**Author:** [@Gordian](https://discourse.itk.org/u/Gordian)\
**Replies:** 6\
**Last updated:** [January 28, 2021, 1:05am UTC](https://discourse.itk.org/t/update-remote-module-in-itk/2615 "2021-01-28T01:05:40Z")
Hello, just a question regarding the updates of remote modules in ITK. I have a remote module in ITK. The \*.remote.cmake points to the \* github repo. Initially ITK load the files from the remote repo and build the remo…
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## [Extract brain from 3D binary mask images](https://discourse.itk.org/t/extract-brain-from-3d-binary-mask-images/3791)
**Author:** [@lisongang-PR](https://discourse.itk.org/u/lisongang-PR)\
**Replies:** 2\
**Last updated:** [January 26, 2021, 12:22pm UTC](https://discourse.itk.org/t/extract-brain-from-3d-binary-mask-images/3791 "2021-01-26T12:22:13Z")
I got the 3D mask of brain by using StripTsImageFilter，How can I use mask to extract brain？
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## [Deformable registration, but only allow deformation in one direction](https://discourse.itk.org/t/deformable-registration-but-only-allow-deformation-in-one-direction/3789)
**Author:** [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)\
**Replies:** 6\
**Last updated:** [January 24, 2021, 11:28pm UTC](https://discourse.itk.org/t/deformable-registration-but-only-allow-deformation-in-one-direction/3789 "2021-01-24T23:28:53Z")
Hi message board, I would like to implement the algorithm described in the first paragraph of section 2.3 of this paper: The algorithm performs deformable registration between two images but only allows for stretch…
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## [SimpleITK doesn't seem to apply rescale intercept/slop](https://discourse.itk.org/t/simpleitk-doesnt-seem-to-apply-rescale-intercept-slop/3768)
**Author:** [@malteekj](https://discourse.itk.org/u/malteekj)\
**Replies:** 8\
**Last updated:** [January 22, 2021, 2:32pm UTC](https://discourse.itk.org/t/simpleitk-doesnt-seem-to-apply-rescale-intercept-slop/3768 "2021-01-22T14:32:14Z")
I’m using the SimpleITK API for python to load medical images in DICOM format (PET and CT). However, it appears that SimpleITK doesn’t apply the rescale slope and rescale intercept. My code right now is: import SimpleIT…
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## [Errors of ITK.js Hello World project](https://discourse.itk.org/t/errors-of-itk-js-hello-world-project/3784)
**Author:** [@K.Matsuzaki](https://discourse.itk.org/u/K.Matsuzaki)\
**Replies:** 3\
**Last updated:** [January 22, 2021, 4:12am UTC](https://discourse.itk.org/t/errors-of-itk-js-hello-world-project/3784 "2021-01-22T04:12:37Z")
Hi, I’m interested in ITK.js and trying a Hello World project.(https://insightsoftwareconsortium.github.io/itk-js/examples/hello\_world\_node.html) I installed tools as instructions. Then I executed “npx itk-js build .”…
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## [ITK Snap Registration - Background turns white with rotation or translation](https://discourse.itk.org/t/itk-snap-registration-background-turns-white-with-rotation-or-translation/3788)
**Author:** [@ckronman](https://discourse.itk.org/u/ckronman)\
**Replies:** 1\
**Last updated:** [January 21, 2021, 8:40pm UTC](https://discourse.itk.org/t/itk-snap-registration-background-turns-white-with-rotation-or-translation/3788 "2021-01-21T20:40:12Z")
Hello there! I’m using ITK Snap to reorient the translation & rotation of a set of MRI images with the manual registration tool. Everything has been working well until recently when I had an image background change from …
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## ["Requested region is (at least partially) outside the largest possible region. Aborted (core dumped)" when calling Update/UpdateLargestPossibleRegion](https://discourse.itk.org/t/requested-region-is-at-least-partially-outside-the-largest-possible-region-aborted-core-dumped-when-calling-update-updatelargestpossibleregion/3732)
**Author:** [@Stefan\_Radonjic](https://discourse.itk.org/u/Stefan_Radonjic)\
**Replies:** 6\
**Last updated:** [January 21, 2021, 9:42am UTC](https://discourse.itk.org/t/requested-region-is-at-least-partially-outside-the-largest-possible-region-aborted-core-dumped-when-calling-update-updatelargestpossibleregion/3732 "2021-01-21T09:42:45Z")
Hello everyone! I am new to ITK and I am trying to create a custom registration filter, but I keep running into following error message: what(): /home/stefan/itk/Modules/Core/Common/src/itkDataObject.cxx:393: Requested…
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## [Cumulative Gausian Optimizer for Registration](https://discourse.itk.org/t/cumulative-gausian-optimizer-for-registration/3777)
**Author:** [@Michael7](https://discourse.itk.org/u/Michael7)\
**Replies:** 5\
**Last updated:** [January 21, 2021, 8:41am UTC](https://discourse.itk.org/t/cumulative-gausian-optimizer-for-registration/3777 "2021-01-21T08:41:59Z")
Hi, I’m trying to configure and set an itk::CumulativeGaussianOptimizer instance to run a registration ( itk::PointSetToPointSetRegistrationMethod\) procedure. Nevertheless, I seem to find n…
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## [Bspline Converging too fast](https://discourse.itk.org/t/bspline-converging-too-fast/3778)
**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 2\
**Last updated:** [January 20, 2021, 1:38am UTC](https://discourse.itk.org/t/bspline-converging-too-fast/3778 "2021-01-20T01:38:59Z")
Hello, I am performing a two-stage registration, being the last stage a deformable one. The deformable stage uses the itkLBFGSBOptimizerv4.h optimizer. The deformable stage is converging too fast and certainly with no…
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## [Binary image to cloud points in physical coordinates](https://discourse.itk.org/t/binary-image-to-cloud-points-in-physical-coordinates/3781)
**Author:** [@ainor](https://discourse.itk.org/u/ainor)\
**Replies:** 5\
**Last updated:** [January 19, 2021, 4:12pm UTC](https://discourse.itk.org/t/binary-image-to-cloud-points-in-physical-coordinates/3781 "2021-01-19T16:12:09Z")
I have a binary 3d image. How can I extract a point cloud from the image surface in physical coordinates?
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## [Closest point of a plane to a 3d image in physical coordinates.](https://discourse.itk.org/t/closest-point-of-a-plane-to-a-3d-image-in-physical-coordinates/3779)
**Author:** [@ainor](https://discourse.itk.org/u/ainor)\
**Replies:** 3\
**Last updated:** [January 19, 2021, 2:41pm UTC](https://discourse.itk.org/t/closest-point-of-a-plane-to-a-3d-image-in-physical-coordinates/3779 "2021-01-19T14:41:15Z")
I have a 3d image formed from a volume of slices. Each Slices in the volume is a binary image (the region of interest has pixels with a value of 255 and the rest of the image is zero). I have a plane in the physical coo…
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## [How to obtain the physical coordinates of the nodes in an ITK :: Mesh obtained from a 3D volume of CT images](https://discourse.itk.org/t/how-to-obtain-the-physical-coordinates-of-the-nodes-in-an-itk-mesh-obtained-from-a-3d-volume-of-ct-images/3773)
**Author:** [@ainor](https://discourse.itk.org/u/ainor)\
**Replies:** 1\
**Last updated:** [January 18, 2021, 10:37pm UTC](https://discourse.itk.org/t/how-to-obtain-the-physical-coordinates-of-the-nodes-in-an-itk-mesh-obtained-from-a-3d-volume-of-ct-images/3773 "2021-01-18T22:37:58Z")
I am using ITK library to get a mesh from a 3D image, the 3D image is a volume of slices. I get the mesh using itk::BinaryMask3DMeshSource . But I need to get its physical coordinate for each mesh node and I don’t know h…
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## [MRI isotropic volume reconstruction from 2D slices](https://discourse.itk.org/t/mri-isotropic-volume-reconstruction-from-2d-slices/3764)
**Author:** [@Fleur](https://discourse.itk.org/u/Fleur)\
**Replies:** 10\
**Last updated:** [January 18, 2021, 10:24pm UTC](https://discourse.itk.org/t/mri-isotropic-volume-reconstruction-from-2d-slices/3764 "2021-01-18T22:24:26Z")
Hello everyone, I have a simple task to achieve: I have 3 sets of anisotropic MRI data per subject (= 2D MRI slices along one axis) and I want to perform volume reconstruction to obtain a single 3D isotropic volume of t…
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## [Reading/Writing Images to/from Memory (Rather than Files)](https://discourse.itk.org/t/reading-writing-images-to-from-memory-rather-than-files/3763)
**Author:** [@harold.absalom](https://discourse.itk.org/u/harold.absalom)\
**Replies:** 2\
**Last updated:** [January 17, 2021, 4:48am UTC](https://discourse.itk.org/t/reading-writing-images-to-from-memory-rather-than-files/3763 "2021-01-17T04:48:27Z")
I’m trying to construct an itk::Image from an in-memory buffer, rather than from a file on disk. The image data itself is formatted as an NRRD. The buffer has been filled by an external program, and at some point I would…
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## [Apple Silicon/M1 Nightly Build](https://discourse.itk.org/t/apple-silicon-m1-nightly-build/3758)
**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 4\
**Last updated:** [January 15, 2021, 10:19pm UTC](https://discourse.itk.org/t/apple-silicon-m1-nightly-build/3758 "2021-01-15T22:19:56Z")
I have acquired an Apple Silicon mac system and I am currently trying to build ITK as a native ARM64 library and running into compile errors. Would it be beneficial to the ITK developers to setup this machine as a nightl…
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## [How to set source to detector distance](https://discourse.itk.org/t/how-to-set-source-to-detector-distance/2984)
**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 5\
**Last updated:** [January 13, 2021, 2:38pm UTC](https://discourse.itk.org/t/how-to-set-source-to-detector-distance/2984 "2021-01-13T14:38:43Z")
Hi, I’m currently looking GetDRRSiddonJacobsRayTracing \[1\] to generate DRR images from 3D-CT volumes. Does this example have a way to set source to detector distance ? If so can you elaborate with an example. \[1\] htt…
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## [Keep an eye on zlib-ng](https://discourse.itk.org/t/keep-an-eye-on-zlib-ng/1199)
**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 3\
**Last updated:** [January 12, 2021, 6:20pm UTC](https://discourse.itk.org/t/keep-an-eye-on-zlib-ng/1199 "2021-01-12T18:20:43Z")
A group of folks are trying to drag zlib into the 21st century, keep an eye on it here:
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## [Build Error when using -DCMAKE\_CXX\_FLAGS\_DEBUG="/MTd" flag in C++](https://discourse.itk.org/t/build-error-when-using-dcmake-cxx-flags-debug-mtd-flag-in-c/3748)
**Author:** [@viki](https://discourse.itk.org/u/viki)\
**Replies:** 5\
**Last updated:** [January 12, 2021, 5:39pm UTC](https://discourse.itk.org/t/build-error-when-using-dcmake-cxx-flags-debug-mtd-flag-in-c/3748 "2021-01-12T17:39:15Z")
Hi, I am facing build error, when using -DCMAKE\_CXX\_FLAGS\_DEBUG="/MTd" . cmake\_code: cmake …\\ITK -DCMAKE\_CXX\_FLAGS\_RELEASE="/MT" -DCMAKE\_CXX\_FLAGS\_DEBUG="/MTd" -DITK\_SKIP\_PATH\_LENGTH\_CHECKS=ON -DModule\_ITKIOGDCM=OFF -…
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## [composite transform convertion problem](https://discourse.itk.org/t/composite-transform-convertion-problem/3749)
**Author:** [@pierrectl](https://discourse.itk.org/u/pierrectl)\
**Replies:** 7\
**Last updated:** [January 11, 2021, 3:24pm UTC](https://discourse.itk.org/t/composite-transform-convertion-problem/3749 "2021-01-11T15:24:26Z")
Hello all, I was wondering if we can convert a CompositeTransformType to a TransformType? Here is my sample of code: using TransformType = itk::Euler3DTransform\< double \>; TransformType::Pointer first\_transformation =…
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## [StatisticsImageFilter does not work with sub region](https://discourse.itk.org/t/statisticsimagefilter-does-not-work-with-sub-region/3752)
**Author:** [@Xinbo\_Li](https://discourse.itk.org/u/Xinbo_Li)\
**Replies:** 2\
**Last updated:** [January 11, 2021, 2:08pm UTC](https://discourse.itk.org/t/statisticsimagefilter-does-not-work-with-sub-region/3752 "2021-01-11T14:08:39Z")
I tried to get mean intensity of a sub region in an image by using the StatisticsImageFilter. Turns out that the filter does not work with sub region. I used the 3 set region methods of the class and tried all possible…
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## [Resampling a displacement-field transformed image](https://discourse.itk.org/t/resampling-a-displacement-field-transformed-image/1884)
**Author:** [@Nino](https://discourse.itk.org/u/Nino)\
**Replies:** 7\
**Last updated:** [January 4, 2021, 12:55am UTC](https://discourse.itk.org/t/resampling-a-displacement-field-transformed-image/1884 "2021-01-04T00:55:38Z")
Hi guys, I am using a DisplacementField transformation and resample the image with the ResampleImageFilter. Everything is working great! Now I am wondering how the resample method is working? Does it invoke the InverseD…
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## [Find default values of parameters for optimizer](https://discourse.itk.org/t/find-default-values-of-parameters-for-optimizer/3738)
**Author:** [@user1](https://discourse.itk.org/u/user1)\
**Replies:** 3\
**Last updated:** [December 31, 2020, 1:31am UTC](https://discourse.itk.org/t/find-default-values-of-parameters-for-optimizer/3738 "2020-12-31T01:31:15Z")
Hi! I’m using SimpleITK with Python and am doing a registration task. I used the Powell optimizer and it’s default values worked very well for me so now I’d like to know what they are. I have yet to find a way to access…
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## [Read Transform - Apply to VersorRigid3DTransform](https://discourse.itk.org/t/read-transform-apply-to-versorrigid3dtransform/3737)
**Author:** [@gattia](https://discourse.itk.org/u/gattia)\
**Replies:** 6\
**Last updated:** [December 30, 2020, 4:36pm UTC](https://discourse.itk.org/t/read-transform-apply-to-versorrigid3dtransform/3737 "2020-12-30T16:36:06Z")
I’ve been trying to read a transform from disk (VersorRigid3DTransform saved previously) and then feed it into the VersorRigid3DTransform class so that I can get access to the original parameters like: Matrix, Translatio…
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## [Nifti read failed?](https://discourse.itk.org/t/nifti-read-failed/3735)
**Author:** [@jeffppp](https://discourse.itk.org/u/jeffppp)\
**Replies:** 2\
**Last updated:** [December 30, 2020, 3:36am UTC](https://discourse.itk.org/t/nifti-read-failed/3735 "2020-12-30T03:36:45Z")
Hello, every one~ I have a question. std::string str=“D:\\Test2.nii”; itk::ImageIOBase::Pointer imageIO = tk::ImageIOFactory::CreateImageIO(str.c\_str(), itk::CommonEnums::IOFileMode::ReadMode); I use ITK 5.1 to read …
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## [How to achieve the following segmentation effect:](https://discourse.itk.org/t/how-to-achieve-the-following-segmentation-effect/3733)
**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 2\
**Last updated:** [December 28, 2020, 10:54pm UTC](https://discourse.itk.org/t/how-to-achieve-the-following-segmentation-effect/3733 "2020-12-28T22:54:10Z")
How to achieve the following segmentation effect:
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## [How to show bones only?](https://discourse.itk.org/t/how-to-show-bones-only/3698)
**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 2\
**Last updated:** [December 28, 2020, 5:57am UTC](https://discourse.itk.org/t/how-to-show-bones-only/3698 "2020-12-28T05:57:17Z")
I have an image sequence now, how can only the bones be displayed after 3D reconstruction like the RadiAnt DICOM Viewer?
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## [Undefined reference to image registers](https://discourse.itk.org/t/undefined-reference-to-image-registers/3717)
**Author:** [@rohit\_inippully](https://discourse.itk.org/u/rohit_inippully)\
**Replies:** 4\
**Last updated:** [December 22, 2020, 4:05pm UTC](https://discourse.itk.org/t/undefined-reference-to-image-registers/3717 "2020-12-22T16:05:19Z")
Hey, I am getting an error when compiling the examples given in the itk software guide. Can anyone advise me how to fix this? Thank you, Rohit Inippully.
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## [AttributeError: module 'SimpleITK' has no attribute 'sitkNearestNeighbour'](https://discourse.itk.org/t/attributeerror-module-simpleitk-has-no-attribute-sitknearestneighbour/3729)
**Author:** [@Eddardaa\_ben\_loussai](https://discourse.itk.org/u/Eddardaa_ben_loussai)\
**Replies:** 1\
**Last updated:** [December 22, 2020, 1:56pm UTC](https://discourse.itk.org/t/attributeerror-module-simpleitk-has-no-attribute-sitknearestneighbour/3729 "2020-12-22T13:56:50Z")
Hi everyone, I trying to resize my medical dataset (format .mhd), however i had this error: AttributeError: module ‘SimpleITK’ has no attribute ‘sitkNearestNeighbour’ anyone have idea, please let me know. thank you i…
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## [Getting error in mhd file reading](https://discourse.itk.org/t/getting-error-in-mhd-file-reading/3727)
**Author:** [@anirban1513](https://discourse.itk.org/u/anirban1513)\
**Replies:** 1\
**Last updated:** [December 22, 2020, 1:51pm UTC](https://discourse.itk.org/t/getting-error-in-mhd-file-reading/3727 "2020-12-22T13:51:15Z")
I am getting this error!! THE mhd File can’t be found or read by the simpleitk 1.2.4 I am getting the same error! What to do?? RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/I…
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## [RFC: Toward supporting distribution of VTK based modules on PyPI](https://discourse.itk.org/t/rfc-toward-supporting-distribution-of-vtk-based-modules-on-pypi/3722)
**Author:** [@jcfr](https://discourse.itk.org/u/jcfr)\
**Replies:** 0\
**Last updated:** [December 21, 2020, 8:20pm UTC](https://discourse.itk.org/t/rfc-toward-supporting-distribution-of-vtk-based-modules-on-pypi/3722 "2020-12-21T20:20:02Z")
At Kitware, we would like to support the ability to package and distribute any VTK based modules on PyPI (Python Package Index). If you would like to see this happen, read and “heart” the following discourse post, and d…
[Previous page](https://discourse.itk.org/latest.md?page=55)
[Next page](https://discourse.itk.org/latest.md?page=57)