# Latest

**URL:** https://discourse.itk.org/latest.md?page=33

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

**Page:** 34

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## [GPUDemon running puzzles.](https://discourse.itk.org/t/gpudemon-running-puzzles/5353)

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**Author:** [@Hongying\_Feng](https://discourse.itk.org/u/Hongying_Feng)\
**Replies:** 0\
**Last updated:** [September 22, 2022, 7:49am UTC](https://discourse.itk.org/t/gpudemon-running-puzzles/5353 "2022-09-22T07:49:00Z")

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Hi, I am trying to use the GPUDemonRegistrationFilter to speed up the Registration. Here is how I implement it. First, I used the following iteration observer. class CommandIterationUpdate : public itk::Command { pu…

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## [3D Affine:Rotate on two different axes one after the other](https://discourse.itk.org/t/3d-affine-rotate-on-two-different-axes-one-after-the-other/5315)

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**Author:** [@wic94016](https://discourse.itk.org/u/wic94016)\
**Replies:** 7\
**Last updated:** [September 21, 2022, 12:11pm UTC](https://discourse.itk.org/t/3d-affine-rotate-on-two-different-axes-one-after-the-other/5315 "2022-09-21T12:11:09Z")

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Hey guys,I have a serious question about my python code. What I want to do is ,if I have a 3D array like this and I want it to be 90 degrees around the -X axis first,then 10 degrees around the y axis. But it seems t…

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## [How to use ImageRegionIterator and ImageRegionConstIteratorWithIndex in python](https://discourse.itk.org/t/how-to-use-imageregioniterator-and-imageregionconstiteratorwithindex-in-python/5346)

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**Author:** [@cnkhanh](https://discourse.itk.org/u/cnkhanh)\
**Replies:** 4\
**Last updated:** [September 21, 2022, 12:05pm UTC](https://discourse.itk.org/t/how-to-use-imageregioniterator-and-imageregionconstiteratorwithindex-in-python/5346 "2022-09-21T12:05:30Z")

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I tried to write something like the below using python, I can’t find equivalence classes in python. Is there any way to do it in python? typedef itk::ImageRegionIterator\< OutputImageType \> OutIteratorType; IteratorTyp…

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## [Normalized mutual information combined with gradient descent as a similarity measure function for 2D/3D registration](https://discourse.itk.org/t/normalized-mutual-information-combined-with-gradient-descent-as-a-similarity-measure-function-for-2d-3d-registration/5351)

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**Author:** [@12qew](https://discourse.itk.org/u/12qew)\
**Replies:** 0\
**Last updated:** [September 21, 2022, 12:00pm UTC](https://discourse.itk.org/t/normalized-mutual-information-combined-with-gradient-descent-as-a-similarity-measure-function-for-2d-3d-registration/5351 "2022-09-21T12:00:18Z")

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Hello everyone, I have been working on 2D/3D registration recently and encountered a problem. In this project of mine, the sum function of normalized mutual information and gradient descent is used as the similarity meas…

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## [How to fix 'itkMatrixD33' object does not support indexing (itk.BinaryMask3DMeshSource)](https://discourse.itk.org/t/how-to-fix-itkmatrixd33-object-does-not-support-indexing-itk-binarymask3dmeshsource/5347)

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**Author:** [@cnkhanh](https://discourse.itk.org/u/cnkhanh)\
**Replies:** 4\
**Last updated:** [September 21, 2022, 1:53am UTC](https://discourse.itk.org/t/how-to-fix-itkmatrixd33-object-does-not-support-indexing-itk-binarymask3dmeshsource/5347 "2022-09-21T01:53:39Z")

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The below is the code in C++ typename ImageType::DirectionType imageDirection=inputImage-\>GetDirection(); //… mesh generated using itk::BinaryMask3DMeshSource typename MeshType::Pointer mesh = meshSource-\>GetOutput()…

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## [insighttoolkit/brigejavascript instruction manual](https://discourse.itk.org/t/insighttoolkit-brigejavascript-instruction-manual/5328)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 7\
**Last updated:** [September 20, 2022, 10:52am UTC](https://discourse.itk.org/t/insighttoolkit-brigejavascript-instruction-manual/5328 "2022-09-20T10:52:09Z")

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@matt.mccormick , Hi mat, I am trying to build and run WatershedSegmentation1.cxx using ITK-WASM/WASI. the code is below. I have just tried to parse input command line with pipeline as in example InputsOutputs example…

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## [ITK 5.2.1 static build Win x64](https://discourse.itk.org/t/itk-5-2-1-static-build-win-x64/5341)

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**Author:** [@DL\_I](https://discourse.itk.org/u/DL_I)\
**Replies:** 3\
**Last updated:** [September 20, 2022, 5:56am UTC](https://discourse.itk.org/t/itk-5-2-1-static-build-win-x64/5341 "2022-09-20T05:56:16Z")

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building ITK tag v5.2.1 static in Visual Studio 2020 x64 build environment. I have Qt 5.15.2, VTK 9.1.0 and GDCM 3.1.0 built statically debug. ITK is configured to use\_system\_gdcm, shared libs off, no testing, no e…

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## [How to open .TRE file?](https://discourse.itk.org/t/how-to-open-tre-file/2538)

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**Author:** [@Duy\_H](https://discourse.itk.org/u/Duy_H)\
**Replies:** 64\
**Last updated:** [September 19, 2022, 11:33am UTC](https://discourse.itk.org/t/how-to-open-tre-file/2538 "2022-09-19T11:33:30Z")

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Dataset at “https://public.kitware.com/Wiki/TubeTK/Data” have “VascularNetwork.tre” file. How can i open this file using Python?

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## [Can we use k-d Tree Based k-Means Clustering in a 3D vector?](https://discourse.itk.org/t/can-we-use-k-d-tree-based-k-means-clustering-in-a-3d-vector/5339)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 0\
**Last updated:** [September 16, 2022, 9:28pm UTC](https://discourse.itk.org/t/can-we-use-k-d-tree-based-k-means-clustering-in-a-3d-vector/5339 "2022-09-16T21:28:12Z")

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I am segmenting the spinal canal in CT images and I need to classify the spinal canal pixels positions in groups. ( “Automatic Segmentation of the Body and the Spinal Canal in CT Images Based on A Priori Information”). …

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## [DRR Generation from 3D Chest CT and Projection of a Mesh onto the DRR](https://discourse.itk.org/t/drr-generation-from-3d-chest-ct-and-projection-of-a-mesh-onto-the-drr/5325)

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**Author:** [@qod\_rec](https://discourse.itk.org/u/qod_rec)\
**Replies:** 7\
**Last updated:** [September 16, 2022, 5:31pm UTC](https://discourse.itk.org/t/drr-generation-from-3d-chest-ct-and-projection-of-a-mesh-onto-the-drr/5325 "2022-09-16T17:31:07Z")

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Hello everyone. I have 3D chest CTs whose lung contour is labeled and I generate the contour meshes. I am trying to complete the following things: Generate the DRR from the 3D chest CTs Project the mesh vertex(points…

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## [Apply deformation to the 3D-CT image volume from mesh displacement](https://discourse.itk.org/t/apply-deformation-to-the-3d-ct-image-volume-from-mesh-displacement/5338)

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**Author:** [@lakmy](https://discourse.itk.org/u/lakmy)\
**Replies:** 1\
**Last updated:** [September 16, 2022, 3:30pm UTC](https://discourse.itk.org/t/apply-deformation-to-the-3d-ct-image-volume-from-mesh-displacement/5338 "2022-09-16T15:30:23Z")

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I have a reference mesh and a deformed version of it (they are unstrcuted grid saved in vtk file format). The reference mesh was acquired from a 3D-CT volume. I would want to apply the same deformation to the reference …

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## [Which of path should set to ITK\_DIR](https://discourse.itk.org/t/which-of-path-should-set-to-itk-dir/4675)

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**Author:** [@xh\_c](https://discourse.itk.org/u/xh_c)\
**Replies:** 8\
**Last updated:** [September 14, 2022, 8:22pm UTC](https://discourse.itk.org/t/which-of-path-should-set-to-itk-dir/4675 "2022-09-14T20:22:25Z")

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Hello, I just build ITK with cmake. Now I have two folder, ITK\_source and ITK\_build. I set my ITK\_DIR to ITK\_build but get no head file error. And I found that some ITK module just have .obj file and no .cxx or .h. In IT…

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## [HU value in dcm series files and itk::Image](https://discourse.itk.org/t/hu-value-in-dcm-series-files-and-itk-image/5333)

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**Author:** [@liguangops](https://discourse.itk.org/u/liguangops)\
**Replies:** 4\
**Last updated:** [September 14, 2022, 1:51am UTC](https://discourse.itk.org/t/hu-value-in-dcm-series-files-and-itk-image/5333 "2022-09-14T01:51:26Z")

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I am a little confused about HU value in dcm series. When I use ITK\_SNAP or 3d slicer to read dcm series files, it shows that the range of HU is \[-1000, 4.303e+004\] But when I use itk::ImageSeriesReader and get it to ou…

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## [Anonymize / De-identify dicom datasets](https://discourse.itk.org/t/anonymize-de-identify-dicom-datasets/2316)

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**Author:** [@Jigabytes](https://discourse.itk.org/u/Jigabytes)\
**Replies:** 6\
**Last updated:** [September 12, 2022, 7:40am UTC](https://discourse.itk.org/t/anonymize-de-identify-dicom-datasets/2316 "2022-09-12T07:40:50Z")

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Hi All, I would like to use de-identified medical dicom datasets for my segmentation process. Any recommendations in this space? Are there standard library available for achieving it? Thanks, Jiten

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## [3D multi-modal medical image registration using user defined function for similarity metric computation](https://discourse.itk.org/t/3d-multi-modal-medical-image-registration-using-user-defined-function-for-similarity-metric-computation/5064)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 41\
**Last updated:** [September 10, 2022, 3:41pm UTC](https://discourse.itk.org/t/3d-multi-modal-medical-image-registration-using-user-defined-function-for-similarity-metric-computation/5064 "2022-09-10T15:41:02Z")

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Hello, I want to register two 3D multi-modal medical images using mutual information. However instead of using the inbuilt MattesMutualInformation or JointHistogramMutualInformation, I want to use my own mutual informat…

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## [LabelMapToLabelImageFilter\`s output is an image with white color](https://discourse.itk.org/t/labelmaptolabelimagefilter-s-output-is-an-image-with-white-color/5316)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 1\
**Last updated:** [September 7, 2022, 7:01am UTC](https://discourse.itk.org/t/labelmaptolabelimagefilter-s-output-is-an-image-with-white-color/5316 "2022-09-07T07:01:01Z")

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I want to use the ConnectedComponentImageFilter to delete the false positive area, and pass the result through other filters (LabelImageToShapeLabelMapFilter,LabelMap,LabelMapToLabelImageFilter namely) to convert into im…

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## [data.kitware.com maintenance tomorrow](https://discourse.itk.org/t/data-kitware-com-maintenance-tomorrow/5317)

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**Author:** [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Replies:** 1\
**Last updated:** [September 6, 2022, 5:56pm UTC](https://discourse.itk.org/t/data-kitware-com-maintenance-tomorrow/5317 "2022-09-06T17:56:48Z")

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Tomorrow, Sept 6th maintenance is planned for data.kitware.com. It is expected to be from 12:30 to 2:00pm Easter Time. Most of ITK test data is hosted here, so interruption to data downloads is likely.

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## [SimpleITK: memory management, and question: select where to write the output of a filter for explicit memory management purposes?](https://discourse.itk.org/t/simpleitk-memory-management-and-question-select-where-to-write-the-output-of-a-filter-for-explicit-memory-management-purposes/5312)

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**Author:** [@vincenzoml](https://discourse.itk.org/u/vincenzoml)\
**Replies:** 6\
**Last updated:** [September 6, 2022, 2:19pm UTC](https://discourse.itk.org/t/simpleitk-memory-management-and-question-select-where-to-write-the-output-of-a-filter-for-explicit-memory-management-purposes/5312 "2022-09-06T14:19:08Z")

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Hi, in making the second version of voxlogica (see https : //github.com/vincenzoml/voxlogica), which is, all in all, the interpreter of a simple domain-specific programming language, we are exploring custom memory manag…

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## [Getting 3D images from stacking 2D axial slices with all important coordinate information](https://discourse.itk.org/t/getting-3d-images-from-stacking-2d-axial-slices-with-all-important-coordinate-information/5313)

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**Author:** [@shadab](https://discourse.itk.org/u/shadab)\
**Replies:** 0\
**Last updated:** [September 2, 2022, 6:27pm UTC](https://discourse.itk.org/t/getting-3d-images-from-stacking-2d-axial-slices-with-all-important-coordinate-information/5313 "2022-09-02T18:27:36Z")

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Hi ITK community, I have a 3D PET/CT dataset with 3D segmentations (GT) (with labels 0, 1, and 2). The CT images are typically 512x512xSizeZ, while the PET images are of various shapes like 128x128xSizeZ' or \`256x256xSi…

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## [Installation problem (ITK3.2.0 in Linux)](https://discourse.itk.org/t/installation-problem-itk3-2-0-in-linux/724)

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**Author:** [@LiuHao-THU](https://discourse.itk.org/u/LiuHao-THU)\
**Replies:** 4\
**Last updated:** [August 30, 2022, 7:51pm UTC](https://discourse.itk.org/t/installation-problem-itk3-2-0-in-linux/724 "2022-08-30T19:51:18Z")

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hi, i am a beginner to ITK, now I am installing itk(3.2) vtk(5.8) in my Linux. and I meet some problem. I even do not know how to solve it. I have successfully installed the latest version ITK and vtk, however the lates…

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## [SimpleITK 2.2.0 Release](https://discourse.itk.org/t/simpleitk-2-2-0-release/5307)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 0\
**Last updated:** [August 30, 2022, 4:03pm UTC](https://discourse.itk.org/t/simpleitk-2-2-0-release/5307 "2022-08-30T16:03:18Z")

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SimpleITK 2.2.0 has been released! The release includes new features, API changes, documentation updates and bug fixes. A highlight of this release is the addition of SimpleElastix as a compile time option in SimpleITK…

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## [Extract gray levels on a given line from a CT](https://discourse.itk.org/t/extract-gray-levels-on-a-given-line-from-a-ct/5297)

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**Author:** [@scarpma](https://discourse.itk.org/u/scarpma)\
**Replies:** 3\
**Last updated:** [August 29, 2022, 9:24pm UTC](https://discourse.itk.org/t/extract-gray-levels-on-a-given-line-from-a-ct/5297 "2022-08-29T21:24:14Z")

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Hello everyone, I want to build a Gray Level Model (GLM) of a set of CT in order to segment the aorta using active shape modeling (see ref for an example). To create the GLM I need to extract gray level profiles, i.e.,…

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## [Simple ITK TransformVector Returning Error](https://discourse.itk.org/t/simple-itk-transformvector-returning-error/5306)

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**Author:** [@natwille1](https://discourse.itk.org/u/natwille1)\
**Replies:** 2\
**Last updated:** [August 29, 2022, 7:35pm UTC](https://discourse.itk.org/t/simple-itk-transformvector-returning-error/5306 "2022-08-29T19:35:38Z")

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Hi, I am trying to apply a 3D euler transform to a vector at a particular point: basis = np.array(\[\[1.0, 0.0, 0.0\], \[0.0, 1.0, 0.0\], \[0.0, 0.0, 1.0\]\]) origin = np.array(\[0.0, 0.0, 0.0\]).reshape(-1, 3) out = transform.Tr…

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## [How to apply mask when using rescale filter](https://discourse.itk.org/t/how-to-apply-mask-when-using-rescale-filter/5295)

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**Author:** [@willi3by](https://discourse.itk.org/u/willi3by)\
**Replies:** 5\
**Last updated:** [August 29, 2022, 1:58pm UTC](https://discourse.itk.org/t/how-to-apply-mask-when-using-rescale-filter/5295 "2022-08-29T13:58:15Z")

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Hi, I am implementing a modified version of the filtering approach in this tutorial: Segment Blood Vessels With Multi-Scale Hessian-Based Measure — v5.3.0 However, my images contain tissue for which I do not want to app…

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## [Is it possible to apply transformation to other images?](https://discourse.itk.org/t/is-it-possible-to-apply-transformation-to-other-images/5302)

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**Author:** [@GrowlingM1ke](https://discourse.itk.org/u/GrowlingM1ke)\
**Replies:** 1\
**Last updated:** [August 29, 2022, 1:07pm UTC](https://discourse.itk.org/t/is-it-possible-to-apply-transformation-to-other-images/5302 "2022-08-29T13:07:43Z")

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Hello, I’ve been using pyelastix toolkit in order to perform non-rigid image registration. I needed to boost the contrast within the images I was using in order to improve registration, however the pyelastix wrapper doe…

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## [Blob Detection](https://discourse.itk.org/t/blob-detection/5299)

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**Author:** [@Mahdiye\_Imanpanah](https://discourse.itk.org/u/Mahdiye_Imanpanah)\
**Replies:** 1\
**Last updated:** [August 29, 2022, 12:46pm UTC](https://discourse.itk.org/t/blob-detection/5299 "2022-08-29T12:46:45Z")

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Hi everybody I want to develop a method to detect shapes in the images(for example blobs). I’ve found Hough-Transform to reach this goal, but I can’t find it in SimpleItk. Does SimpleItk support Hough-Transform? If i…

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## [SimpleITK writing NIfTI with invalid header](https://discourse.itk.org/t/simpleitk-writing-nifti-with-invalid-header/2498)

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**Author:** [@fepegar](https://discourse.itk.org/u/fepegar)\
**Replies:** 12\
**Last updated:** [August 26, 2022, 6:07pm UTC](https://discourse.itk.org/t/simpleitk-writing-nifti-with-invalid-header/2498 "2022-08-26T18:07:17Z")

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Hello, I’m using SimpleITK 1.2.4 to read and write NIfTI images. NIfTI docs say that it “should not occur” that qfac is 0. qfac is the first value of the pixdim array in the header and is expected to be -1 or 1. When I…

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## [itk-wasm wasi build for c++ program](https://discourse.itk.org/t/itk-wasm-wasi-build-for-c-program/5153)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 3\
**Last updated:** [August 26, 2022, 5:44pm UTC](https://discourse.itk.org/t/itk-wasm-wasi-build-for-c-program/5153 "2022-08-26T17:44:10Z")

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@matt.mccormick , @dzenanz , Hi, I need help to link hdf5 libraries of ITK-5.2.1/ITK-5.3 to a itk-wasm/wasi build. It seems to complain about hdf5 libraries. the c++ code: include \<itkImageFileReader.h\> causes the fd…

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## [itk::JSONImageIO class missing from ITK library?](https://discourse.itk.org/t/itk-jsonimageio-class-missing-from-itk-library/5275)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 2\
**Last updated:** [August 26, 2022, 2:02pm UTC](https://discourse.itk.org/t/itk-jsonimageio-class-missing-from-itk-library/5275 "2022-08-26T14:02:48Z")

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Hi, I am trying to convert \<image.png\> file into \<image.png.json\> file. Can anyone in the forum help me to find the class, i have been searching for it for last two days and nothing found. Thank you @sag

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## [ITK-JS && ITK-WASM](https://discourse.itk.org/t/itk-js-itk-wasm/5021)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 14\
**Last updated:** [August 26, 2022, 2:01pm UTC](https://discourse.itk.org/t/itk-js-itk-wasm/5021 "2022-08-26T14:01:54Z")

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@matt.mccormick Hi Mat, I am trying to use both ITK-JS and ITK-WASM. I have failed in both. please help me with following questions: +I have followed this Node.js HelloWorld, and i failed with the error cannot find mo…

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