# Latest

**URL:** https://discourse.itk.org/latest.md?page=38

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

**Page:** 39

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## [ITK Examples Hackathon 2022 Summary](https://discourse.itk.org/t/itk-examples-hackathon-2022-summary/5007)

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**Author:** [@Tom\_Birdsong](https://discourse.itk.org/u/Tom_Birdsong)\
**Replies:** 0\
**Last updated:** [May 25, 2022, 12:58pm UTC](https://discourse.itk.org/t/itk-examples-hackathon-2022-summary/5007 "2022-05-25T12:58:21Z")

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Thank you to everyone who attended the ITK Examples Hackathon 2022 this past Friday! We had a great time with significant updates from remote and in-person attendees, including new C++ and Python examples, bug fixes, an …

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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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## [SimpeElastix affine registration throws error](https://discourse.itk.org/t/simpeelastix-affine-registration-throws-error/4962)

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**Author:** [@KateDelb](https://discourse.itk.org/u/KateDelb)\
**Replies:** 2\
**Last updated:** [May 23, 2022, 10:52am UTC](https://discourse.itk.org/t/simpeelastix-affine-registration-throws-error/4962 "2022-05-23T10:52:03Z")

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Trying to execute an affine registration with SimpleElastix: elastixImageFilter = sitk.ElastixImageFilter() elastixImageFilter.SetFixedImage(t1) elastixImageFilter.SetMovingImage(fet) elastixImageFilter.SetParameterMap(…

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## [How should I write a function for (flood filled image function iterator) ?](https://discourse.itk.org/t/how-should-i-write-a-function-for-flood-filled-image-function-iterator/4965)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 1\
**Last updated:** [May 23, 2022, 9:10am UTC](https://discourse.itk.org/t/how-should-i-write-a-function-for-flood-filled-image-function-iterator/4965 "2022-05-23T09:10:44Z")

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I would like to write a new function for the floodfilledimagefunctioniterator but I don’t know how should I write one. I am following what has been suggested here: Floodfill segmentation or is there an other possibillit…

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## [readImageFile - webworker](https://discourse.itk.org/t/readimagefile-webworker/4248)

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**Author:** [@sam](https://discourse.itk.org/u/sam)\
**Replies:** 5\
**Last updated:** [May 20, 2022, 1:19pm UTC](https://discourse.itk.org/t/readimagefile-webworker/4248 "2022-05-20T13:19:12Z")

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Hello everyone, I work on an application that allows to read medical images (DICOM format) and I use a itk js (readImageFile) that allows to read these images but that returns a webworker to each image read the problem i…

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## [3d segmentation refinement](https://discourse.itk.org/t/3d-segmentation-refinement/4993)

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**Author:** [@AmericaBG](https://discourse.itk.org/u/AmericaBG)\
**Replies:** 4\
**Last updated:** [May 19, 2022, 5:34pm UTC](https://discourse.itk.org/t/3d-segmentation-refinement/4993 "2022-05-19T17:34:29Z")

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Hi! I’ve a 3d mask segmentation that I would like to improve by using some method. For example, something like use the mask like a “seed” and refine the segmentation with the original image information. Original image …

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## [Resampling to volume to smaller size and smaller voxel spacing](https://discourse.itk.org/t/resampling-to-volume-to-smaller-size-and-smaller-voxel-spacing/4984)

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**Author:** [@shadab](https://discourse.itk.org/u/shadab)\
**Replies:** 10\
**Last updated:** [May 19, 2022, 1:55pm UTC](https://discourse.itk.org/t/resampling-to-volume-to-smaller-size-and-smaller-voxel-spacing/4984 "2022-05-19T13:55:21Z")

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Hi ITK community, I have recently started learning SimpleITK and have been stuck on a specific type of Resampling that I have been trying to implement. I have PET/CT Nifti images. My typical PET and CT volumes have the …

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## [numpy arrays with color normalization](https://discourse.itk.org/t/numpy-arrays-with-color-normalization/4946)

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**Author:** [@Jon](https://discourse.itk.org/u/Jon)\
**Replies:** 16\
**Last updated:** [May 16, 2022, 7:30pm UTC](https://discourse.itk.org/t/numpy-arrays-with-color-normalization/4946 "2022-05-16T19:30:09Z")

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… python script trying to use numpy arrays in ‘.npy’ files as input to color normalization, ie args for ‘itk.structure\_preserving\_color\_normalization\_filter’ flist is a list of input paths npy\_inp\_img = np.load(inp\_flist…

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## [How do i implement a feature such as (mask=segmentaion==c python language) with c++ itk](https://discourse.itk.org/t/how-do-i-implement-a-feature-such-as-mask-segmentaion-c-python-language-with-c-itk/4985)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 2\
**Last updated:** [May 16, 2022, 12:58am UTC](https://discourse.itk.org/t/how-do-i-implement-a-feature-such-as-mask-segmentaion-c-python-language-with-c-itk/4985 "2022-05-16T00:58:24Z")

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I want to transform the following code into ITK(c++ version), But I do not know which functions could do it. HELP! for c in labels: # labels is list that stores the labelmap's unique value mask = segmentation==c …

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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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## [Failure to get a file lock reading HF5: Singularity Container: NFSv4: ANTS](https://discourse.itk.org/t/failure-to-get-a-file-lock-reading-hf5-singularity-container-nfsv4-ants/4973)

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**Author:** [@toomanycats](https://discourse.itk.org/u/toomanycats)\
**Replies:** 2\
**Last updated:** [May 13, 2022, 6:49pm UTC](https://discourse.itk.org/t/failure-to-get-a-file-lock-reading-hf5-singularity-container-nfsv4-ants/4973 "2022-05-13T18:49:29Z")

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I’m running the NiPreps project, FmriPrep inside of a Singularity container. There’s a lot wrappers, including Nipype, but I do get an ITKv5 failure to read an HF5 transform because of a file lock issue. I’m wondering i…

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## [ITK 5.3.0 Release Candidate 3 available for testing](https://discourse.itk.org/t/itk-5-3-0-release-candidate-3-available-for-testing/4989)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [May 13, 2022, 4:48pm UTC](https://discourse.itk.org/t/itk-5-3-0-release-candidate-3-available-for-testing/4989 "2022-05-13T16:48:55Z")

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ITK 5.3 Release Candidate 3 Release Notes We are happy to announce the Insight Toolkit (ITK) 5.3 Release Candidate 3 is available for testing! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scient…

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## [itk-python weird time consuming](https://discourse.itk.org/t/itk-python-weird-time-consuming/4975)

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**Author:** [@HiunIce](https://discourse.itk.org/u/HiunIce)\
**Replies:** 4\
**Last updated:** [May 13, 2022, 12:20pm UTC](https://discourse.itk.org/t/itk-python-weird-time-consuming/4975 "2022-05-13T12:20:08Z")

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Hi teams, I tried some itk.filter both in cpp and python. The cpp version is ok but python version is quite time consuming(for New statement) ‘’’ cost 15 second for this code itk.RescaleIntensityImageFilter\[self.inpu…

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## [itk montage tiff without ome-tiff header](https://discourse.itk.org/t/itk-montage-tiff-without-ome-tiff-header/4948)

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**Author:** [@allen](https://discourse.itk.org/u/allen)\
**Replies:** 3\
**Last updated:** [May 13, 2022, 10:35am UTC](https://discourse.itk.org/t/itk-montage-tiff-without-ome-tiff-header/4948 "2022-05-13T10:35:48Z")

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hello, i use the itk montage stitching tiles and get a tiff file, but it is not standard tiff format i think, which can not be opened in openslide is there a way to get a OME-XML metadata to the tiff file of itk monta…

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## [VectorImageToImageMetricTraitsv4 with VectorImage - dynamic number of components](https://discourse.itk.org/t/vectorimagetoimagemetrictraitsv4-with-vectorimage-dynamic-number-of-components/4980)

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**Author:** [@zbjornson](https://discourse.itk.org/u/zbjornson)\
**Replies:** 1\
**Last updated:** [May 13, 2022, 9:43am UTC](https://discourse.itk.org/t/vectorimagetoimagemetrictraitsv4-with-vectorimage-dynamic-number-of-components/4980 "2022-05-13T09:43:29Z")

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Hello, The intro text to Perform Registration on Vector Images — v5.3.0 suggests that that code can be used with a VectorImage. It uses VectorImageToImageMetricTraitsv4, and the docs for that class say it works with Vec…

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## [Mesh visualization itk](https://discourse.itk.org/t/mesh-visualization-itk/4964)

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**Author:** [@Jakub\_Mitura](https://discourse.itk.org/u/Jakub_Mitura)\
**Replies:** 8\
**Last updated:** [May 11, 2022, 3:43pm UTC](https://discourse.itk.org/t/mesh-visualization-itk/4964 "2022-05-11T15:43:11Z")

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Hello i would like to use some external visualization tool with multiview, scroling and mesh visualization using python I have a problem that as far as I understand meshes are only in itk, and all visualization examples…

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## [Registration of volume Ct-Scans with different morphology/anatomical structures](https://discourse.itk.org/t/registration-of-volume-ct-scans-with-different-morphology-anatomical-structures/4971)

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**Author:** [@Le\_Warman](https://discourse.itk.org/u/Le_Warman)\
**Replies:** 1\
**Last updated:** [May 10, 2022, 11:20pm UTC](https://discourse.itk.org/t/registration-of-volume-ct-scans-with-different-morphology-anatomical-structures/4971 "2022-05-10T23:20:43Z")

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Hello, I’m currently working with a dataset with different patients. Each one of them is a 3D CT-scan volume with different properties such as pixel spacing, hounsfield units range (but I’m doing a clipping between -102…

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## [Overlaying Segmented mask with color over Input Vtkimagedata 3D (Dicom series)](https://discourse.itk.org/t/overlaying-segmented-mask-with-color-over-input-vtkimagedata-3d-dicom-series/4912)

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**Author:** [@SREERAG\_H](https://discourse.itk.org/u/SREERAG_H)\
**Replies:** 14\
**Last updated:** [May 9, 2022, 6:18am UTC](https://discourse.itk.org/t/overlaying-segmented-mask-with-color-over-input-vtkimagedata-3d-dicom-series/4912 "2022-05-09T06:18:51Z")

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Hi all , I am working with ITK Segmentation algorithm’s. My input is a Dicom series and I used VtkDicomReader to get the vtkimagedata and then I converted to itkimage(Short, dmension=3) and I used connected threshold re…

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## [Installation from Git sources (master, 5.3rc03) with double vector support](https://discourse.itk.org/t/installation-from-git-sources-master-5-3rc03-with-double-vector-support/4957)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 6\
**Last updated:** [May 7, 2022, 10:56am UTC](https://discourse.itk.org/t/installation-from-git-sources-master-5-3rc03-with-double-vector-support/4957 "2022-05-07T10:56:32Z")

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Installation from Git sources (master, 5.3rc03) with double vector support Dear developers, I am trying to get a deformable transformation. I am now using Arch (see below) and “regular” compilation flags (as provided by…

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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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## [Is ITKStrain still supported?](https://discourse.itk.org/t/is-itkstrain-still-supported/4956)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 3\
**Last updated:** [May 6, 2022, 3:03pm UTC](https://discourse.itk.org/t/is-itkstrain-still-supported/4956 "2022-05-06T15:03:10Z")

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Continuing the discussion from Installation of ITKElastix with pip Installing and using Python wrapped Remote Module: Hello! I am trying to install itk-strain with pip, but I got an error (see below). Thus, I clicked o…

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## [SimpleITK: Extract largest Connected component from binary image](https://discourse.itk.org/t/simpleitk-extract-largest-connected-component-from-binary-image/4958)

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**Author:** [@pythonuser](https://discourse.itk.org/u/pythonuser)\
**Replies:** 2\
**Last updated:** [May 3, 2022, 5:21pm UTC](https://discourse.itk.org/t/simpleitk-extract-largest-connected-component-from-binary-image/4958 "2022-05-03T17:21:39Z")

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Hi, I am trying to extract the largest connected component from a binary image / (delete all connected components but the largest one), I tried using the Label filters, but couldn’t make it work. Thanks in advance!

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## [Image quality after registration](https://discourse.itk.org/t/image-quality-after-registration/4947)

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**Author:** [@Moha\_data](https://discourse.itk.org/u/Moha_data)\
**Replies:** 4\
**Last updated:** [May 2, 2022, 5:35pm UTC](https://discourse.itk.org/t/image-quality-after-registration/4947 "2022-05-02T17:35:04Z")

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Hello, I applied affine registration to images, and the result shows that images are successfully registered. However, when I compare the fixed image with the registered moving image, I can see that the fixed image is b…

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## [Binary Morphological Filter with Padding](https://discourse.itk.org/t/binary-morphological-filter-with-padding/4921)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 6\
**Last updated:** [May 2, 2022, 5:31pm UTC](https://discourse.itk.org/t/binary-morphological-filter-with-padding/4921 "2022-05-02T17:31:52Z")

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I am using binary morphological image filter with large structuring element radius to find the convex hull between the lungs. However I haven’t been able to build a satsfatory convex hull yet as some holes have remai…

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## [Simple ITK Crop Image](https://discourse.itk.org/t/simple-itk-crop-image/4246)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 4\
**Last updated:** [April 28, 2022, 5:31pm UTC](https://discourse.itk.org/t/simple-itk-crop-image/4246 "2022-04-28T17:31:03Z")

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Hey guys: I have a 3D grey-level image (256, 256, 192); I have a 3D label-image binary (1 and 0) to define a segmentation (256, 256, 192); I use LabelShapeStatisticsImageFilter to get a bounding box or region for my l…

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## [Simple region-growing segmentation of the small intestine is terrible, using many seed points and 3D T2 MRI data](https://discourse.itk.org/t/simple-region-growing-segmentation-of-the-small-intestine-is-terrible-using-many-seed-points-and-3d-t2-mri-data/4942)

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**Author:** [@aliabidi](https://discourse.itk.org/u/aliabidi)\
**Replies:** 8\
**Last updated:** [April 28, 2022, 4:55pm UTC](https://discourse.itk.org/t/simple-region-growing-segmentation-of-the-small-intestine-is-terrible-using-many-seed-points-and-3d-t2-mri-data/4942 "2022-04-28T16:55:15Z")

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I am currently trying to apply region growing to 3D T2 MRI scans which I have been given, to segment the end of the small intenstine (i.e. the terminal ileum). I am using several features from SimpleITK. The problem is, …

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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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## [Calculating mutual information of two images](https://discourse.itk.org/t/calculating-mutual-information-of-two-images/4931)

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**Author:** [@Flo](https://discourse.itk.org/u/Flo)\
**Replies:** 4\
**Last updated:** [April 26, 2022, 12:09pm UTC](https://discourse.itk.org/t/calculating-mutual-information-of-two-images/4931 "2022-04-26T12:09:43Z")

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I have corresponding MRI and CT image volumes. I have registered them using the mattes mutual information metric. The results seem fine but I would like to be able to calculate the metric of two 3D images that are alread…

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## [How to call the FEM module in Python?](https://discourse.itk.org/t/how-to-call-the-fem-module-in-python/4937)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 2\
**Last updated:** [April 26, 2022, 9:45am UTC](https://discourse.itk.org/t/how-to-call-the-fem-module-in-python/4937 "2022-04-26T09:45:47Z")

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How to use the FEM module? I must be doing something terribly silly. Can you please help me to access the FEM module? I was just trying to translate DeformableRegistration1.cxx into Python. Thanks. import itk itk.fem …

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