's causing the problem. I tried to do a set() but it >> didn't seem to fix it. >> >> Can somebody please advise? >> >> 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 > _____________________________________ 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 tammy.diprima at stonybrook.edu Tue Aug 30 19:52:56 2016 From: tammy.diprima at stonybrook.edu (Tammy Diprima) Date: Tue, 30 Aug 2016 19:52:56 -0400 Subject: [ITK] [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: Hi Matt, Thank you for the advice. You're right, in that I need not include any OpenCV dirs; it's all about ITK. The problem is, I'm already doing the: find_package( ITK REQUIRED ) include( ${ITK_USE_FILE} ) The compiler's not happy unless I physically copy the header and source files (itkOpenCVImageBridge.*) from [ ITK-SOURCE-DIR]/Modules/Video/BridgeOpenCV/include to a location CMakeLists knows about (in an include directory). Which makes sense, but I would have thought when I built ITK with the BridgeOpenCV flag turned on that it would have been copied during that particular process. Oh well. At least it's working now. Cheers, thanks a lot. Tammy On 30 August 2016 at 13:28, Matt McCormick wrote: > Hi Tammy, > > Your project's CMakeLists.txt needs: > > find_package(ITK) > include(${ITK_USE_FILE}) > > The "include(${ITK_USE_FILE})" command calls "include_directories" > with the directories containing itkOpenCVImageBridge.h. > > HTH, > Matt > > On Tue, Aug 30, 2016 at 12:35 PM, Tammy Diprima > wrote: > > OK I have an update. So, set() worked to reset the broken variable > > (workaround). And then I had to locate itkOpenCVImageBridge.* and copy > the > > files to the location. > > > > That worked. > > > > But -- does anybody have an idea how I could have broken > OpenCV_INCLUDE_DIRS > > in the first place? > > And also -- something tells me I shouldn't have had to copy the source > files > > to the OpenCV_INCLUDE_DIRS. What did I do wrong? > > > > Thanks again. > > > > > > > > 30 August 2016 at 12:25: > > > >> I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. > >> I recompiled using make. > >> > >> In my C++ program I'm including the headers: > >> #include > >> #include "itkOpenCVImageBridge.h" > >> > >> But it's saying "cannot find itkOpenCVImageBridge.h" > >> > >> I put messaging output in my CMakeLists.txt: > >> include_directories(${OpenCV_INCLUDE_DIRS}) > >> MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) > >> > >> And the output shows that the directory is incorrect: > >> OpenCV_INCLUDE_DIRS /usr/local/include/opencv/usr/local/include > >> > >> This might be what's causing the problem. I tried to do a set() but it > >> didn't seem to fix it. > >> > >> Can somebody please advise? > >> > >> 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 -------------- _____________________________________ 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 tammy.diprima at stonybrook.edu Wed Aug 31 09:32:11 2016 From: tammy.diprima at stonybrook.edu (Tammy Diprima) Date: Wed, 31 Aug 2016 09:32:11 -0400 Subject: [ITK] [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: I think I just answered my own question. I forgot *sudo make install*. Now both itkOpenCVImageBridge files are where they're supposed to be, in /usr/local/include/ITK-4.8. Matt, the chat with you totally helped. Sorry to interrupt your day, but -- Thanks very much. I really appreciate it. -- T *30 August 2016 at 19:52:* > Hi Matt, > > Thank you for the advice. You're right, in that I need not include any > OpenCV dirs; it's all about ITK. > The problem is, I'm already doing the: > > find_package( ITK REQUIRED ) > include( ${ITK_USE_FILE} ) > > The compiler's not happy unless I physically copy the header and source > files (itkOpenCVImageBridge.*) from [ITK-SOURCE-DIR]/Modules/ > Video/BridgeOpenCV/include to a location CMakeLists knows about (in an > include directory). Which makes sense, but I would have thought when I > built ITK with the BridgeOpenCV flag turned on that it would have been > copied during that particular process. Oh well. At least it's working now. > > Cheers, thanks a lot. > Tammy > > > On 30 August 2016 at 13:28, Matt McCormick > wrote: > >> Hi Tammy, >> >> Your project's CMakeLists.txt needs: >> >> find_package(ITK) >> include(${ITK_USE_FILE}) >> >> The "include(${ITK_USE_FILE})" command calls "include_directories" >> with the directories containing itkOpenCVImageBridge.h. >> >> HTH, >> Matt >> >> On Tue, Aug 30, 2016 at 12:35 PM, Tammy Diprima >> wrote: >> > OK I have an update. So, set() worked to reset the broken variable >> > (workaround). And then I had to locate itkOpenCVImageBridge.* and copy >> the >> > files to the location. >> > >> > That worked. >> > >> > But -- does anybody have an idea how I could have broken >> OpenCV_INCLUDE_DIRS >> > in the first place? >> > And also -- something tells me I shouldn't have had to copy the source >> files >> > to the OpenCV_INCLUDE_DIRS. What did I do wrong? >> > >> > Thanks again. >> > >> > >> > >> > 30 August 2016 at 12:25: >> > >> >> I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. >> >> I recompiled using make. >> >> >> >> In my C++ program I'm including the headers: >> >> #include >> >> #include "itkOpenCVImageBridge.h" >> >> >> >> But it's saying "cannot find itkOpenCVImageBridge.h" >> >> >> >> I put messaging output in my CMakeLists.txt: >> >> include_directories(${OpenCV_INCLUDE_DIRS}) >> >> MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) >> >> >> >> And the output shows that the directory is incorrect: >> >> OpenCV_INCLUDE_DIRS /usr/local/include/opencv/usr/local/include >> >> >> >> This might be what's causing the problem. I tried to do a set() but it >> >> didn't seem to fix it. >> >> >> >> Can somebody please advise? >> >> >> >> 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 -------------- _____________________________________ 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 Wed Aug 31 10:09:38 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 31 Aug 2016 10:09:38 -0400 Subject: [ITK] [ITK-users] built opencv bridge but can't find In-Reply-To: References: Message-ID: Hi Tammy, Thanks for sharing your progress and the update! Welcome to ITK :-) Matt On Wed, Aug 31, 2016 at 9:32 AM, Tammy Diprima wrote: > I think I just answered my own question. I forgot sudo make install. Now > both itkOpenCVImageBridge files are where they're supposed to be, in > /usr/local/include/ITK-4.8. > > Matt, the chat with you totally helped. Sorry to interrupt your day, but -- > Thanks very much. I really appreciate it. -- T > > > 30 August 2016 at 19:52: > >> Hi Matt, >> >> Thank you for the advice. You're right, in that I need not include any >> OpenCV dirs; it's all about ITK. >> The problem is, I'm already doing the: >> >> find_package( ITK REQUIRED ) >> include( ${ITK_USE_FILE} ) >> >> The compiler's not happy unless I physically copy the header and source >> files (itkOpenCVImageBridge.*) from >> [ITK-SOURCE-DIR]/Modules/Video/BridgeOpenCV/include to a location CMakeLists >> knows about (in an include directory). Which makes sense, but I would have >> thought when I built ITK with the BridgeOpenCV flag turned on that it would >> have been copied during that particular process. Oh well. At least it's >> working now. >> >> Cheers, thanks a lot. >> Tammy >> >> >> On 30 August 2016 at 13:28, Matt McCormick >> wrote: >>> >>> Hi Tammy, >>> >>> Your project's CMakeLists.txt needs: >>> >>> find_package(ITK) >>> include(${ITK_USE_FILE}) >>> >>> The "include(${ITK_USE_FILE})" command calls "include_directories" >>> with the directories containing itkOpenCVImageBridge.h. >>> >>> HTH, >>> Matt >>> >>> On Tue, Aug 30, 2016 at 12:35 PM, Tammy Diprima >>> wrote: >>> > OK I have an update. So, set() worked to reset the broken variable >>> > (workaround). And then I had to locate itkOpenCVImageBridge.* and copy >>> > the >>> > files to the location. >>> > >>> > That worked. >>> > >>> > But -- does anybody have an idea how I could have broken >>> > OpenCV_INCLUDE_DIRS >>> > in the first place? >>> > And also -- something tells me I shouldn't have had to copy the source >>> > files >>> > to the OpenCV_INCLUDE_DIRS. What did I do wrong? >>> > >>> > Thanks again. >>> > >>> > >>> > >>> > 30 August 2016 at 12:25: >>> > >>> >> I re-ran ccmake on ITK with Module_ITKVideoBridgeOpenCV:BOOL=ON. >>> >> I recompiled using make. >>> >> >>> >> In my C++ program I'm including the headers: >>> >> #include >>> >> #include "itkOpenCVImageBridge.h" >>> >> >>> >> But it's saying "cannot find itkOpenCVImageBridge.h" >>> >> >>> >> I put messaging output in my CMakeLists.txt: >>> >> include_directories(${OpenCV_INCLUDE_DIRS}) >>> >> MESSAGE( STATUS "OpenCV_INCLUDE_DIRS " ${OpenCV_INCLUDE_DIRS} ) >>> >> >>> >> And the output shows that the directory is incorrect: >>> >> OpenCV_INCLUDE_DIRS /usr/local/include/opencv/usr/local/include >>> >> >>> >> This might be what's causing the problem. I tried to do a set() but >>> >> it >>> >> didn't seem to fix it. >>> >> >>> >> Can somebody please advise? >>> >> >>> >> 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 >>> > >> >> > _____________________________________ 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 Wed Aug 31 10:16:38 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 31 Aug 2016 10:16:38 -0400 Subject: [ITK] [ITK-users] QVtkWidget beginner questions In-Reply-To: <1472626890697-37451.post@n7.nabble.com> References: <1472626890697-37451.post@n7.nabble.com> Message-ID: Hello Ibraheem, Welcome to ITK :-) Please see comments inline below. On Wed, Aug 31, 2016 at 3:01 AM, Ibraheem via Insight-users wrote: > Dear all, > I am writing some ITK examples while learning it following different > tutorials . I have Ubuntu 14.04. I build these tools from the source: ITK > 4.10, VTK 7.0, QT5.7 and CMake 3.6.1 > In example 2, I wrote a simple GUI application that read a DICOM volume from > a folder, displays it in a QVtkWidget, thresholds the slice and displays it > in another QVtkWidget. Save the resulted thresholded volume in a new folder. > I had some problems that I was able to solve like the dark output and the > flipping, see the bellow code comments. Excellent. Thanks for sharing your efforts! > My questions: > 1- Is there a way to filter and write all the images at once instead of > using the for loop? To write to an image series in general, there is an itk::ImageSeriesWriter. > 2- Writing the way I did make the output volume lost some origin > information i.e value, 0,0 . What did I do wrong? Writing DICOMs (correctly) is currently a very tricky endeavour. There are currently some experiments underway to make this easier. However, until that time, it is recommended to use another format, like MetaImage, for writing files. > 3- I read some posts about using QVtkWidget2 and QVtkWidget3 but I > couldn't find them in my vtk build, is there some options I missed when I > built vtk? > 4- How can I display a specific plane instead of the axial slices e.g. > display a coronal slice. > 5- How can I get the voxel information when I point in the QVTkWidget? I > am not sure if the mapping I used is correct. These questions are welcome, but the VTK mailing list is a better place to discuss these issues. Matt _____________________________________ 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 tevain at telecom-paristech.fr Wed Aug 31 11:47:47 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Wed, 31 Aug 2016 17:47:47 +0200 (CEST) Subject: [ITK] Registration framework v3 / v4 and Slicer In-Reply-To: <1547929136.51028728.1472657178193.JavaMail.zimbra@enst.fr> Message-ID: <184910079.51087910.1472658467552.JavaMail.zimbra@enst.fr> Hello everybody, Question about the difference between the v3 and v4 registration frameworks: I conducted some experiments on registration in Slicer with the GeneralRegistration module (from the BRAINS suite), and now I try to get the same result in my own program. I've learned from Github that the module use the v4 framework, but I'm working with ITK 4.5, and unfortunately this version doesn't bring all that's needed for copying the Slicer code. So, I've tried to mimick the pipeline with the v3 framework, staying as close as possible (same metrics, same optimizers, same transformation chain, same parameters, etc). But results are quite differents, not bad but definetely not as accurate as the Slicer one (even after toying with the parameters). I haven't found a clear comparison document, so does the difference between the two frameworks can explain such results ? Thanks, Tim From abou_zeid_wassim at hotmail.com Wed Aug 31 12:21:00 2016 From: abou_zeid_wassim at hotmail.com (wassim bouzeid) Date: Wed, 31 Aug 2016 16:21:00 +0000 Subject: [ITK] Joint Entropy for Mutual Information Message-ID: Hello Everyone, I want to compute the normalized mutual information between two images X and Y to be registered using the joint histograms. For this purpose, I want to compute the joint entropy of the process X with its upper neighbor in the lattice H(X,Xu) and the joint entropy of the process Y in lattice Y with its upper neighbor of its corresponding process in lattice X H(Y,Xu) using the NormalizedMutualInformationHistogramImageToImageMetric Class. This Class computes the histograms by iterating through the bins and not through each image dimensions i, j and k. I have computed the joint entropy of X and Y H(X,Y) but I am not able to go further with computing H(X,Xu) and H(Y,Xu). Thanks for your help, Wassim -------------- next part -------------- An HTML attachment was scrubbed... URL: From lasso at queensu.ca Wed Aug 31 12:30:41 2016 From: lasso at queensu.ca (Andras Lasso) Date: Wed, 31 Aug 2016 16:30:41 +0000 Subject: [ITK] Registration framework v3 / v4 and Slicer In-Reply-To: <184910079.51087910.1472658467552.JavaMail.zimbra@enst.fr> References: <1547929136.51028728.1472657178193.JavaMail.zimbra@enst.fr> <184910079.51087910.1472658467552.JavaMail.zimbra@enst.fr> Message-ID: Registration optimizers and metrics have been changed in ITKv4, so regardless of what parameters you choose, you won't get the same results. We've worked a lot on getting similar results with ITKv4 as with ITKv3 but the closest was to get slightly more accurate results with not significantly longer computation time. See some of the discussion here: http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html If you want to use the ITKv3 registration framework then you may check out an older BRAINS version that still used ITKv3. Andras -----Original Message----- From: Community [mailto:community-bounces at itk.org] On Behalf Of Timothee Evain Sent: August 31, 2016 11:48 To: community at itk.org Subject: [ITK] Registration framework v3 / v4 and Slicer Hello everybody, Question about the difference between the v3 and v4 registration frameworks: I conducted some experiments on registration in Slicer with the GeneralRegistration module (from the BRAINS suite), and now I try to get the same result in my own program. I've learned from Github that the module use the v4 framework, but I'm working with ITK 4.5, and unfortunately this version doesn't bring all that's needed for copying the Slicer code. So, I've tried to mimick the pipeline with the v3 framework, staying as close as possible (same metrics, same optimizers, same transformation chain, same parameters, etc). But results are quite differents, not bad but definetely not as accurate as the Slicer one (even after toying with the parameters). I haven't found a clear comparison document, so does the difference between the two frameworks can explain such results ? Thanks, Tim _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From noreply at insightsoftwareconsortium.org Wed Aug 31 17:15:49 2016 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Wed, 31 Aug 2016 17:15:49 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Two Luis Miguel fans walk into a bar in Nagoya ---> (yada, yada, yada) ---> an ITK-implementation of a popular patch-based denoising filter Message-ID: <20160831211549.9CC363D620C4@insight-journal.org> Hello, A new submission has been added to the Insight Journal. Title: Two Luis Miguel fans walk into a bar in Nagoya ---> (yada, yada, yada) ---> an ITK-implementation of a popular patch-based denoising filter Authors: Tustison N., Manjon Herrera J. Abstract: This document describes an ITK implementation of the adaptive patch-based image denoising algorithm described in cite{Manjon:2010aa}. This offering consists of the templated class itkPatchBasedDenoisingImageFilter interfaced through the DenoiseImage program which includes its own interface program. We include a couple of examples. Download and review this publication at: http://hdl.handle.net/10380/3564 Generated by the Insight Journal You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://insight-journal.org/ . _____________________________________ 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 jeannasheen at gmail.com Wed Aug 10 00:01:57 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Wed, 10 Aug 2016 04:01:57 -0000 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Thanks for letting me know. I've changed the output image type to float and now it no longer shows up as just black. I've attached my output image (the image on the left is the input image; the image on the right is the output image). However, the filter seems not to detect blood vessels like I hoped, even after testing various values of Alpha, Beta, and Gamma. I was wondering if anybody has suggestions on how to improve the vessel detection? Thanks, Jeanna On Tue, Aug 9, 2016 at 6:29 AM, D?enan Zuki? wrote: > Hi Jeanna, > > output of this filter is in [0,1] range, and if your output image type is > not float then you will get an all-black image. Here is an example > invocation: > > typedef itk::HessianToObjectnessMeasureImageFilter< HessianImageType, > FloatImageType > ObjectnessFilterType; > ObjectnessFilterType::Pointer objectnessFilter = > ObjectnessFilterType::New(); > objectnessFilter->SetBrightObject(true); > objectnessFilter->SetScaleObjectnessMeasure(false); > objectnessFilter->SetObjectDimension(2.5); > objectnessFilter->SetAlpha(0.5); > objectnessFilter->SetBeta(1.0); > objectnessFilter->SetGamma(5.0); > objectnessFilter->SetInput(hc->GetOutput()); > objectnessFilter->Update(); > FloatImageType::Pointer objectness = objectnessFilter->GetOutput(); > > On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. wrote: > >> Actually, I found a way to display the images to the screen. However, I >> am still not quite sure how to detect the blood vessels in my image. When I >> apply the itkHessianToObjectnessMeasureImageFilter on my image, it just >> turns out black. I was wondering if this is because there is not enough >> contrast between the vessels and the background. If so, is there any >> setting or threshold on the filter I can change so that it can detect the >> blood vessels? >> >> Thanks, >> Jeanna >> >> On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. wrote: >> >>> Hi Timothee, >>> >>> I'm using the itk:HessianToObjectnessMeasureImageFilter that you >>> suggested. I was wondering if there is any way for me to view the image on >>> the screen after it has been run through the filter, and if you have any >>> examples of the filter working on an image. >>> >>> Thanks, >>> Jeanna >>> >>> On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. wrote: >>> >>>> Hi Timothee, >>>> >>>> Thank you for replying. I will look into these methods. >>>> >>>> Jeanna >>>> >>>> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < >>>> tevain at telecom-paristech.fr> wrote: >>>> >>>>> Hello Jeanna, >>>>> >>>>> I think this will be difficult just with the LabelMap framework. >>>>> Usually to filter vessels you rely on some measures based on their >>>>> shape, but in the ShapeLabelObject, the elongation measure is "the ratio of >>>>> the longest physical size of the region [i.e. the bounding box] on one >>>>> dimension and its smallest physical size". This is a quite coarse measure, >>>>> sensitive to rotation, and I doubt it will be useful in your case. >>>>> Aside from the attribute problem, you also have to detect the vessels >>>>> prior to filtering them (i.e. getting a binary or a label image of >>>>> vessels), and the LabelMap framework doesn't do that. >>>>> >>>>> I would suggest taking a look at these other methods: >>>>> -Frangi's vesselness (implemented in itk through these filter : >>>>> itkHessianToObjectnessMeasureImageFilter or >>>>> itkHessian3DToVesselnessMeasureImageFilter) >>>>> -Ranking Orientation Responses of Path Openings, aka RORPO ( >>>>> http://path-openings.github.io/RORPO/) >>>>> -Fast Marching (itkFastMarchingImageFilter) >>>>> >>>>> HTH, >>>>> >>>>> Tim >>>>> >>>>> ----- Mail original ----- >>>>> De: "Jeanna S." >>>>> ?: community at itk.org >>>>> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >>>>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >>>>> >>>>> Hello, >>>>> >>>>> I am trying to process the attached image using the >>>>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >>>>> retina, and I want to use the image filter to remove the blood vessels from >>>>> the picture (the blood vessels are the long, skinny, branching lines). I >>>>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >>>>> ) would be able to do this with a little modification, and if so, which >>>>> attribute would be the most useful to identify and remove the blood vessels. >>>>> >>>>> Thanks in advance. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>>> >>>> >>>> >>>> -- >>>> when the rich wage war, it's the poor who die >>>> >>> >>> >>> >>> -- >>> when the rich wage war, it's the poor who die >>> >> >> >> >> -- >> when the rich wage war, it's the poor who die >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: HessianToObjectnessMeasureImageFilter.png Type: image/png Size: 273518 bytes Desc: not available URL: From jeannasheen at gmail.com Wed Aug 10 21:31:14 2016 From: jeannasheen at gmail.com (Jeanna S.) Date: Thu, 11 Aug 2016 01:31:14 -0000 Subject: [ITK] ITK Example ShapeOpeningLabelMapFilter In-Reply-To: References: <1629031236.37139606.1470214761548.JavaMail.zimbra@enst.fr> Message-ID: Hi D?enan, I actually found that I had to put objectnessFilter->SetScaleObjectnessMeasure(false);. I already had objectnessFilter->SetBrightObject(false); and objectnessFilter->SetObjectDimension(1);. Now the output, which I've attached, is much better, though it still shows some of the blobs. Thanks for all your help. Jeanna On Wed, Aug 10, 2016 at 4:59 AM, D?enan Zuki? wrote: > Hi Jeanna, > > by taking a look at the output, you need objectnessFilter-> > SetBrightObject(false); and a larger size of > objectnessFilter->SetObjectDimension(); > > HTH, > D?enan > > On Wed, Aug 10, 2016 at 12:01 AM, Jeanna S. wrote: > >> Thanks for letting me know. I've changed the output image type to float >> and now it no longer shows up as just black. I've attached my output image >> (the image on the left is the input image; the image on the right is the >> output image). However, the filter seems not to detect blood vessels like I >> hoped, even after testing various values of Alpha, Beta, and Gamma. I was >> wondering if anybody has suggestions on how to improve the vessel detection? >> >> Thanks, >> Jeanna >> >> On Tue, Aug 9, 2016 at 6:29 AM, D?enan Zuki? wrote: >> >>> Hi Jeanna, >>> >>> output of this filter is in [0,1] range, and if your output image type >>> is not float then you will get an all-black image. Here is an example >>> invocation: >>> >>> typedef itk::HessianToObjectnessMeasureImageFilter< >>> HessianImageType, FloatImageType > ObjectnessFilterType; >>> ObjectnessFilterType::Pointer objectnessFilter = >>> ObjectnessFilterType::New(); >>> objectnessFilter->SetBrightObject(true); >>> objectnessFilter->SetScaleObjectnessMeasure(false); >>> objectnessFilter->SetObjectDimension(2.5); >>> objectnessFilter->SetAlpha(0.5); >>> objectnessFilter->SetBeta(1.0); >>> objectnessFilter->SetGamma(5.0); >>> objectnessFilter->SetInput(hc->GetOutput()); >>> objectnessFilter->Update(); >>> FloatImageType::Pointer objectness = objectnessFilter->GetOutput(); >>> >>> On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. wrote: >>> >>>> Actually, I found a way to display the images to the screen. However, I >>>> am still not quite sure how to detect the blood vessels in my image. When I >>>> apply the itkHessianToObjectnessMeasureImageFilter on my image, it >>>> just turns out black. I was wondering if this is because there is not >>>> enough contrast between the vessels and the background. If so, is there any >>>> setting or threshold on the filter I can change so that it can detect the >>>> blood vessels? >>>> >>>> Thanks, >>>> Jeanna >>>> >>>> On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. >>>> wrote: >>>> >>>>> Hi Timothee, >>>>> >>>>> I'm using the itk:HessianToObjectnessMeasureImageFilter that you >>>>> suggested. I was wondering if there is any way for me to view the image on >>>>> the screen after it has been run through the filter, and if you have any >>>>> examples of the filter working on an image. >>>>> >>>>> Thanks, >>>>> Jeanna >>>>> >>>>> On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. >>>>> wrote: >>>>> >>>>>> Hi Timothee, >>>>>> >>>>>> Thank you for replying. I will look into these methods. >>>>>> >>>>>> Jeanna >>>>>> >>>>>> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain < >>>>>> tevain at telecom-paristech.fr> wrote: >>>>>> >>>>>>> Hello Jeanna, >>>>>>> >>>>>>> I think this will be difficult just with the LabelMap framework. >>>>>>> Usually to filter vessels you rely on some measures based on their >>>>>>> shape, but in the ShapeLabelObject, the elongation measure is "the ratio of >>>>>>> the longest physical size of the region [i.e. the bounding box] on one >>>>>>> dimension and its smallest physical size". This is a quite coarse measure, >>>>>>> sensitive to rotation, and I doubt it will be useful in your case. >>>>>>> Aside from the attribute problem, you also have to detect the >>>>>>> vessels prior to filtering them (i.e. getting a binary or a label image of >>>>>>> vessels), and the LabelMap framework doesn't do that. >>>>>>> >>>>>>> I would suggest taking a look at these other methods: >>>>>>> -Frangi's vesselness (implemented in itk through these filter : >>>>>>> itkHessianToObjectnessMeasureImageFilter or >>>>>>> itkHessian3DToVesselnessMeasureImageFilter) >>>>>>> -Ranking Orientation Responses of Path Openings, aka RORPO ( >>>>>>> http://path-openings.github.io/RORPO/) >>>>>>> -Fast Marching (itkFastMarchingImageFilter) >>>>>>> >>>>>>> HTH, >>>>>>> >>>>>>> Tim >>>>>>> >>>>>>> ----- Mail original ----- >>>>>>> De: "Jeanna S." >>>>>>> ?: community at itk.org >>>>>>> Envoy?: Mercredi 3 Ao?t 2016 03:08:42 >>>>>>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter >>>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I am trying to process the attached image using the >>>>>>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a >>>>>>> retina, and I want to use the image filter to remove the blood vessels from >>>>>>> the picture (the blood vessels are the long, skinny, branching lines). I >>>>>>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here >>>>>>> ) would be able to do this with a little modification, and if so, which >>>>>>> attribute would be the most useful to identify and remove the blood vessels. >>>>>>> >>>>>>> Thanks in advance. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Community mailing list >>>>>>> Community at itk.org >>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> when the rich wage war, it's the poor who die >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> when the rich wage war, it's the poor who die >>>>> >>>> >>>> >>>> >>>> -- >>>> when the rich wage war, it's the poor who die >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >>>> >>> >> >> >> -- >> when the rich wage war, it's the poor who die >> > > -- when the rich wage war, it's the poor who die -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eyetest.png Type: image/png Size: 241152 bytes Desc: not available URL: From xzhao21 at lsu.edu Sat Aug 20 00:37:35 2016 From: xzhao21 at lsu.edu (Xiaodong Zhao) Date: Sat, 20 Aug 2016 04:37:35 -0000 Subject: [ITK] (beginner question) How to get transform matrix then apply it to another volume In-Reply-To: References: Message-ID: <4B2A0549-3D6C-4E92-9BB9-AE81FFD7A181@lsu.edu> Hi Dzenan, Thanks for your reply! I tried to edit the example ImageRegistration20.cxx a bit. Basically I just input the the fixed MR, the moving MR, and the CT that?s pre-registered with the moving MR, and after the affine transformation is done b/w the 2 MR volumes, I just applied the same transformation matrix to the CT, or at least that?s what i was trying to do(i just copied the resampling part and changed some variables)... The MR looks good, but I got all these streaking artifacts from the CT, and the CT numbers seems to be rescaled to from 0 to around 250, which happens to be about the same range of the difference image(the min and max of the IntensityRescaler in line 451). I attached a screenshot of one CT slice, and the code(excuse my POOOOOR programming skills!). Did I use a wrong resampling filter or?? Thanks again, Neo -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2016-08-19 at 11.10.25 PM.png Type: image/png Size: 471682 bytes Desc: Screen Shot 2016-08-19 at 11.10.25 PM.png URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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