# Latest

**URL:** https://discourse.itk.org/latest.md?page=46

[Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md)

**Page:** 47

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## [NCI Imaging Data Commons @ MICCAI 2021](https://discourse.itk.org/t/nci-imaging-data-commons-miccai-2021/4447)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 0\
**Last updated:** [September 24, 2021, 2:56am UTC](https://discourse.itk.org/t/nci-imaging-data-commons-miccai-2021/4447 "2021-09-24T02:56:42Z")

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If you are interested to get a brief introduction and hopefully engaging demonstrations of the NCI Imaging Data Commons functionality, please join us at the “NIH Cancer Imaging Data Repositories for Biomedical Data Scie…

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## [Displacement field to (BSpline) Transform](https://discourse.itk.org/t/displacement-field-to-bspline-transform/4434)

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**Author:** [@Mikhail](https://discourse.itk.org/u/Mikhail)\
**Replies:** 8\
**Last updated:** [September 23, 2021, 8:13pm UTC](https://discourse.itk.org/t/displacement-field-to-bspline-transform/4434 "2021-09-23T20:13:01Z")

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Dear community, I am looking for a way to obtain a (bspline) transformation given a displacement field (x y z 3) defined on a regular grid. The reason I want to obtain this transformation is to reduce the memory consump…

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## [ITK issue, HDF5 CXX compiler wrapper, ANTs installation](https://discourse.itk.org/t/itk-issue-hdf5-cxx-compiler-wrapper-ants-installation/4439)

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**Author:** [@Surendra\_Maharjan](https://discourse.itk.org/u/Surendra_Maharjan)\
**Replies:** 1\
**Last updated:** [September 22, 2021, 9:54pm UTC](https://discourse.itk.org/t/itk-issue-hdf5-cxx-compiler-wrapper-ants-installation/4439 "2021-09-22T21:54:15Z")

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Hello ITKers, My name is Suren. I am having an issue while installing ANTs in Mac Big Sur. It says "HDF5 CXX compiler wrapper is unable to compile a minimal HDF5 program. “HDF5 C compiler wrapper is unable to compile …

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## [Poor affine registration results using LandmarkBasedTransformInitializer](https://discourse.itk.org/t/poor-affine-registration-results-using-landmarkbasedtransforminitializer/4403)

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**Author:** [@ctorti](https://discourse.itk.org/u/ctorti)\
**Replies:** 8\
**Last updated:** [September 22, 2021, 4:23pm UTC](https://discourse.itk.org/t/poor-affine-registration-results-using-landmarkbasedtransforminitializer/4403 "2021-09-22T16:23:16Z")

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Hi all, I’m getting bad affine registration results for certain combinations of moving and fixed images. To rule out the possibility of poor initial alignment, I considered affine and bspline CT-to-MR registrations us…

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## [GetImageViewFromArray in SimpleITK](https://discourse.itk.org/t/getimageviewfromarray-in-simpleitk/4436)

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**Author:** [@rogertrullo](https://discourse.itk.org/u/rogertrullo)\
**Replies:** 7\
**Last updated:** [September 22, 2021, 2:03pm UTC](https://discourse.itk.org/t/getimageviewfromarray-in-simpleitk/4436 "2021-09-22T14:03:22Z")

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Hi all, I am using Simpleitk and it seems that there is no GetImageViewFromArray funciton. I have the GetArrayViewFromImage function though. Is there any reason on why is this function not available? When I do GetImageF…

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## [Create DRR image from Chest CT scan](https://discourse.itk.org/t/create-drr-image-from-chest-ct-scan/1370)

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**Author:** [@sumedha\_singla](https://discourse.itk.org/u/sumedha_singla)\
**Replies:** 11\
**Last updated:** [September 22, 2021, 1:51pm UTC](https://discourse.itk.org/t/create-drr-image-from-chest-ct-scan/1370 "2021-09-22T13:51:14Z")

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Hi everyone, We are trying to convert 3D volumetric CT images to chest Xray (for a sake of comparison with another dataset). We use this example: The projection results in radiography-looking images but it is visuall…

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## [About ImageGraphCut3DSegmentationExample and ImageMultiLabelGraphCut3DSegmentationExample, How to use?](https://discourse.itk.org/t/about-imagegraphcut3dsegmentationexample-and-imagemultilabelgraphcut3dsegmentationexample-how-to-use/4417)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 1\
**Last updated:** [September 22, 2021, 12:43pm UTC](https://discourse.itk.org/t/about-imagegraphcut3dsegmentationexample-and-imagemultilabelgraphcut3dsegmentationexample-how-to-use/4417 "2021-09-22T12:43:16Z")

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I have recently study the " ImageMultiLabelGraphCut3DSegmentationExample", But I did not know how to use the The demo, especially how to make" image.mhd multiLabelMask.mhd backgroundMask.mhd" parameters! Can you give m…

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## [mask during image registration](https://discourse.itk.org/t/mask-during-image-registration/4413)

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**Author:** [@Anesh](https://discourse.itk.org/u/Anesh)\
**Replies:** 2\
**Last updated:** [September 21, 2021, 2:32pm UTC](https://discourse.itk.org/t/mask-during-image-registration/4413 "2021-09-21T14:32:54Z")

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Hi All, I have a basic question on registration using spatial object mask. Let’s say I have an image where the background is zero or close to zero and my mask is all ones, as illustrated below. When I run registration, …

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## [AffineGeometryFrame class is removed as part of migration from v4 to v5](https://discourse.itk.org/t/affinegeometryframe-class-is-removed-as-part-of-migration-from-v4-to-v5/4433)

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**Author:** [@Mahesh\_Timmanagoudar](https://discourse.itk.org/u/Mahesh_Timmanagoudar)\
**Replies:** 3\
**Last updated:** [September 20, 2021, 3:24pm UTC](https://discourse.itk.org/t/affinegeometryframe-class-is-removed-as-part-of-migration-from-v4-to-v5/4433 "2021-09-20T15:24:24Z")

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I need that transform on its own. How can i make use of AffineGeometryFrame class functionalities in new ITK version (v5). I have debugged below things. typedef itk::TubeSpatialObject\< Dimension \> TubeType; typename Tu…

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## [Difference between numberofFixedImageSamples and numberofSpatialSamples](https://discourse.itk.org/t/difference-between-numberoffixedimagesamples-and-numberofspatialsamples/4431)

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**Author:** [@c.spanakis83](https://discourse.itk.org/u/c.spanakis83)\
**Replies:** 1\
**Last updated:** [September 20, 2021, 1:26pm UTC](https://discourse.itk.org/t/difference-between-numberoffixedimagesamples-and-numberofspatialsamples/4431 "2021-09-20T13:26:58Z")

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Hello I want to use Mutual Information (specifically Mattes’ Mutual Information) in order to align 2 medical images. However, I found that it has two methods: SetNumberofFixedImageSamples (unsigned int num) SetNumberof…

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## [Transform Point from Affine Transform](https://discourse.itk.org/t/transform-point-from-affine-transform/4429)

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**Author:** [@kleingeo](https://discourse.itk.org/u/kleingeo)\
**Replies:** 1\
**Last updated:** [September 17, 2021, 6:53pm UTC](https://discourse.itk.org/t/transform-point-from-affine-transform/4429 "2021-09-17T18:53:32Z")

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I have a question regarding transforming a point with an affine transform. I have applied an affine transform (translation, rotation, scaling) two images (image and its segmentations) and after resampling it is working a…

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## [ITK not loading NRRD files any more](https://discourse.itk.org/t/itk-not-loading-nrrd-files-any-more/4224)

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**Author:** [@Fijoy\_Vadakkumpadan](https://discourse.itk.org/u/Fijoy_Vadakkumpadan)\
**Replies:** 12\
**Last updated:** [September 17, 2021, 2:54pm UTC](https://discourse.itk.org/t/itk-not-loading-nrrd-files-any-more/4224 "2021-09-17T14:54:29Z")

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Hello, Does ITK no longer fully support NRRD files? I’m trying to upgrade the ITK version in my application from 4.10.1 to 5.1.1. Unfortunately, the new ITK version is throwing a floating point exception when attemptin…

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## [Does anyone know where to download the file "GraphCut3D/ImageMultiLabelGridCutFilter.h".](https://discourse.itk.org/t/does-anyone-know-where-to-download-the-file-graphcut3d-imagemultilabelgridcutfilter-h/4353)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 9\
**Last updated:** [September 15, 2021, 6:35pm UTC](https://discourse.itk.org/t/does-anyone-know-where-to-download-the-file-graphcut3d-imagemultilabelgridcutfilter-h/4353 "2021-09-15T18:35:03Z")

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Whe I download and build the project “”, I can not find the file “AlphaExpansion\_3D\_6C\_MT.h”, where include in “GraphCut3D/ImageMultiLabelGridCutFilter.h” like this: can anyone give me a websit to download this file…

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## [M\_ReadElementsData: data not read completelyideal = 5734400 : actual = 2700286M](https://discourse.itk.org/t/m-readelementsdata-data-not-read-completelyideal-5734400-actual-2700286m/4424)

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**Author:** [@Will\_G](https://discourse.itk.org/u/Will_G)\
**Replies:** 5\
**Last updated:** [September 15, 2021, 3:23pm UTC](https://discourse.itk.org/t/m-readelementsdata-data-not-read-completelyideal-5734400-actual-2700286m/4424 "2021-09-15T15:23:22Z")

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Hi, I’m very new to using simpleITK for image conversion, my model now seemingly runs but with this one error message been presented. M\_ReadElementsData: data not read completelyideal = 5734400 : actual = 2700286 Has a…

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## [Understanding sitk.Euler3DTransform convention](https://discourse.itk.org/t/understanding-sitk-euler3dtransform-convention/4422)

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**Author:** [@MMdeB](https://discourse.itk.org/u/MMdeB)\
**Replies:** 1\
**Last updated:** [September 15, 2021, 1:20pm UTC](https://discourse.itk.org/t/understanding-sitk-euler3dtransform-convention/4422 "2021-09-15T13:20:35Z")

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Hi, I’m using sitk.Euler3DTransform to rotate my 3D image, but I am confused regarding which euler convention is used. I found that sitk.Euler3DTransform uses the ZXY or ZYX convention. However, is this using extrinsic…

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## [ITK 5.3 Release Candidate 1 available for testing](https://discourse.itk.org/t/itk-5-3-release-candidate-1-available-for-testing/4421)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [September 14, 2021, 10:16pm UTC](https://discourse.itk.org/t/itk-5-3-release-candidate-1-available-for-testing/4421 "2021-09-14T22:16:18Z")

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We are happy to announce the Insight Toolkit (ITK) 5.3 Release Candidate 1 is available for testing! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and r…

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## [ITKCudaCommon automatic linking error](https://discourse.itk.org/t/itkcudacommon-automatic-linking-error/4418)

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**Author:** [@Gabriele\_Belotti](https://discourse.itk.org/u/Gabriele_Belotti)\
**Replies:** 1\
**Last updated:** [September 14, 2021, 9:55am UTC](https://discourse.itk.org/t/itkcudacommon-automatic-linking-error/4418 "2021-09-14T09:55:16Z")

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Hi, I’m trying to update a script that was once linked to RTK module directly (around 1.4). I linked against my 5.2 build with only one issue: ITKCudaCommon seems to be referred to without relative path to build\\lib\\Re…

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## [Unexpected Results for "MultiResImageRegistration1.cxx."](https://discourse.itk.org/t/unexpected-results-for-multiresimageregistration1-cxx/4411)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 2\
**Last updated:** [September 13, 2021, 7:49am UTC](https://discourse.itk.org/t/unexpected-results-for-multiresimageregistration1-cxx/4411 "2021-09-13T07:49:03Z")

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Hello everyone! I just started out with ITK, with base knowledge from VTK. I wanted to work through some Registration examples towards Multi-Resolution Registration. The Hello World Registration example worked for me, …

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## [GCC 9/11 Compiler Error or Assembler Error?](https://discourse.itk.org/t/gcc-9-11-compiler-error-or-assembler-error/4412)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 0\
**Last updated:** [September 10, 2021, 10:11pm UTC](https://discourse.itk.org/t/gcc-9-11-compiler-error-or-assembler-error/4412 "2021-09-10T22:11:05Z")

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has anyone seen this error from GCC 9 or 11? FAILED: Plugins/ITKImageProcessing/CMakeFiles/ITKImageProcessingServer.dir/ITKImageProcessingFilters/ITKImageReader.cpp.o $BUILD\_PREFIX/bin/x86\_64-conda-linux-gnu-c++ -DH5Su…

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## [Why to invert the order of the indices between numpy and SimpleITK?](https://discourse.itk.org/t/why-to-invert-the-order-of-the-indices-between-numpy-and-simpleitk/809)

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**Author:** [@Diego\_C](https://discourse.itk.org/u/Diego_C)\
**Replies:** 15\
**Last updated:** [May 31, 2020, 12:46pm UTC](https://discourse.itk.org/t/why-to-invert-the-order-of-the-indices-between-numpy-and-simpleitk/809 "2020-05-31T12:46:35Z")

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HI, Can anyone explain the logic between this: \[image\] This is taken from the SimpleITK Notebooks It states that the order of the indices is the opposite in numpy. But in fact this is an arbitrary choice. For instanc…

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## [Thread safety of itk::ObjectFactoryBase::Initialize()](https://discourse.itk.org/t/thread-safety-of-itk-initialize/4404)

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**Author:** [@seanm](https://discourse.itk.org/u/seanm)\
**Replies:** 7\
**Last updated:** [September 9, 2021, 8:38pm UTC](https://discourse.itk.org/t/thread-safety-of-itk-initialize/4404 "2021-09-09T20:38:38Z")

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Hi all, In testing my own app with clang thread sanitizer (TSan) I hit a race condition with ITK. I reduced it to many threads running this code: typedef itk::Image\<float, 2\> MyTypedef; MyTypedef::New(); The issue is…

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## [Bug in itk.image\_duplicator?](https://discourse.itk.org/t/bug-in-itk-image-duplicator/4408)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 2\
**Last updated:** [September 9, 2021, 1:56pm UTC](https://discourse.itk.org/t/bug-in-itk-image-duplicator/4408 "2021-09-09T13:56:43Z")

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I load an image like import itk img = itk.imread("/path/to/image.nii.gz") print(type(img)) print(img.shape) The type is a itk.itkImagePython.itkImageF3. The shape is (310,310,310). Then I duplicate the image: img\_t =…

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## [Detailed description of statistics available in SimpleITK LabelShapeStatisticsImageFilter?](https://discourse.itk.org/t/detailed-description-of-statistics-available-in-simpleitk-labelshapestatisticsimagefilter/4405)

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**Author:** [@jni](https://discourse.itk.org/u/jni)\
**Replies:** 2\
**Last updated:** [September 9, 2021, 12:39pm UTC](https://discourse.itk.org/t/detailed-description-of-statistics-available-in-simpleitk-labelshapestatisticsimagefilter/4405 "2021-09-09T12:39:32Z")

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Hi everyone, Is there any place that lists what each of the available stats in LabelShapeStatisticsImageFilter is actually computing? My searching for what “flatness” is has taken me here: https://simpleitk.org/SPIE201…

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## [SimpleITK Euler3D Transform, Adjust Image Origin and Direction](https://discourse.itk.org/t/simpleitk-euler3d-transform-adjust-image-origin-and-direction/3966)

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**Author:** [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)\
**Replies:** 24\
**Last updated:** [September 8, 2021, 2:39pm UTC](https://discourse.itk.org/t/simpleitk-euler3d-transform-adjust-image-origin-and-direction/3966 "2021-09-08T14:39:21Z")

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Hi board, I have a 3D volume that I registered to another volume with ITK’s registration methods. My moving-\>fixed transformation is an Euler3DTransform. I’d like to adjust the Origin and Direction of my moving image w…

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## [Progress reporting with strange behaviour](https://discourse.itk.org/t/progress-reporting-with-strange-behaviour/4398)

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**Author:** [@Anders\_G](https://discourse.itk.org/u/Anders_G)\
**Replies:** 1\
**Last updated:** [September 8, 2021, 1:48pm UTC](https://discourse.itk.org/t/progress-reporting-with-strange-behaviour/4398 "2021-09-08T13:48:01Z")

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Im quite new to simpleITK so this is perhaps simple. But I just don’t get it. When I look at the progress of a filter, (I register a Command so I can follow the progress) it behaves strangely. For most filters like the …

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## [Convert CT mask to PET mask](https://discourse.itk.org/t/convert-ct-mask-to-pet-mask/3775)

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**Author:** [@Jakob\_Riber\_Rasmusse](https://discourse.itk.org/u/Jakob_Riber_Rasmusse)\
**Replies:** 6\
**Last updated:** [September 8, 2021, 9:42am UTC](https://discourse.itk.org/t/convert-ct-mask-to-pet-mask/3775 "2021-09-08T09:42:25Z")

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Hello Apoligies if my question is outside the scope of this forum, but here it goes: I am in a situation where I have to convert a mask created on a CT image in to a mask that applies to a PET image. E.g. from 480x480x…

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## [conda-forge release of 5.21?](https://discourse.itk.org/t/conda-forge-release-of-5-21/4402)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 2\
**Last updated:** [September 7, 2021, 3:25pm UTC](https://discourse.itk.org/t/conda-forge-release-of-5-21/4402 "2021-09-07T15:25:01Z")

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I was curious what it takes to track down the errors preventing ITK 5.2.1 from being updated on conda-forge? Thoughts? Mike Jackson

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## [ITK, Matt at CppCast](https://discourse.itk.org/t/itk-matt-at-cppcast/4388)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 2\
**Last updated:** [September 5, 2021, 3:01pm UTC](https://discourse.itk.org/t/itk-matt-at-cppcast/4388 "2021-09-05T15:01:29Z")

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Well done, @matt.mccormick :+1: :+1: :+1: Nice discussion of you with those C++ specialists, Rob Irving and Jason Turner at Insight Toolkit with Matt McCormick • CppCast - Podcast Addict ! My LKEB colleague Baldur va…

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## [Understanding 3DVersor rotation output](https://discourse.itk.org/t/understanding-3dversor-rotation-output/4389)

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**Author:** [@emilljungberg](https://discourse.itk.org/u/emilljungberg)\
**Replies:** 5\
**Last updated:** [September 4, 2021, 9:44am UTC](https://discourse.itk.org/t/understanding-3dversor-rotation-output/4389 "2021-09-04T09:44:37Z")

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Hi! I’m working on a project where I use a Versor3DRigidTransform for registering 3D MRI images, and I’m having some issues interpreting the output from the registration results. My end goal is to get a transformation w…

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## [No such module: "MinimalPathExtraction"](https://discourse.itk.org/t/no-such-module-minimalpathextraction/4393)

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**Author:** [@Mahesh\_Timmanagoudar](https://discourse.itk.org/u/Mahesh_Timmanagoudar)\
**Replies:** 8\
**Last updated:** [September 3, 2021, 11:50am UTC](https://discourse.itk.org/t/no-such-module-minimalpathextraction/4393 "2021-09-03T11:50:50Z")

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– Configuring extension directory: TubeTK – Checking EXTENSION\_NAME variable – Checking EXTENSION\_NAME variable - TubeTK – Configuring Launcher script – Configuring Launcher script - ok \[windows\] – Configuring SEM C…

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