# Engineering

**URL:** https://discourse.itk.org/c/engineering/6.md?page=9

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

**Page:** 10

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## [Missing libITKIOGDCM-5.3.a file for GATE build](https://discourse.itk.org/t/missing-libitkiogdcm-5-3-a-file-for-gate-build/4090)

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**Author:** [@thestrangefruition](https://discourse.itk.org/u/thestrangefruition)\
**Replies:** 1\
**Last updated:** [May 3, 2021, 6:01pm UTC](https://discourse.itk.org/t/missing-libitkiogdcm-5-3-a-file-for-gate-build/4090 "2021-05-03T18:01:03Z")

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Hello all, I am attempting to install and compile GATE which used ITK alongside it. When running make to compile GATE, I get this error regarding a missing ITK file: strangefruition@WORK:~/Gate-9.1/gate\_v9.1-build$ mak…

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## [Using "short" data directly as input to the N4BiasFieldCorrectionImageFilter](https://discourse.itk.org/t/using-short-data-directly-as-input-to-the-n4biasfieldcorrectionimagefilter/4081)

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**Author:** [@Tamar](https://discourse.itk.org/u/Tamar)\
**Replies:** 2\
**Last updated:** [April 28, 2021, 3:16pm UTC](https://discourse.itk.org/t/using-short-data-directly-as-input-to-the-n4biasfieldcorrectionimagefilter/4081 "2021-04-28T15:16:13Z")

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I am incorporating the simpleITK N4BiasFieldCorrectionImageFilter into an existing c# application as part of the image processing chain. Is there is a way to read the input data directly from a “short” array that is sto…

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## [Trouble building Lesion Sizing Toolkit](https://discourse.itk.org/t/trouble-building-lesion-sizing-toolkit/4069)

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**Author:** [@clicq](https://discourse.itk.org/u/clicq)\
**Replies:** 1\
**Last updated:** [April 26, 2021, 8:59pm UTC](https://discourse.itk.org/t/trouble-building-lesion-sizing-toolkit/4069 "2021-04-26T20:59:34Z")

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I am having trouble trying to build the Lesion Sizing Toolkit module. I first tried the latest released version of ITK, 5.1.2, enabling the LesionSizingToolkit and ITKVTKglue modules. While the dependencies build correct…

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## [\[solved\] Disable python wrapping for a specific remote module](https://discourse.itk.org/t/solved-disable-python-wrapping-for-a-specific-remote-module/4055)

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**Author:** [@eric](https://discourse.itk.org/u/eric)\
**Replies:** 5\
**Last updated:** [April 20, 2021, 11:54pm UTC](https://discourse.itk.org/t/solved-disable-python-wrapping-for-a-specific-remote-module/4055 "2021-04-20T23:54:22Z")

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Hi, I’m trying to compile ITK with the remote module RTK and python wrapping. I’m having issues with building the RTK python wrapper with multiple symbol definition on Windows, I tried tackling it to no avail. In the m…

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## [method "GetLogBiasFieldAsImage" missing in N4BiasFieldCorrection c# implementation](https://discourse.itk.org/t/method-getlogbiasfieldasimage-missing-in-n4biasfieldcorrection-c-implementation/4033)

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**Author:** [@Tamar](https://discourse.itk.org/u/Tamar)\
**Replies:** 5\
**Last updated:** [April 20, 2021, 1:47pm UTC](https://discourse.itk.org/t/method-getlogbiasfieldasimage-missing-in-n4biasfieldcorrection-c-implementation/4033 "2021-04-20T13:47:49Z")

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Hello, I have the N4BiasFieldCorrectionImageFilter implemented in c# (visual studio) and it is working correctly and improving images. However, when I attempt to use the method GetLogBiasFieldAsImage() I get the follo…

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## [Build ITKPython module with additional supported data types](https://discourse.itk.org/t/build-itkpython-module-with-additional-supported-data-types/4042)

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**Author:** [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)\
**Replies:** 6\
**Last updated:** [April 20, 2021, 9:01am UTC](https://discourse.itk.org/t/build-itkpython-module-with-additional-supported-data-types/4042 "2021-04-20T09:01:59Z")

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Dear ITK community, after generating radially distorted images of lung tissue for my PhD project with ITKPython, I have realized that multiple filters I use do not support certain ITK data types. In order to solve this …

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## [KeyError: 'ITKSmoothing' when initializing RegularStepGradientDescentOptimizerv4](https://discourse.itk.org/t/keyerror-itksmoothing-when-initializing-regularstepgradientdescentoptimizerv4/3973)

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**Author:** [@Soren\_Christensen](https://discourse.itk.org/u/Soren_Christensen)\
**Replies:** 5\
**Last updated:** [April 7, 2021, 1:54am UTC](https://discourse.itk.org/t/keyerror-itksmoothing-when-initializing-regularstepgradientdescentoptimizerv4/3973 "2021-04-07T01:54:56Z")

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Hi, I have a fresh pip install of 5.1.1 and get this error when creating an ImageRegistrationMethodv4 object: registration = itk.ImageRegistrationMethodv4.REGv4F3F3.New(FixedImage=fixed, …

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## [FFTW, MKL, CUFFT and USE\_GPU](https://discourse.itk.org/t/fftw-mkl-cufft-and-use-gpu/3348)

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**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 10\
**Last updated:** [April 1, 2021, 6:43pm UTC](https://discourse.itk.org/t/fftw-mkl-cufft-and-use-gpu/3348 "2021-04-01T18:43:39Z")

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I notice there’s quite a few “accelerator” type options for ITK builds, but the documentation regarding what they do/impact is very sparse to non-existent. Can anyone point me at some docs, or enlighten me as to how muc…

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## [multi-Grid Bspline Image Registration error](https://discourse.itk.org/t/multi-grid-bspline-image-registration-error/3980)

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**Author:** [@hfeng](https://discourse.itk.org/u/hfeng)\
**Replies:** 6\
**Last updated:** [March 25, 2021, 1:53pm UTC](https://discourse.itk.org/t/multi-grid-bspline-image-registration-error/3980 "2021-03-25T13:53:58Z")

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Hi, I am testing the examples provided officially, DeformableRegistration6.cxx. The first 2 stages went well. But the third stage stopped at step 15 and exited with an error information “Optimizer stop condition = A rou…

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## [Multi-resolution Demons Registration](https://discourse.itk.org/t/multi-resolution-demons-registration/3981)

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**Author:** [@hfeng](https://discourse.itk.org/u/hfeng)\
**Replies:** 0\
**Last updated:** [March 24, 2021, 8:57pm UTC](https://discourse.itk.org/t/multi-resolution-demons-registration/3981 "2021-03-24T20:57:41Z")

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Hi, I am trying to do the deformable image registration using demons, simply extending the example “DeformableRegistration16.cxx” to 3d images. A multi-resolution scheme is used here with 4 levels. Where can I find the …

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## [Unable to use ITK filters when packaging my Python project that lists ITK as a requirement.](https://discourse.itk.org/t/unable-to-use-itk-filters-when-packaging-my-python-project-that-lists-itk-as-a-requirement/3977)

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**Author:** [@joeykleingers](https://discourse.itk.org/u/joeykleingers)\
**Replies:** 1\
**Last updated:** [March 24, 2021, 3:44pm UTC](https://discourse.itk.org/t/unable-to-use-itk-filters-when-packaging-my-python-project-that-lists-itk-as-a-requirement/3977 "2021-03-24T15:44:02Z")

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Hello, I am relatively new to Python and I have a Python project with a requirements.txt file and a setup.py file inside of it. My requirements.txt file has itk listed as a requirement. The code in my setup.py file re…

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## [Drop support for GCC 4.x?](https://discourse.itk.org/t/drop-support-for-gcc-4-x/3874)

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**Author:** [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Replies:** 10\
**Last updated:** [March 19, 2021, 2:27pm UTC](https://discourse.itk.org/t/drop-support-for-gcc-4-x/3874 "2021-03-19T14:27:29Z")

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PR2231 caused a lot of build errors on a nightly machine with GCC 4.8.4. GCC 4.8.4 does not seem to support C++11 well enough for the latest GTest to compile. Should we upgrade the compiler on this machine and say that …

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## [Git Help: ITK and ITKExamples](https://discourse.itk.org/t/git-help-itk-and-itkexamples/3963)

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**Author:** [@melrobin](https://discourse.itk.org/u/melrobin)\
**Replies:** 1\
**Last updated:** [March 17, 2021, 2:54pm UTC](https://discourse.itk.org/t/git-help-itk-and-itkexamples/3963 "2021-03-17T14:54:33Z")

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Can you give me just a little git help on a simple question? I forked ITKExamples and updated the fork. I have BUILD\_EXAMPLES turned on in ITK. A subsequent build of ITK creates a detached head in Modules/Remote/Sphin…

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## [Unsupported JPEG data precision 12](https://discourse.itk.org/t/unsupported-jpeg-data-precision-12/348)

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**Author:** [@madsdk](https://discourse.itk.org/u/madsdk)\
**Replies:** 7\
**Last updated:** [March 16, 2021, 10:17pm UTC](https://discourse.itk.org/t/unsupported-jpeg-data-precision-12/348 "2021-03-16T22:17:44Z")

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Hello, I’m hoping someone here has had this problem before and can help me figure out how to deal with it. I’m attempting to load a DICOM image series, but when I try to load it I get the following message: Unsupported…

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## [Image Registration using BSplines with order greater than 3](https://discourse.itk.org/t/image-registration-using-bsplines-with-order-greater-than-3/3955)

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**Author:** [@Felippe\_Trigueiro\_An](https://discourse.itk.org/u/Felippe_Trigueiro_An)\
**Replies:** 3\
**Last updated:** [March 15, 2021, 2:46pm UTC](https://discourse.itk.org/t/image-registration-using-bsplines-with-order-greater-than-3/3955 "2021-03-15T14:46:38Z")

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Hi, I’m trying to do a registration using BSplines of order 4. However, when I set 4 to the parameter ‘order’ in the BSplineTransformInitializer constructor, I got the following message: “sitk::ERROR: Invalid Order: 4 on…

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## [ITK Code Coverage \> 90%!](https://discourse.itk.org/t/itk-code-coverage-90/3946)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [March 9, 2021, 3:36pm UTC](https://discourse.itk.org/t/itk-code-coverage-90/3946 "2021-03-09T15:36:09Z")

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Thanks to the hard work of @jhlegarreta and others in the community, we just passed a major milestone: ITK Code Coverage is \> 90% :tada: :champagne: :sheep: :man\_cartwheeling: Well done!

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## [Seg fault in CharLS](https://discourse.itk.org/t/seg-fault-in-charls/3940)

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**Author:** [@gcsharp](https://discourse.itk.org/u/gcsharp)\
**Replies:** 2\
**Last updated:** [March 8, 2021, 8:47pm UTC](https://discourse.itk.org/t/seg-fault-in-charls/3940 "2021-03-08T20:47:00Z")

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Hi, I have a segmentation fault on program exit when linking to both ITK and dcmtk on Fedora 33. ITK is built from source whereas dcmtk is supplied by the OS package manager. The crash is a double free of static variab…

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## [Trying to extract stats from a DICOM image after using watershed segmentation and relabeling components](https://discourse.itk.org/t/trying-to-extract-stats-from-a-dicom-image-after-using-watershed-segmentation-and-relabeling-components/3930)

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**Author:** [@Diego\_C](https://discourse.itk.org/u/Diego_C)\
**Replies:** 1\
**Last updated:** [March 5, 2021, 6:17am UTC](https://discourse.itk.org/t/trying-to-extract-stats-from-a-dicom-image-after-using-watershed-segmentation-and-relabeling-components/3930 "2021-03-05T06:17:08Z")

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Hi! I have a pipeline where I do watershed segmentation and then I filter the number of components retaining only those with a given size. My code looks like this: im\_watershed = sitk.MorphologicalWatershed(im\_gradient…

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## [Using LabelIntensityStatisticsImageFilter in SimpleITK](https://discourse.itk.org/t/using-labelintensitystatisticsimagefilter-in-simpleitk/3910)

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**Author:** [@Diego\_C](https://discourse.itk.org/u/Diego_C)\
**Replies:** 6\
**Last updated:** [March 2, 2021, 9:52pm UTC](https://discourse.itk.org/t/using-labelintensitystatisticsimagefilter-in-simpleitk/3910 "2021-03-02T21:52:48Z")

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Hi! I am looking for an example of how to use LabelIntensityStatisticsImageFilter, to get stats from my connected components. I have this code: cc = sitk.ConnectedComponentsImageFilter() im\_cc = cc.Execute(image) sta…

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## [Link C++ library into cmake project](https://discourse.itk.org/t/link-c-library-into-cmake-project/3886)

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**Author:** [@PauloFavero](https://discourse.itk.org/u/PauloFavero)\
**Replies:** 6\
**Last updated:** [March 2, 2021, 10:55am UTC](https://discourse.itk.org/t/link-c-library-into-cmake-project/3886 "2021-03-02T10:55:14Z")

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Hello everyone, I created an MVC in a python notebook and then I want to translate it to C++. In order to do that, I followed the building instructions and I successfully compiled simpeITK. I am using CLion as an IDE. …

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## [Creating a module group with custom modules not compiling for ITK 4.13](https://discourse.itk.org/t/creating-a-module-group-with-custom-modules-not-compiling-for-itk-4-13/3906)

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**Author:** [@al-sabr](https://discourse.itk.org/u/al-sabr)\
**Replies:** 0\
**Last updated:** [February 25, 2021, 10:41am UTC](https://discourse.itk.org/t/creating-a-module-group-with-custom-modules-not-compiling-for-itk-4-13/3906 "2021-02-25T10:41:21Z")

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I tried the same exercise on ITK 5.1+ and was able to have a successful compilation. I had to downgrade to ITK 4.13 and the same work doesn’t compile because of linking error. I’m wondering if there’s any difference betw…

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## [Working with label maps](https://discourse.itk.org/t/working-with-label-maps/3901)

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**Author:** [@Diego\_C](https://discourse.itk.org/u/Diego_C)\
**Replies:** 2\
**Last updated:** [February 24, 2021, 8:41pm UTC](https://discourse.itk.org/t/working-with-label-maps/3901 "2021-02-24T20:41:49Z")

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Hi! I am wondering if I can use Label Maps to get simple stats of my connected components. I have a binary image img and I have done this: cc = sitk.ConnectedComponentImageFilter() img2 = cc.Execute(img) This giv…

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## [ITKMontage and Regular Grid Montages Requirement](https://discourse.itk.org/t/itkmontage-and-regular-grid-montages-requirement/3884)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 2\
**Last updated:** [February 24, 2021, 6:22pm UTC](https://discourse.itk.org/t/itkmontage-and-regular-grid-montages-requirement/3884 "2021-02-24T18:22:21Z")

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Is there a requirement that the ITKMontage filters require a montage on a regular grid? And by that I mean if I have a montage that is 20 Tiles Wide by 10 Tiles High but let’s say that the each of the corner tile images …

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## [SimpleITK BinaryDilateImageFilter](https://discourse.itk.org/t/simpleitk-binarydilateimagefilter/3894)

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**Author:** [@Diego\_C](https://discourse.itk.org/u/Diego_C)\
**Replies:** 1\
**Last updated:** [February 24, 2021, 1:59pm UTC](https://discourse.itk.org/t/simpleitk-binarydilateimagefilter/3894 "2021-02-24T13:59:13Z")

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Hi :wave: Where can I find an example of BinaryDilateImageFilter in SimpleITK? In particular, how to set the structuring element? Thanks, Diego

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## [Missing Examples ImportPixelBufferIntoAnImage/Code.py, and WRAP\_PYTHON question](https://discourse.itk.org/t/missing-examples-importpixelbufferintoanimage-code-py-and-wrap-python-question/3409)

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**Author:** [@fissell](https://discourse.itk.org/u/fissell)\
**Replies:** 4\
**Last updated:** [February 22, 2021, 9:39pm UTC](https://discourse.itk.org/t/missing-examples-importpixelbufferintoanimage-code-py-and-wrap-python-question/3409 "2021-02-22T21:39:26Z")

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Hi, I’m building InsightToolkit-5.1.0 on Ubuntu 20.04 with BUILD\_EXAMPLES ON and ITK\_WRAP\_PYTHON ON. Two questions. The make command succeeded. The make install command generated an errror: Make Error at Modules…

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## ['nullptr' error in ITK compiling](https://discourse.itk.org/t/nullptr-error-in-itk-compiling/3888)

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**Author:** [@zhuangming.shen](https://discourse.itk.org/u/zhuangming.shen)\
**Replies:** 1\
**Last updated:** [February 22, 2021, 7:52am UTC](https://discourse.itk.org/t/nullptr-error-in-itk-compiling/3888 "2021-02-22T07:52:09Z")

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Hi all, When I compiled ITK-4.13.3, I met a lot of "nullptr’ errors if I enable Module\_ITKVtkGlue in cmake. The VTK version and gcc version I used is 8.2.0 and 4.8.5. It seems I missed something. Does anybody know the s…

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## [PatchBased Denoising Filter Failures on ARM64 MacOS](https://discourse.itk.org/t/patchbased-denoising-filter-failures-on-arm64-macos/3878)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 3\
**Last updated:** [February 18, 2021, 2:11pm UTC](https://discourse.itk.org/t/patchbased-denoising-filter-failures-on-arm64-macos/3878 "2021-02-18T14:11:59Z")

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We have an ARM64 Build for MacOS Big Sur up on open.cdash.org and there has been a consistent 4 failures for a few weeks. Patch Based Denoising fails. The build bot is called “silicon.bluequartz.net” and is under the exp…

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## [How do I install the montaging remote module so that I can use it in my Python virtual environment?](https://discourse.itk.org/t/how-do-i-install-the-montaging-remote-module-so-that-i-can-use-it-in-my-python-virtual-environment/3873)

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**Author:** [@joeykleingers](https://discourse.itk.org/u/joeykleingers)\
**Replies:** 3\
**Last updated:** [February 16, 2021, 8:28pm UTC](https://discourse.itk.org/t/how-do-i-install-the-montaging-remote-module-so-that-i-can-use-it-in-my-python-virtual-environment/3873 "2021-02-16T20:28:54Z")

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Hello, I created a Python virtual environment and ran these commands: pip install itk pip install itk-montage However, when I try to create a TileMontage in my code import itk montage = itk.TileMontage.New() it fai…

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## [Python writing is not working correctly](https://discourse.itk.org/t/python-writing-is-not-working-correctly/3864)

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**Author:** [@sarthakpati](https://discourse.itk.org/u/sarthakpati)\
**Replies:** 5\
**Last updated:** [February 16, 2021, 4:15pm UTC](https://discourse.itk.org/t/python-writing-is-not-working-correctly/3864 "2021-02-16T16:15:00Z")

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Hi, The write image function in both SimpleITK and ITK python wrapping is broken. I am having a very weird issue when writing images whose information has changed: \>\>\> import SimpleITK as sitk \>\>\> base\_image = sitk.Re…

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## [Bump minimum CMake version for 5.2?](https://discourse.itk.org/t/bump-minimum-cmake-version-for-5-2/3856)

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**Author:** [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Replies:** 1\
**Last updated:** [February 12, 2021, 3:57pm UTC](https://discourse.itk.org/t/bump-minimum-cmake-version-for-5-2/3856 "2021-02-12T15:57:03Z")

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A recent PR to update bundled HDF5 version implicitly increases minimum CMake version to 3.14 in the default configuration. ITK currently requires 3.10.2. Should we bump minimum CMake version? If so, should we go for CMa…

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