# Uncategorized

**URL:** https://discourse.itk.org/c/uncategorized/1.md?no_subcategories=false&page=5

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

**Page:** 6

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## [ITK.js](https://discourse.itk.org/t/itk-js/622)

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**Author:** [@lolo](https://discourse.itk.org/u/lolo)\
**Replies:** 5\
**Last updated:** [August 15, 2022, 8:49pm UTC](https://discourse.itk.org/t/itk-js/622 "2022-08-15T20:49:22Z")

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Hi all, I’m an old ITK / VTK user (in time not age!). I was very enthusiatic when I found out ITK.js, VTK.js and the ITK-VTK-image-Viewer.js. I’m now a bit confused on what could be achieved… VTK.js looks like a powerf…

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## [largestpossibile region is bigger than request region and m\_buffered region](https://discourse.itk.org/t/largestpossibile-region-is-bigger-than-request-region-and-m-buffered-region/5222)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 3\
**Last updated:** [July 29, 2022, 1:23am UTC](https://discourse.itk.org/t/largestpossibile-region-is-bigger-than-request-region-and-m-buffered-region/5222 "2022-07-29T01:23:23Z")

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hi I load a nii.gz file using ITK, and I find this file\`s largest possible region(531,531,604) is bigger than request and m\_buffer region (both of them are 512,512,604). I know this can be fixed by setrequest() or setmy…

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## [simple ITK in windows container](https://discourse.itk.org/t/simple-itk-in-windows-container/5169)

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**Author:** [@Sowmya\_Rajesh](https://discourse.itk.org/u/Sowmya_Rajesh)\
**Replies:** 5\
**Last updated:** [July 18, 2022, 6:45pm UTC](https://discourse.itk.org/t/simple-itk-in-windows-container/5169 "2022-07-18T18:45:26Z")

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I am trying to use simpleITK inside the docker windows container. The container is built without any error. But when I run the container, I am getting the following error. Traceback (most recent call last): File “c:\\h…

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## [Remove multiple labels in 1 bone and have only 1 label per bone](https://discourse.itk.org/t/remove-multiple-labels-in-1-bone-and-have-only-1-label-per-bone/5186)

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**Author:** [@Vilma\_Bozgo](https://discourse.itk.org/u/Vilma_Bozgo)\
**Replies:** 5\
**Last updated:** [July 15, 2022, 2:14pm UTC](https://discourse.itk.org/t/remove-multiple-labels-in-1-bone-and-have-only-1-label-per-bone/5186 "2022-07-15T14:14:29Z")

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Hello! I have a multilabel skeleton mask for MRI images of the skeleton. But for the same bone I sometimes get different labels, like in the image attached where the first bone gets a red label and a green label. But in …

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## [Include ITK in own project in Visual studio 2022](https://discourse.itk.org/t/include-itk-in-own-project-in-visual-studio-2022/5178)

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**Author:** [@KateDelb](https://discourse.itk.org/u/KateDelb)\
**Replies:** 1\
**Last updated:** [July 14, 2022, 12:49pm UTC](https://discourse.itk.org/t/include-itk-in-own-project-in-visual-studio-2022/5178 "2022-07-14T12:49:54Z")

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This might be a stupid question, but I’m new so bare with me. I’m trying to include ITK into my on visual studio project: project-\>properties-\>c/c+±\>general-\>Additional Include But I’m not quite sure what to include? I…

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## [How to do “Annotation&Measurement” on MPR like MITK or 3D Slicer?](https://discourse.itk.org/t/how-to-do-annotation-measurement-on-mpr-like-mitk-or-3d-slicer/5174)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 1\
**Last updated:** [July 13, 2022, 4:55pm UTC](https://discourse.itk.org/t/how-to-do-annotation-measurement-on-mpr-like-mitk-or-3d-slicer/5174 "2022-07-13T16:55:45Z")

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How to do “Annotation&Measurement” on MPR like MITK or 3D Slicer?

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## [3D Affine registration: different datasets](https://discourse.itk.org/t/3d-affine-registration-different-datasets/5127)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 23\
**Last updated:** [July 1, 2022, 7:09pm UTC](https://discourse.itk.org/t/3d-affine-registration-different-datasets/5127 "2022-07-01T19:09:44Z")

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Hello, I am working on 3D CT images. I need to perform registration on two different datasets. I randomly selected a scan from dataset 1 as the fixed\_image and perform a 3d affine registration to register all the scans …

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## [Is it possible to extract an array of the image intensities in Sitk?](https://discourse.itk.org/t/is-it-possible-to-extract-an-array-of-the-image-intensities-in-sitk/5147)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 1\
**Last updated:** [June 30, 2022, 3:44pm UTC](https://discourse.itk.org/t/is-it-possible-to-extract-an-array-of-the-image-intensities-in-sitk/5147 "2022-06-30T15:44:32Z")

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I am working with 3D images(300) of size (128x128x128). I want to extract the image area/an array of the image intensities (remove the background), do some transformation, and plug the transformed image intensities back …

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## [ITK 5.2.0 Known Issues location](https://discourse.itk.org/t/itk-5-2-0-known-issues-location/5105)

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**Author:** [@Francois](https://discourse.itk.org/u/Francois)\
**Replies:** 2\
**Last updated:** [June 29, 2022, 3:29pm UTC](https://discourse.itk.org/t/itk-5-2-0-known-issues-location/5105 "2022-06-29T15:29:42Z")

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Hello, I need to validate ITK 5.2.0 in our software as a third party library. As we are validating ITK I will need to know what are the known issues for that particular version. The github page for the issues just ref…

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## [check is the origin and spacing data present](https://discourse.itk.org/t/check-is-the-origin-and-spacing-data-present/5089)

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**Author:** [@Jakub\_Mitura](https://discourse.itk.org/u/Jakub_Mitura)\
**Replies:** 4\
**Last updated:** [June 27, 2022, 5:43pm UTC](https://discourse.itk.org/t/check-is-the-origin-and-spacing-data-present/5089 "2022-06-27T17:43:42Z")

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I have relatively big dataset from various sources all in MHA I want to be check that all have correctly set spacing,origin and direction - is there a way to check it ? To clarify I read already all of the origin and s…

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## [groupwise registration with labels](https://discourse.itk.org/t/groupwise-registration-with-labels/5128)

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**Author:** [@Jakub\_Mitura](https://discourse.itk.org/u/Jakub_Mitura)\
**Replies:** 1\
**Last updated:** [June 27, 2022, 1:57pm UTC](https://discourse.itk.org/t/groupwise-registration-with-labels/5128 "2022-06-27T13:57:03Z")

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Hello I have dataset with 5 MRI images per patient plus label associated with one of them It seems that groupwise registration could be best option for me like in for example \[1\], but I can not find a way to perform gro…

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## [itk-wasm, hellow world , nodejs, not working](https://discourse.itk.org/t/itk-wasm-hellow-world-nodejs-not-working/5115)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 9\
**Last updated:** [June 26, 2022, 7:45pm UTC](https://discourse.itk.org/t/itk-wasm-hellow-world-nodejs-not-working/5115 "2022-06-26T19:45:54Z")

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@lassoan Dear Anders, I have a beginner question. I spent almost two weeks to put together my development environment in windows, wsl+ubuntu2004, macos. I use virtual wsl2 subsystem in windows as linux backend. my fro…

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## [What is the difference between a rotation transform and SetDirection?](https://discourse.itk.org/t/what-is-the-difference-between-a-rotation-transform-and-setdirection/5083)

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**Author:** [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)\
**Replies:** 1\
**Last updated:** [June 10, 2022, 8:03am UTC](https://discourse.itk.org/t/what-is-the-difference-between-a-rotation-transform-and-setdirection/5083 "2022-06-10T08:03:31Z")

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Hello, I am trying to understand the basics of SimpleITK. I am having doubts as to how a translation transform differs from a SetOffset and a rotation transform differs from a SetDirection. What I am hoping to obtain is…

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## [Combining overlapping 3D images](https://discourse.itk.org/t/combining-overlapping-3d-images/5059)

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**Author:** [@Ale\_Ballester](https://discourse.itk.org/u/Ale_Ballester)\
**Replies:** 2\
**Last updated:** [June 6, 2022, 4:38pm UTC](https://discourse.itk.org/t/combining-overlapping-3d-images/5059 "2022-06-06T16:38:52Z")

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Let’s say I have two 3D ultrasound images representing two overlapping regions. How can I combine those images into a single 3D image? I want to preserve spatial information.

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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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## [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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## [Geodesic Active contour Level set image filter error](https://discourse.itk.org/t/geodesic-active-contour-level-set-image-filter-error/2182)

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**Author:** [@Pooja\_Virkar](https://discourse.itk.org/u/Pooja_Virkar)\
**Replies:** 10\
**Last updated:** [March 15, 2022, 1:26am UTC](https://discourse.itk.org/t/geodesic-active-contour-level-set-image-filter-error/2182 "2022-03-15T01:26:59Z")

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Hello, I am trying to use Geodesic Active contour Level set image filter from https://itk.org/ITKExamples/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Documentation.html First I was trying to wo…

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## [dicom nrrd nifti spacing, origin mismatch.](https://discourse.itk.org/t/dicom-nrrd-nifti-spacing-origin-mismatch/4311)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 10\
**Last updated:** [March 7, 2022, 3:52pm UTC](https://discourse.itk.org/t/dicom-nrrd-nifti-spacing-origin-mismatch/4311 "2022-03-07T15:52:30Z")

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Hello I am working with dicom and nrrd image file formats. Usually nrrd files are segmentations and in different spacing and origin compared to the dicoms. So my workflow is: resample the nrrd file on dicom to match di…

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## [ITK ERROR: Hematoxylin and Eosin are getting mixed up; failed](https://discourse.itk.org/t/itk-error-hematoxylin-and-eosin-are-getting-mixed-up-failed/4767)

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**Author:** [@Jon](https://discourse.itk.org/u/Jon)\
**Replies:** 37\
**Last updated:** [March 1, 2022, 9:59am UTC](https://discourse.itk.org/t/itk-error-hematoxylin-and-eosin-are-getting-mixed-up-failed/4767 "2022-03-01T09:59:56Z")

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I’m trying to help my doctor daughter by using machine learning to find tumors in her osteosarcoma histology slides. The H&E staining is poor — quite low but visible to humans – compared to that of the public domain data…

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## [Rotation Around a Specified Axis](https://discourse.itk.org/t/rotation-around-a-specified-axis/1875)

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**Author:** [@DrJessop](https://discourse.itk.org/u/DrJessop)\
**Replies:** 9\
**Last updated:** [February 24, 2022, 1:43pm UTC](https://discourse.itk.org/t/rotation-around-a-specified-axis/1875 "2022-02-24T13:43:43Z")

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I am trying to rotate an MRI image around the z-axis by 90 degrees. I can specify the center of rotation using an Euler3DTransform, however I cannot specify the direction of rotation (the image is diagonally rotated). Ho…

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## [Can I get the index of a point in a point container?](https://discourse.itk.org/t/can-i-get-the-index-of-a-point-in-a-point-container/4828)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 1\
**Last updated:** [February 23, 2022, 3:47pm UTC](https://discourse.itk.org/t/can-i-get-the-index-of-a-point-in-a-point-container/4828 "2022-02-23T15:47:29Z")

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Can I get the index of a point in a point container?

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## [custom struturing element](https://discourse.itk.org/t/custom-struturing-element/4797)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 1\
**Last updated:** [February 9, 2022, 9:19pm UTC](https://discourse.itk.org/t/custom-struturing-element/4797 "2022-02-09T21:19:47Z")

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How do I build a custom flat struturing element assinging a different number to each of its cells?

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## [How to store a 3d deformation field array into an mhd image](https://discourse.itk.org/t/how-to-store-a-3d-deformation-field-array-into-an-mhd-image/4761)

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**Author:** [@Hongying\_Feng](https://discourse.itk.org/u/Hongying_Feng)\
**Replies:** 2\
**Last updated:** [January 28, 2022, 2:38pm UTC](https://discourse.itk.org/t/how-to-store-a-3d-deformation-field-array-into-an-mhd-image/4761 "2022-01-28T14:38:33Z")

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I have a numpy array of size (160,512,512,3), standing for a 3D deformation field. I am trying to save this array to an image (desired type is itk.Image\[itk.Vector\[itk.F,3\],3\]) by using itk.GetImageFromArray. The code …

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## [Regarding C++11 noexcept](https://discourse.itk.org/t/regarding-c-11-noexcept/1517)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 23\
**Last updated:** [January 7, 2022, 6:34pm UTC](https://discourse.itk.org/t/regarding-c-11-noexcept/1517 "2022-01-07T18:34:41Z")

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It was an unpleasant surprise to me, to read here at the forum (December 2017) that noexcept might sometimes harm the performance. As noted by @matt.mccormick at warning: dynamic exception specifications are deprecated i…

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## [While building the code I'm getting this error undefined reference to \`vtable for itk::ImageFileReaderException'](https://discourse.itk.org/t/while-building-the-code-im-getting-this-error-undefined-reference-to-vtable-for-itk-imagefilereaderexception/4679)

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**Author:** [@priyanka](https://discourse.itk.org/u/priyanka)\
**Replies:** 4\
**Last updated:** [December 20, 2021, 1:45pm UTC](https://discourse.itk.org/t/while-building-the-code-im-getting-this-error-undefined-reference-to-vtable-for-itk-imagefilereaderexception/4679 "2021-12-20T13:45:19Z")

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‘’’ libexample-postgresql-lib.a(UserService.cpp.o): In function itk::ImageFileReaderException::ImageFileReaderException(char const\*, unsigned int, char const\*, char const\*)': UserService.cpp:(.text.\_ZN3itk24ImageFileRea…

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## [Bspline FFD registration](https://discourse.itk.org/t/bspline-ffd-registration/4682)

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**Author:** [@VeerBal](https://discourse.itk.org/u/VeerBal)\
**Replies:** 0\
**Last updated:** [December 17, 2021, 5:29pm UTC](https://discourse.itk.org/t/bspline-ffd-registration/4682 "2021-12-17T17:29:38Z")

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Hi there So I’m registering 2 lung CT images of same subject at different time points using the Bspline FFD approach . These lung images are in .mha format and I’m using the same approach as done in the POPI model. So …

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## [Error while configuring itk example with vcpkg](https://discourse.itk.org/t/error-while-configuring-itk-example-with-vcpkg/4672)

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**Author:** [@priyanka](https://discourse.itk.org/u/priyanka)\
**Replies:** 5\
**Last updated:** [December 17, 2021, 6:54am UTC](https://discourse.itk.org/t/error-while-configuring-itk-example-with-vcpkg/4672 "2021-12-17T06:54:32Z")

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Please see the image below for the error I’m facing.

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## [Contouring with having initial curve using filters in Simple ITK module?](https://discourse.itk.org/t/contouring-with-having-initial-curve-using-filters-in-simple-itk-module/4620)

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**Author:** [@shahrokh\_nasseri](https://discourse.itk.org/u/shahrokh_nasseri)\
**Replies:** 18\
**Last updated:** [December 15, 2021, 4:16pm UTC](https://discourse.itk.org/t/contouring-with-having-initial-curve-using-filters-in-simple-itk-module/4620 "2021-12-15T16:16:55Z")

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Hello Dear Developers and Users Consider the following figure. This screenshot contains a 2D image of EPID, named EPID. Consider the following figure. This screenshot contains the contour of the pelvic bone extracte…

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## [use of SimpleFilter in 3dslicer](https://discourse.itk.org/t/use-of-simplefilter-in-3dslicer/4664)

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**Author:** [@mahi](https://discourse.itk.org/u/mahi)\
**Replies:** 1\
**Last updated:** [December 10, 2021, 9:35pm UTC](https://discourse.itk.org/t/use-of-simplefilter-in-3dslicer/4664 "2021-12-10T21:35:02Z")

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heloo. i want to use from SimpleFilter module in 3dslicer but it doesnt have any documentation . can any one help me?

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## [DRR image](https://discourse.itk.org/t/drr-image/4638)

<div class="topic-metadata">

**Author:** [@wangjun456](https://discourse.itk.org/u/wangjun456)\
**Replies:** 6\
**Last updated:** [December 8, 2021, 3:18am UTC](https://discourse.itk.org/t/drr-image/4638 "2021-12-08T03:18:13Z")

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I use the example GetDRRSiddonJacobsRayTracing.cxx to generate DRR images. The data in the example can generate DRR images. when I used my own data, I can only generate an all black image. Does anyone know why?

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