# Engineering

**URL:** https://discourse.itk.org/c/engineering/6.md?page=6

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

**Page:** 7

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## [Modify an element in a matrix](https://discourse.itk.org/t/modify-an-element-in-a-matrix/5398)

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**Author:** [@zhuangming.shen](https://discourse.itk.org/u/zhuangming.shen)\
**Replies:** 7\
**Last updated:** [October 11, 2022, 9:53am UTC](https://discourse.itk.org/t/modify-an-element-in-a-matrix/5398 "2022-10-11T09:53:56Z")

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Hi, if I want to modify an element in a matrix, in ITK 4.13.3, I can code like But in ITK 5.2.1, the same code seems fail to change the element. I’d like to know what’s the way to do this in ITK 5. Thanks in advan…

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## [itkwidgets large images](https://discourse.itk.org/t/itkwidgets-large-images/5401)

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**Author:** [@darrent1974](https://discourse.itk.org/u/darrent1974)\
**Replies:** 2\
**Last updated:** [October 10, 2022, 7:02pm UTC](https://discourse.itk.org/t/itkwidgets-large-images/5401 "2022-10-10T19:02:37Z")

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Hi, I’m currently using itkwidgets 1.0a6 and was wondering if there is any internal limit on displaying 2D images above a certain size? In my current testing I’ve discovered that the view widget stops rendering images …

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## [Reduced dependencies for ITK external modules](https://discourse.itk.org/t/reduced-dependencies-for-itk-external-modules/5391)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 7\
**Last updated:** [October 7, 2022, 12:54pm UTC](https://discourse.itk.org/t/reduced-dependencies-for-itk-external-modules/5391 "2022-10-07T12:54:06Z")

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I would like to reduce dependencies to only the minimal ITK modules, instead of pulling in all of itk from pypi. Since my code only depends on ITKCommon I tried using itk-core as dependency. I did pip install itk\_dis…

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## [\`Apply Morphological Closing on Specific Label Object\` Example, Label value? radius value?](https://discourse.itk.org/t/apply-morphological-closing-on-specific-label-object-example-label-value-radius-value/5387)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [October 6, 2022, 6:49pm UTC](https://discourse.itk.org/t/apply-morphological-closing-on-specific-label-object-example-label-value-radius-value/5387 "2022-10-06T18:49:00Z")

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Hi, what values for label and radius should be used? I am working on Labeling objects for segmentation of 2D/3D and i came accros Labeling concept. I know usually Label would be in range of 0-255 so i figured it is abo…

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## [itk::imageSeriesReader return nullptr](https://discourse.itk.org/t/itk-imageseriesreader-return-nullptr/5367)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 2\
**Last updated:** [September 27, 2022, 1:55pm UTC](https://discourse.itk.org/t/itk-imageseriesreader-return-nullptr/5367 "2022-09-27T13:55:54Z")

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using InputImageTypeCuda = itk::CudaImage\<float, 3\>; using ReaderTypeCuda = itk::ImageSeriesReader; ReaderTypeCuda::Pointer reader = ReaderTypeCuda::New(); ReaderTypeCuda::New() failed it return nullptr, anyone know w…

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## [Does sery share the same rescale slope?](https://discourse.itk.org/t/does-sery-share-the-same-rescale-slope/5348)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 4\
**Last updated:** [September 22, 2022, 1:38pm UTC](https://discourse.itk.org/t/does-sery-share-the-same-rescale-slope/5348 "2022-09-22T13:38:41Z")

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I want to read dicom files, and I want to know whether the sery share the same rescale slope/intercept? Or two image in one sery may have different rescale slope/intercept.

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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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## [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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## [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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## [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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## [How to understand the coordinate system of dicom](https://discourse.itk.org/t/how-to-understand-the-coordinate-system-of-dicom/5180)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 11\
**Last updated:** [August 26, 2022, 2:25am UTC](https://discourse.itk.org/t/how-to-understand-the-coordinate-system-of-dicom/5180 "2022-08-26T02:25:15Z")

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I am confuzed in the understanding of dicom coordinate system. I display dicom information with SimpleITK: import SimpleITK as sitk path1 = 'C:\\\\Users\\\\Administrator\\\\Desktop\\\\medspro\\\\Data\\\\dce1\\\\IMG-0001-00001.dcm' …

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## [Doxygen with Github Actions and Pages.](https://discourse.itk.org/t/doxygen-with-github-actions-and-pages/4790)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 23\
**Last updated:** [August 24, 2022, 6:52pm UTC](https://discourse.itk.org/t/doxygen-with-github-actions-and-pages/4790 "2022-08-24T18:52:49Z")

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I recently made some changes with the ITK Doxygen configuration to minimize the about of changes from night to night in the HTML generated by Doxygen. Minimizing the number of files modified each day enabled regular web …

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## [pythonic api: issue calling filter with two input types](https://discourse.itk.org/t/pythonic-api-issue-calling-filter-with-two-input-types/5280)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 2\
**Last updated:** [August 23, 2022, 1:14am UTC](https://discourse.itk.org/t/pythonic-api-issue-calling-filter-with-two-input-types/5280 "2022-08-23T01:14:39Z")

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I created a new ITK external module to benefit from the nice packaging and pypi distribution. My filter is templated over the input image types (a scalar image and a mask image). The wrapping instructions looks like: …

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## [itk::JSONImageIO](https://discourse.itk.org/t/itk-jsonimageio/5276)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 2\
**Last updated:** [August 18, 2022, 5:09pm UTC](https://discourse.itk.org/t/itk-jsonimageio/5276 "2022-08-18T17:09:20Z")

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Hi @dzenanz , I have problem finding class itk::JSONImageIO, i wanna convert png images to png.json files. I know we can use itk::JSONImageIO class. thank you @sag

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## [The image is full of zero after using resample filter.](https://discourse.itk.org/t/the-image-is-full-of-zero-after-using-resample-filter/5232)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 10\
**Last updated:** [August 12, 2022, 12:55pm UTC](https://discourse.itk.org/t/the-image-is-full-of-zero-after-using-resample-filter/5232 "2022-08-12T12:55:00Z")

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Hi, I am sorry for troubling you so many times. I am trying to resize my image from (530,530,604) -\>(512,512,604), then i use ResampleImageFilter, ScaleTransform and BSplineInterpolateImageFunction to do it. The conve…

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## [Python wrapping for 64-bit double \`itk::Mesh\` coordinates?](https://discourse.itk.org/t/python-wrapping-for-64-bit-double-itk-mesh-coordinates/5241)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 4\
**Last updated:** [August 5, 2022, 9:12pm UTC](https://discourse.itk.org/t/python-wrapping-for-64-bit-double-itk-mesh-coordinates/5241 "2022-08-05T21:12:21Z")

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Is there a Python wrapping of itk::Mesh for 64-bit floating point (double) coordinates of its points? In C++, an itk::Mesh has 32-bit float coordinates by default, but it can be set to 64-bit double by some “mesh trait…

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## [how to convert a tensor with libtorch into a ITK image?](https://discourse.itk.org/t/how-to-convert-a-tensor-with-libtorch-into-a-itk-image/5176)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 10\
**Last updated:** [August 1, 2022, 8:34am UTC](https://discourse.itk.org/t/how-to-convert-a-tensor-with-libtorch-into-a-itk-image/5176 "2022-08-01T08:34:29Z")

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I have created a tensor by libtorch , which it’s shape is 688,688,450, and I want to transfer this tensor into image.

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## [MedianFilterTest, ITK-WASM, ITK-JS, ITK-JS-VTK, crashed when running npx node index.mjs ./cthead.png ./cthead1.out.png 4](https://discourse.itk.org/t/medianfiltertest-itk-wasm-itk-js-itk-js-vtk-crashed-when-running-npx-node-index-mjs-cthead-png-cthead1-out-png-4/5223)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 2\
**Last updated:** [July 28, 2022, 12:29pm UTC](https://discourse.itk.org/t/medianfiltertest-itk-wasm-itk-js-itk-js-vtk-crashed-when-running-npx-node-index-mjs-cthead-png-cthead1-out-png-4/5223 "2022-07-28T12:29:30Z")

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Hi @dzenanz, I am stuck in ITK-JS, ITK-WASM. Environment: VSCODE: latest version Node version: node.js 16.15.1 npm version: 8.11.0 EDI: Visual studio code/WSL2(widows linux subsystem) works fine. docker desktop: i…

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## [VersorTransformation does not work correctly with CompositeTransform after version 2.0.0](https://discourse.itk.org/t/versortransformation-does-not-work-correctly-with-compositetransform-after-version-2-0-0/5194)

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**Author:** [@rraayyii](https://discourse.itk.org/u/rraayyii)\
**Replies:** 11\
**Last updated:** [July 18, 2022, 7:12pm UTC](https://discourse.itk.org/t/versortransformation-does-not-work-correctly-with-compositetransform-after-version-2-0-0/5194 "2022-07-18T19:12:39Z")

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My code with VersorTransform & CompositeTransform doesn’t work anymore after I updated SimpleITK from 1.2.4 to anything above 2.0.0. Diving into the issue, I found that for some reason by adding VersorTransform into a C…

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## [Generating ITK CMake Requires from project code?](https://discourse.itk.org/t/generating-itk-cmake-requires-from-project-code/5154)

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**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 2\
**Last updated:** [July 4, 2022, 2:17pm UTC](https://discourse.itk.org/t/generating-itk-cmake-requires-from-project-code/5154 "2022-07-04T14:17:59Z")

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I recall seeing a script once upon a time that can parse a project’s includes and generate a minimal ITK CMake REQUIRES, does this exist or did I dream it? My google-fu is unable to conjure it up.

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## [operator \<\< is not clear ??](https://discourse.itk.org/t/operator-is-not-clear/5087)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 2\
**Last updated:** [June 15, 2022, 3:06am UTC](https://discourse.itk.org/t/operator-is-not-clear/5087 "2022-06-15T03:06:18Z")

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The weirdest thing is yesterday the project ran safely, today it throw an error: operator \<\< is not clear!. And vs located this error on BSplineDecompositionImageFilter function in itkBSplineDecompositionImageFilter.hxx…

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## [how to speed up resample interpolator?](https://discourse.itk.org/t/how-to-speed-up-resample-interpolator/5026)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 1\
**Last updated:** [May 31, 2022, 3:31am UTC](https://discourse.itk.org/t/how-to-speed-up-resample-interpolator/5026 "2022-05-31T03:31:44Z")

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When i use BsplineInterpolator to resample my nifit file(315x512x512) to (369X663x663), it takes almost 20 min, that is too low. how can i to speed up this? cpu: i5-4590 3.3ghz The following is my resample code: typ…

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## [Read Image](https://discourse.itk.org/t/read-image/5002)

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**Author:** [@Enrico\_Sarneri](https://discourse.itk.org/u/Enrico_Sarneri)\
**Replies:** 1\
**Last updated:** [May 23, 2022, 2:22pm UTC](https://discourse.itk.org/t/read-image/5002 "2022-05-23T14:22:21Z")

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Hello, I’m dealing with the following problem. I’ve a single 2D .dcm image and I want to read it through SITK. The problem is that SITK automatically applies the modality LUT when reading images, while usually when I rea…

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## [MacOS GitHub Actions, Azure Pipelines: itkeigen/Eigen/Core: fatal error: ‘omp.h’ file not found](https://discourse.itk.org/t/macos-github-actions-azure-pipelines-itkeigen-eigen-core-fatal-error-omp-h-file-not-found/4986)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 3\
**Last updated:** [May 14, 2022, 2:45pm UTC](https://discourse.itk.org/t/macos-github-actions-azure-pipelines-itkeigen-eigen-core-fatal-error-omp-h-file-not-found/4986 "2022-05-14T14:45:58Z")

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From this week it appears that new commits to elastix (using ITK and OpenMP), fail to compile on MacOS, both on GitHub Actions and Azure Pipelines, saying: Modules/ThirdParty/Eigen3/src/itkeigen/…/itkeigen/Eigen/Core:7…

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## [Will data.kitware.com get a GitHub login?](https://discourse.itk.org/t/will-data-kitware-com-get-a-github-login/4968)

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**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 1\
**Last updated:** [May 6, 2022, 4:27pm UTC](https://discourse.itk.org/t/will-data-kitware-com-get-a-github-login/4968 "2022-05-06T16:27:48Z")

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I just noticed having to grab my API key that it only has Google integration, any plans for GitHub?

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## [How to address const correctness build issues associated with ITKUltrasound module ?](https://discourse.itk.org/t/how-to-address-const-correctness-build-issues-associated-with-itkultrasound-module/4949)

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**Author:** [@jcfr](https://discourse.itk.org/u/jcfr)\
**Replies:** 2\
**Last updated:** [April 28, 2022, 1:52pm UTC](https://discourse.itk.org/t/how-to-address-const-correctness-build-issues-associated-with-itkultrasound-module/4949 "2022-04-28T13:52:39Z")

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Issues are summarized in https://github.com/KitwareMedical/ITKUltrasound/pull/198 and also copied below for convenience. These are errors reported when building SlicerITKUltrasound based of PR SlicerITKUltrasound#78 In…

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## [Drop support for Visual Studio 2017?](https://discourse.itk.org/t/drop-support-for-visual-studio-2017/4944)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 5\
**Last updated:** [April 26, 2022, 3:11pm UTC](https://discourse.itk.org/t/drop-support-for-visual-studio-2017/4944 "2022-04-26T15:11:40Z")

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Microsoft is dropping “vs2017-win2016” from their hosted pipelines for Azure Pipelines. An attempt to use it to test elastix produced the following error message: ##\[error\]This is a scheduled windows-2016 brownout. The…

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## [The exception(Requested region is (at least partially) outside the largest possible region) in orImageFilter.](https://discourse.itk.org/t/the-exception-requested-region-is-at-least-partially-outside-the-largest-possible-region-in-orimagefilter/4889)

<div class="topic-metadata">

**Author:** [@SummerZ2020](https://discourse.itk.org/u/SummerZ2020)\
**Replies:** 5\
**Last updated:** [March 29, 2022, 1:19pm UTC](https://discourse.itk.org/t/the-exception-requested-region-is-at-least-partially-outside-the-largest-possible-region-in-orimagefilter/4889 "2022-03-29T13:19:43Z")

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Hello, I am working on medical image processing , ITK is a great tool to help me in the implementation. But I have got the exception when the OrImageFilter was using. Here is my example code segment: using OrImageFi…

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## [How to get voxel coordinates(as in ITK snap ) from vtkimage viewer from mouse click](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719)

<div class="topic-metadata">

**Author:** [@SREERAG\_H](https://discourse.itk.org/u/SREERAG_H)\
**Replies:** 6\
**Last updated:** [March 3, 2022, 4:25pm UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719 "2022-03-03T16:25:34Z")

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Hello, I am trying to use ITK’s region growing algorithm for medical image segmentation. So to put the seedpoint i need exact voxel coordinates of the mouse click position in my vtkimageviewer. So how can I get those vo…

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