# Latest

**URL:** https://discourse.itk.org/latest.md?page=23

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

**Page:** 24

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## [I need to extract only the brain portion excluding the skull from the CTA image. How can I do it using simpleITK filters? I tried otsu thresholding filters followed by connected components largest label but haven't got result i expected. Can someone help?](https://discourse.itk.org/t/i-need-to-extract-only-the-brain-portion-excluding-the-skull-from-the-cta-image-how-can-i-do-it-using-simpleitk-filters-i-tried-otsu-thresholding-filters-followed-by-connected-components-largest-label-but-havent-got-result-i-expected-can-someone-help/5935)

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**Author:** [@arpan56](https://discourse.itk.org/u/arpan56)\
**Replies:** 4\
**Last updated:** [May 12, 2023, 5:10am UTC](https://discourse.itk.org/t/i-need-to-extract-only-the-brain-portion-excluding-the-skull-from-the-cta-image-how-can-i-do-it-using-simpleitk-filters-i-tried-otsu-thresholding-filters-followed-by-connected-components-largest-label-but-havent-got-result-i-expected-can-someone-help/5935 "2023-05-12T05:10:10Z")

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otsu\_filter = sitk.OtsuThresholdImageFilter() otsu\_filter.SetInsideValue(0) otsu\_filter.SetOutsideValue(1) binary\_image = otsu\_filter.Execute(input\_image) cc\_filter = sitk.ConnectedComponentImageFilter() brain\_mask = cc…

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## [Concept checking in MultiResolutionPyramidImageFilter](https://discourse.itk.org/t/concept-checking-in-multiresolutionpyramidimagefilter/5929)

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**Author:** [@ericrhenry](https://discourse.itk.org/u/ericrhenry)\
**Replies:** 9\
**Last updated:** [May 11, 2023, 2:44am UTC](https://discourse.itk.org/t/concept-checking-in-multiresolutionpyramidimagefilter/5929 "2023-05-11T02:44:38Z")

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I am attempting to use this filter in a registration implementation requiring moving/fixed image pixels which have a vector PixelType (e.g. Itk::Vector\<double,3\>). My first assumption is that this filter should work with…

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## [wasi-build-debug debugging InputsOutputs.wasi.wasm using lldb14](https://discourse.itk.org/t/wasi-build-debug-debugging-inputsoutputs-wasi-wasm-using-lldb14/5897)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 3\
**Last updated:** [May 9, 2023, 9:43am UTC](https://discourse.itk.org/t/wasi-build-debug-debugging-inputsoutputs-wasi-wasm-using-lldb14/5897 "2023-05-09T09:43:07Z")

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@matt.mccormick Hi, I am having a lot of problems with watershed Segmentation even now with wasi build. I will explain this in my next message, I did try to debug a wasi-build-debug of InputsOutputs.wasi.wasm module a…

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## [Only the first image was used for RTK reconstruction](https://discourse.itk.org/t/only-the-first-image-was-used-for-rtk-reconstruction/5923)

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**Author:** [@ma1282029525](https://discourse.itk.org/u/ma1282029525)\
**Replies:** 4\
**Last updated:** [May 8, 2023, 8:15pm UTC](https://discourse.itk.org/t/only-the-first-image-was-used-for-rtk-reconstruction/5923 "2023-05-08T20:15:26Z")

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Regarding the RTK reconstruction, only the first image was used. I used the images collected by our device for CBCT reconstruction, but I still couldn’t obtain the correct results. I found that all the images in the reco…

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## [How to build python module?](https://discourse.itk.org/t/how-to-build-python-module/5925)

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**Author:** [@nnzzll](https://discourse.itk.org/u/nnzzll)\
**Replies:** 2\
**Last updated:** [May 8, 2023, 2:04pm UTC](https://discourse.itk.org/t/how-to-build-python-module/5925 "2023-05-08T14:04:54Z")

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I need to use ITKTwoProjectionRegistration with python3.9, however, the binary wheel from pypi only support for python\<=3.8. So I tried to build it myself following this tutorial I have successfully download docker then…

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## [About GPU Version Compilation of RTK](https://discourse.itk.org/t/about-gpu-version-compilation-of-rtk/5905)

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**Author:** [@ma1282029525](https://discourse.itk.org/u/ma1282029525)\
**Replies:** 8\
**Last updated:** [May 5, 2023, 2:43pm UTC](https://discourse.itk.org/t/about-gpu-version-compilation-of-rtk/5905 "2023-05-05T14:43:02Z")

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Recently, I have been learning RTK, and there are no issues with the CPU version compilation. However, after installing Cuda, I marked RTK in the cmake option\_ USE\_ CUDA, I can’t compile it anymore. I am sure Cuda has be…

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## [Optimizer's stopping condition is rounding error. Registration framework](https://discourse.itk.org/t/optimizers-stopping-condition-is-rounding-error-registration-framework/4603)

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**Author:** [@Luciano\_Rivetti](https://discourse.itk.org/u/Luciano_Rivetti)\
**Replies:** 4\
**Last updated:** [May 3, 2023, 8:19pm UTC](https://discourse.itk.org/t/optimizers-stopping-condition-is-rounding-error-registration-framework/4603 "2023-05-03T20:19:11Z")

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Hi everyone, I’m doing B-Spline registration of CT vs CBCT images. The Registration method Im using is: registration\_method = sitk.ImageRegistrationMethod() grid\_physical\_spacing = \[15.0\]\*3 image\_physical\_size …

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## [PyQt6 conversion to pixmap](https://discourse.itk.org/t/pyqt6-conversion-to-pixmap/5919)

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**Author:** [@CaptainHaddock](https://discourse.itk.org/u/CaptainHaddock)\
**Replies:** 2\
**Last updated:** [May 3, 2023, 12:52pm UTC](https://discourse.itk.org/t/pyqt6-conversion-to-pixmap/5919 "2023-05-03T12:52:53Z")

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How do I convert a DICOM image to a QPixmap in memory? I found an example of writing to disk in e.g. png (Resample and Convert DICOM to Common Image Formats — SimpleITK 2.0rc2 documentation), but looking to be able to co…

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## [Diffeomorphic demons registration algorithms work with vector image types?](https://discourse.itk.org/t/diffeomorphic-demons-registration-algorithms-work-with-vector-image-types/5920)

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**Author:** [@ericrhenry](https://discourse.itk.org/u/ericrhenry)\
**Replies:** 0\
**Last updated:** [May 2, 2023, 7:36pm UTC](https://discourse.itk.org/t/diffeomorphic-demons-registration-algorithms-work-with-vector-image-types/5920 "2023-05-02T19:36:14Z")

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I might be able to figure this out by plumbing the internals, or maybe trying to template a filter using a vector image, but I just wanted to see if anybody has the answer “at the ready”. In principle, registration by op…

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## [Output MRI images have value 0 (almost) everywhere after resampling using SimpleITK](https://discourse.itk.org/t/output-mri-images-have-value-0-almost-everywhere-after-resampling-using-simpleitk/5912)

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**Author:** [@bluefire](https://discourse.itk.org/u/bluefire)\
**Replies:** 2\
**Last updated:** [May 2, 2023, 7:40am UTC](https://discourse.itk.org/t/output-mri-images-have-value-0-almost-everywhere-after-resampling-using-simpleitk/5912 "2023-05-02T07:40:28Z")

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Hey! I have 3-dimensional NIfTI MRI images that I would like to resample to uniform voxel size (1, 1, 1). This works fine: img = sitk.ReadImage(img\_path) output\_spacing = \[1.0, 1.0, 1.0\] input\_spacing = img.GetSpacin…

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## [We are happy to announce the 2nd Get Your Brain Together Hackathon!](https://discourse.itk.org/t/we-are-happy-to-announce-the-2nd-get-your-brain-together-hackathon/5917)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [May 2, 2023, 12:34am UTC](https://discourse.itk.org/t/we-are-happy-to-announce-the-2nd-get-your-brain-together-hackathon/5917 "2023-05-02T00:34:19Z")

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2nd Get Your Brain Together Hackathon What? The Get Your Brain Together hackathons bring together neuroimage data generators, image registration researchers, and neurodata compute infrastructure providers for a hands-o…

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## [Node Emscripten for watershed segmentation, unexpected pixel type](https://discourse.itk.org/t/node-emscripten-for-watershed-segmentation-unexpected-pixel-type/5915)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [May 1, 2023, 9:17pm UTC](https://discourse.itk.org/t/node-emscripten-for-watershed-segmentation-unexpected-pixel-type/5915 "2023-05-01T21:17:55Z")

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@matt.mccormick Hi, I have following cxx code which does watershed segmentation, wasi is working now, but the node, inspect debugging, etc. not working, I have build node-emscripten debug, and node-inspect, node-emscri…

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## [Gantry tilt correction for list of DICOM images](https://discourse.itk.org/t/gantry-tilt-correction-for-list-of-dicom-images/5907)

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**Author:** [@EthanHarvey98](https://discourse.itk.org/u/EthanHarvey98)\
**Replies:** 3\
**Last updated:** [May 1, 2023, 7:47pm UTC](https://discourse.itk.org/t/gantry-tilt-correction-for-list-of-dicom-images/5907 "2023-05-01T19:47:25Z")

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Hello, I am working on writing my own gantry tilt correction function in Python. The function takes in a list of correctly ordered DICOM images loaded by pydicom, corrects each slice, and returns a corrected 3D image. d…

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## [Free form deformation or B-spline](https://discourse.itk.org/t/free-form-deformation-or-b-spline/5895)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 2\
**Last updated:** [May 1, 2023, 4:59pm UTC](https://discourse.itk.org/t/free-form-deformation-or-b-spline/5895 "2023-05-01T16:59:54Z")

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I am trying to perform multi-resolution free form deformation/B-spline between two 2D images by following this: http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/Python\_html/65\_Registration\_FFD.html I don’t…

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## [It's been chaotic lately. My purpose is to calculate the normalized mutual information of pre-registration and post-registration images, and make a comparison to observe the registration effect.](https://discourse.itk.org/t/its-been-chaotic-lately-my-purpose-is-to-calculate-the-normalized-mutual-information-of-pre-registration-and-post-registration-images-and-make-a-comparison-to-observe-the-registration-effect/5910)

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**Author:** [@ljjiayou](https://discourse.itk.org/u/ljjiayou)\
**Replies:** 1\
**Last updated:** [April 30, 2023, 9:01pm UTC](https://discourse.itk.org/t/its-been-chaotic-lately-my-purpose-is-to-calculate-the-normalized-mutual-information-of-pre-registration-and-post-registration-images-and-make-a-comparison-to-observe-the-registration-effect/5910 "2023-04-30T21:01:19Z")

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It’s been chaotic lately. My purpose is to calculate the normalized mutual information of pre-registration and post-registration images, and make a comparison to observe the registration effect. This is my code for cal…

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## [C++17 breaks Visual Studio 2017 -\> drop support?](https://discourse.itk.org/t/c-17-breaks-visual-studio-2017-drop-support/5884)

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**Author:** [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Replies:** 5\
**Last updated:** [April 28, 2023, 7:33pm UTC](https://discourse.itk.org/t/c-17-breaks-visual-studio-2017-drop-support/5884 "2023-04-28T19:33:55Z")

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Enabling C++17 seems to have broken VS2017 due to numerous bugs, some of which we have encountered and fixed before. See details in draft PR 4021. Should we drop it as a supported compiler?

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## [How to get properly-typed second input for BinaryGeneratorImageFilter?](https://discourse.itk.org/t/how-to-get-properly-typed-second-input-for-binarygeneratorimagefilter/5902)

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**Author:** [@SteveRobbins](https://discourse.itk.org/u/SteveRobbins)\
**Replies:** 4\
**Last updated:** [April 28, 2023, 4:34pm UTC](https://discourse.itk.org/t/how-to-get-properly-typed-second-input-for-binarygeneratorimagefilter/5902 "2023-04-28T16:34:01Z")

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I’m working with ITK 5.2.1. I created a 2-input filter that subclasses BinaryGeneratorImageFilter. It is instantiated with three separate template types: BinaryGeneratorImageFilter\<TIn1, TIn2, Tout\>. Inside my filter, …

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## [itkzlib-ng on windows name mangling](https://discourse.itk.org/t/itkzlib-ng-on-windows-name-mangling/5898)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 3\
**Last updated:** [April 28, 2023, 2:07pm UTC](https://discourse.itk.org/t/itkzlib-ng-on-windows-name-mangling/5898 "2023-04-28T14:07:13Z")

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I am building SimpleITK on vanilla Conda with the ITK third party zlib library. Other libraries are coming from conda and appear to use the Conda zlib library. I am seeing the following linking error on windows: ITKTest…

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## [Why is it normal for the SheppLogan created through rtk to have particularly low contrast](https://discourse.itk.org/t/why-is-it-normal-for-the-shepplogan-created-through-rtk-to-have-particularly-low-contrast/5904)

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**Author:** [@ma1282029525](https://discourse.itk.org/u/ma1282029525)\
**Replies:** 2\
**Last updated:** [April 28, 2023, 8:05am UTC](https://discourse.itk.org/t/why-is-it-normal-for-the-shepplogan-created-through-rtk-to-have-particularly-low-contrast/5904 "2023-04-28T08:05:01Z")

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using DSLType = rtk::DrawSheppLoganFilter\<OutputImageType, OutputImageType\>; DSLType::Pointer dsl2 = DSLType::New(); dsl2-\>InPlaceOff(); dsl2-\>SetInput(tomographySource-\>GetOutput()); dsl2-\>Update();

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## [reads DCM volume with grid transform, python](https://discourse.itk.org/t/reads-dcm-volume-with-grid-transform-python/5878)

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**Author:** [@Thirawat](https://discourse.itk.org/u/Thirawat)\
**Replies:** 2\
**Last updated:** [April 28, 2023, 4:38am UTC](https://discourse.itk.org/t/reads-dcm-volume-with-grid-transform-python/5878 "2023-04-28T04:38:25Z")

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Hi all, I have Dicom file that contains Dicom volume grid transform so, I want to read Dicom with that transformation. now I can only read raw Dicom My code: def readDCM(folder\_path, win\_level=50, win\_width=100): …

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## [Loading .bin files originated from OCTA devices](https://discourse.itk.org/t/loading-bin-files-originated-from-octa-devices/5900)

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**Author:** [@aliyavari](https://discourse.itk.org/u/aliyavari)\
**Replies:** 1\
**Last updated:** [April 26, 2023, 1:00pm UTC](https://discourse.itk.org/t/loading-bin-files-originated-from-octa-devices/5900 "2023-04-26T13:00:47Z")

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Dear All, I hope you are doing well. I am a PhD student and working on a project related to medical image segmentation. one of my tasks is to compare annotation/segmentation tools. To compare the tools, first I should …

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## [Explanation of principal axis and principal moments](https://discourse.itk.org/t/explanation-of-principal-axis-and-principal-moments/5882)

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**Author:** [@marabuuu](https://discourse.itk.org/u/marabuuu)\
**Replies:** 4\
**Last updated:** [April 25, 2023, 4:57pm UTC](https://discourse.itk.org/t/explanation-of-principal-axis-and-principal-moments/5882 "2023-04-25T16:57:23Z")

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Dear all, I am writing a blog post for biologists about different measurements including the ones provided by simpleITK and have problems to understand the measurements for principal axis and principal moments. I know t…

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## [ITK/SimpleITK code spell checking](https://discourse.itk.org/t/itk-simpleitk-code-spell-checking/5893)

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**Author:** [@dchen](https://discourse.itk.org/u/dchen)\
**Replies:** 4\
**Last updated:** [April 25, 2023, 1:01pm UTC](https://discourse.itk.org/t/itk-simpleitk-code-spell-checking/5893 "2023-04-25T13:01:02Z")

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Recently, I’ve been working on spell checking the headers in ITK’s code base. My goal has been to improve the ITK/SimpleITK documentation which gets pulled from the headers. I’m posting here just to memorialize my work…

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## [how to build watershed segmentation using itk-wasm](https://discourse.itk.org/t/how-to-build-watershed-segmentation-using-itk-wasm/5894)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [April 24, 2023, 8:36pm UTC](https://discourse.itk.org/t/how-to-build-watershed-segmentation-using-itk-wasm/5894 "2023-04-24T20:36:27Z")

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@matt.mccormick Hi, I already appreciate your help matt. I have a big question about build watershed segmentation in itk-wasm/emscripten(JS). i did manage to get the wasi-build working and segmented several png images…

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## [itk-wasm debugging example problem](https://discourse.itk.org/t/itk-wasm-debugging-example-problem/5870)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 7\
**Last updated:** [April 24, 2023, 8:25pm UTC](https://discourse.itk.org/t/itk-wasm-debugging-example-problem/5870 "2023-04-24T20:25:59Z")

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@matt.mccormick , Hi matt, I have been reading about the WebAssembly and emscripten to understand how ITK-WASM works for last two months. two months ago I got stuck in build watershed segmentation 2d for node.js, it si…

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## [Refactor code in a function](https://discourse.itk.org/t/refactor-code-in-a-function/5887)

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**Author:** [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)\
**Replies:** 2\
**Last updated:** [April 24, 2023, 1:06pm UTC](https://discourse.itk.org/t/refactor-code-in-a-function/5887 "2023-04-24T13:06:47Z")

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Hi, I’m trying to refactor some code in a function. The function is: ITKImgLabelType2D::Pointer GetLabelImageFilter(const ITKImgLabelType2D::Pointer& labelMap) { using LabelMapToLabelImageFilterType = itk::LabelMapToL…

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## [ITK examples, datasets](https://discourse.itk.org/t/itk-examples-datasets/5889)

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**Author:** [@kalpathi60](https://discourse.itk.org/u/kalpathi60)\
**Replies:** 1\
**Last updated:** [April 23, 2023, 8:57pm UTC](https://discourse.itk.org/t/itk-examples-datasets/5889 "2023-04-23T20:57:00Z")

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Havent used ITK in a very long time. I was interested in the levelsets example in the User guide. Are those examples part of the distribution? I dont see the source and the image used as part of that. Similar question …

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## [TransformContinuousIndexToPhysicalPoint got a different result](https://discourse.itk.org/t/transformcontinuousindextophysicalpoint-got-a-different-result/5885)

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**Author:** [@ljjiayou](https://discourse.itk.org/u/ljjiayou)\
**Replies:** 4\
**Last updated:** [April 21, 2023, 8:08pm UTC](https://discourse.itk.org/t/transformcontinuousindextophysicalpoint-got-a-different-result/5885 "2023-04-21T20:08:40Z")

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I took this line of code directly and got a different result than the world coordinates I saw in ITKsnap. Same image and index. why? this is my code : TransformContinuousIndexToPhysicalPoint

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## [Check that two images are at the same physical location](https://discourse.itk.org/t/check-that-two-images-are-at-the-same-physical-location/5883)

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**Author:** [@arobert01](https://discourse.itk.org/u/arobert01)\
**Replies:** 1\
**Last updated:** [April 20, 2023, 2:04pm UTC](https://discourse.itk.org/t/check-that-two-images-are-at-the-same-physical-location/5883 "2023-04-20T14:04:03Z")

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Hello, In itkImageToImageFilter the method VerifyInputInformation check that all the inputs are in the same physical location. When filters do not expect all input images to be at the same physical location, this method…

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## [FFTNormalizedCrossCorrelation: Edges and Filtering](https://discourse.itk.org/t/fftnormalizedcrosscorrelation-edges-and-filtering/5879)

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**Author:** [@elapins](https://discourse.itk.org/u/elapins)\
**Replies:** 2\
**Last updated:** [April 20, 2023, 1:16pm UTC](https://discourse.itk.org/t/fftnormalizedcrosscorrelation-edges-and-filtering/5879 "2023-04-20T13:16:15Z")

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I know that in most FFT based work, users often need to apply some sort of filter (often butterworth) to fade the edges of the image since FFT assumes infinite space. how does SimpleITK FFTNormalizedCrossCorrelation fun…

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