# Latest

**URL:** https://discourse.itk.org/latest.md?page=39

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

**Page:** 40

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## [Installation of ITKElastix with pip](https://discourse.itk.org/t/installation-of-itkelastix-with-pip/4936)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 2\
**Last updated:** [April 26, 2022, 9:44am UTC](https://discourse.itk.org/t/installation-of-itkelastix-with-pip/4936 "2022-04-26T09:44:58Z")

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Hello! I tried to look into ITKElastix. As posted on the repository, I did pip install itk-elastix but I also installed TubeTK, ITKStrain, SciPy, Scikit-image and Scikit-learn pip install itk-tubetk itk-strain pip in…

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## [How detect missing files in a DICOM series.](https://discourse.itk.org/t/how-detect-missing-files-in-a-dicom-series/4935)

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**Author:** [@ainor](https://discourse.itk.org/u/ainor)\
**Replies:** 3\
**Last updated:** [April 26, 2022, 5:50am UTC](https://discourse.itk.org/t/how-detect-missing-files-in-a-dicom-series/4935 "2022-04-26T05:50:39Z")

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Hi, I know that the itk::GDCMSeriesFileNames class allows you to generate an ordering sequence of filenames from a DICOM series. But if I have a series that should consist of, for example, 100 slices and some of those sl…

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## [access meta dictionary using simpleitk](https://discourse.itk.org/t/access-meta-dictionary-using-simpleitk/4939)

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**Author:** [@sehreen](https://discourse.itk.org/u/sehreen)\
**Replies:** 3\
**Last updated:** [April 25, 2022, 11:57pm UTC](https://discourse.itk.org/t/access-meta-dictionary-using-simpleitk/4939 "2022-04-25T23:57:53Z")

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how can I change the following code to read image in Simpleitk set meta data and save as simpleitk dicom = dcmread(dcm\_path) #load it from simplitk and read it in simplitk instead dcmread for key,value in meta\_dict.ite…

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## [Scientist II - Computational Neuroanatomy @ Allen Institute for Brain Science](https://discourse.itk.org/t/scientist-ii-computational-neuroanatomy-allen-institute-for-brain-science/4933)

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**Author:** [@lydiang](https://discourse.itk.org/u/lydiang)\
**Replies:** 0\
**Last updated:** [April 23, 2022, 6:19am UTC](https://discourse.itk.org/t/scientist-ii-computational-neuroanatomy-allen-institute-for-brain-science/4933 "2022-04-23T06:19:40Z")

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Scientist II - Computational Neuroanatomy TLDR: create 3D models for next-generation brain atlases We seek to hire an exceptional scientist to create accurate 3D anatomical models of mouse brain structures based on mul…

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## [write a tif file](https://discourse.itk.org/t/write-a-tif-file/4923)

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**Author:** [@assia855](https://discourse.itk.org/u/assia855)\
**Replies:** 6\
**Last updated:** [April 19, 2022, 2:02pm UTC](https://discourse.itk.org/t/write-a-tif-file/4923 "2022-04-19T14:02:25Z")

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Hello, I’m trying to save my processed data in tif format using this code, but all what I got is a black image. any suggestion to solve this error. thanks in advance. \` writer = sitk.ImageFileWriter() writer.SetFileNa…

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## [BinaryPruningImageFilter](https://discourse.itk.org/t/binarypruningimagefilter/4924)

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**Author:** [@assia855](https://discourse.itk.org/u/assia855)\
**Replies:** 4\
**Last updated:** [April 19, 2022, 1:40pm UTC](https://discourse.itk.org/t/binarypruningimagefilter/4924 "2022-04-19T13:40:05Z")

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Hello, I want to apply this function on my data, but I couldn’t understand the documentation and there’s no example. I would like an example on how can I apply it. Thanks in advance.

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## [How to convert 3D rgb to grascale](https://discourse.itk.org/t/how-to-convert-3d-rgb-to-grascale/4908)

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**Author:** [@assia855](https://discourse.itk.org/u/assia855)\
**Replies:** 7\
**Last updated:** [April 19, 2022, 10:38am UTC](https://discourse.itk.org/t/how-to-convert-3d-rgb-to-grascale/4908 "2022-04-19T10:38:07Z")

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Hello Folks, I’m searching for how to convert my 3D data to grayscale. I can’t find how on the documentation. Thanks in advance.

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## [How to calculate the reverse 3d affine transform?](https://discourse.itk.org/t/how-to-calculate-the-reverse-3d-affine-transform/4916)

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**Author:** [@yding58](https://discourse.itk.org/u/yding58)\
**Replies:** 1\
**Last updated:** [April 15, 2022, 3:14pm UTC](https://discourse.itk.org/t/how-to-calculate-the-reverse-3d-affine-transform/4916 "2022-04-15T15:14:44Z")

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Hi all, I tried to calculate the reverse affine transform matrix and the returned translation vector is always wrong, which bother me a lot. Anyone has any ideas? I appreciate for any suggestions. Thank you! Here are s…

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## [ITK Examples Hackathon 2022](https://discourse.itk.org/t/itk-examples-hackathon-2022/4913)

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**Author:** [@Tom\_Birdsong](https://discourse.itk.org/u/Tom_Birdsong)\
**Replies:** 0\
**Last updated:** [April 14, 2022, 2:30pm UTC](https://discourse.itk.org/t/itk-examples-hackathon-2022/4913 "2022-04-14T14:30:58Z")

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The ITK Examples hackathon aims to bring together ITK developers and new users to expand documentation and learn to use ITK tools for scientific image processing. We will focus on expanding and adding new examples to th…

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## [Extracting displacement fields from rigid registration](https://discourse.itk.org/t/extracting-displacement-fields-from-rigid-registration/4834)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 16\
**Last updated:** [April 14, 2022, 9:20am UTC](https://discourse.itk.org/t/extracting-displacement-fields-from-rigid-registration/4834 "2022-04-14T09:20:57Z")

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Hello! Continuing the discussion from 3D image registration with Python and without SimpleITK: Once I have a registration, what is the best way to extract the deformation field (a.k.a. displacement field) with ITK Py…

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## [ITK not working in Python](https://discourse.itk.org/t/itk-not-working-in-python/4733)

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**Author:** [@ogdenk](https://discourse.itk.org/u/ogdenk)\
**Replies:** 22\
**Last updated:** [April 13, 2022, 1:42pm UTC](https://discourse.itk.org/t/itk-not-working-in-python/4733 "2022-04-13T13:42:06Z")

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Hi all, I have a very basic question. I am learning to use ITK in Python, and I can’t seem to get it to work. In a simple example, I am just trying to use a median image filter, but copying online examples doesn’t work…

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## [Compiling TubeTK v1.1 or v1.0.0 with ITK 5.3rc03](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 13\
**Last updated:** [April 12, 2022, 7:20pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853 "2022-04-12T19:20:57Z")

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Continuing the discussion from Compiling ~MinimalPathExtraction~ with ITK 5.2.1: Hello! (This is not a request for help) I’m getting this error with v1.1 (8cb12a20) and v1.0.0 of TubeTK. samu: file is missing and no…

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## [Integrate some remote modules into ITK proper](https://discourse.itk.org/t/integrate-some-remote-modules-into-itk-proper/4909)

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**Author:** [@dzenanz](https://discourse.itk.org/u/dzenanz)\
**Replies:** 0\
**Last updated:** [April 12, 2022, 4:38pm UTC](https://discourse.itk.org/t/integrate-some-remote-modules-into-itk-proper/4909 "2022-04-12T16:38:16Z")

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Some remote modules have been in use for a long time, and should be integrated into the main repository (i.e. InsightSoftwareConsortium/ITK). Some examples are InsightSoftwareConsortium/ITKSplitComponents#50 and InsightS…

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## [How to normalize a 3D volume](https://discourse.itk.org/t/how-to-normalize-a-3d-volume/4906)

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**Author:** [@assia855](https://discourse.itk.org/u/assia855)\
**Replies:** 6\
**Last updated:** [April 7, 2022, 3:30pm UTC](https://discourse.itk.org/t/how-to-normalize-a-3d-volume/4906 "2022-04-07T15:30:32Z")

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Hello folks, I would like to normalize a 3D volume but I can’t find a ressource. Please can you suggest to me a code or library, I would be grateful. Thanks in advance.

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## [NCI Imaging Data Commons April 2022 release](https://discourse.itk.org/t/nci-imaging-data-commons-april-2022-release/4904)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 0\
**Last updated:** [April 6, 2022, 5:42pm UTC](https://discourse.itk.org/t/nci-imaging-data-commons-april-2022-release/4904 "2022-04-06T17:42:09Z")

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NCI Imaging Data Commons April 2022 release is out! Here are some of the highlights: Data: slide microscopy imaging data is now available for all of the TCGA collections and for the NLST collection - that’s the total…

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## [Multiresolution Registration with 2D Affine Transformation on pairs of 2D images](https://discourse.itk.org/t/multiresolution-registration-with-2d-affine-transformation-on-pairs-of-2d-images/3096)

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**Author:** [@ScottP](https://discourse.itk.org/u/ScottP)\
**Replies:** 20\
**Last updated:** [April 3, 2022, 7:21pm UTC](https://discourse.itk.org/t/multiresolution-registration-with-2d-affine-transformation-on-pairs-of-2d-images/3096 "2022-04-03T19:21:15Z")

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Hello, I’m a beginner to registration (1 month experience) and semi-beginner to Python (4 months). I need to do multiresolution registration in Python with 2D Affine transformation on pairs of 2D fixed and 2D moving ima…

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## [Apply 2D Affine transformation to a 3D image](https://discourse.itk.org/t/apply-2d-affine-transformation-to-a-3d-image/4899)

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**Author:** [@Moha\_data](https://discourse.itk.org/u/Moha_data)\
**Replies:** 3\
**Last updated:** [April 1, 2022, 7:05pm UTC](https://discourse.itk.org/t/apply-2d-affine-transformation-to-a-3d-image/4899 "2022-04-01T19:05:09Z")

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Hello, How can I apply the result of 2D affine registration to a 3D image? For now, I just consider a 3D image as a series of 2D images and apply the transformation to each of them, which is not efficient. I appreciate …

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## [BinaryFillholeImageFilter: Insight Journal Paper](https://discourse.itk.org/t/binaryfillholeimagefilter-insight-journal-paper/4891)

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**Author:** [@Sharada](https://discourse.itk.org/u/Sharada)\
**Replies:** 7\
**Last updated:** [April 1, 2022, 2:02pm UTC](https://discourse.itk.org/t/binaryfillholeimagefilter-insight-journal-paper/4891 "2022-04-01T14:02:09Z")

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Hello, I am trying to access this insight journal article, but it does not load. Unfortunately, I am also not able to access chapter 6 of Pierre Soille’s book “Morphological Image Analysis: Principles and Applications”. …

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## [what is the difference between using DCMTKImageIO and GDCMImageIO ?](https://discourse.itk.org/t/what-is-the-difference-between-using-dcmtkimageio-and-gdcmimageio/4897)

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**Author:** [@mmeltsner](https://discourse.itk.org/u/mmeltsner)\
**Replies:** 1\
**Last updated:** [April 1, 2022, 1:23pm UTC](https://discourse.itk.org/t/what-is-the-difference-between-using-dcmtkimageio-and-gdcmimageio/4897 "2022-04-01T13:23:39Z")

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I have been using generally GDCMImageIO for the ImageFileReader for reading dicom files from disk, but I recently discovered another ImageIO called DCMTKImageIO which seems to use the dcmtk toolkit instead of the gdcm to…

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## [The exception(Requested region is (at least partially) outside the largest possible region) in orImageFilter.](https://discourse.itk.org/t/the-exception-requested-region-is-at-least-partially-outside-the-largest-possible-region-in-orimagefilter/4889)

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**Author:** [@SummerZ2020](https://discourse.itk.org/u/SummerZ2020)\
**Replies:** 5\
**Last updated:** [March 29, 2022, 1:19pm UTC](https://discourse.itk.org/t/the-exception-requested-region-is-at-least-partially-outside-the-largest-possible-region-in-orimagefilter/4889 "2022-03-29T13:19:43Z")

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Hello, I am working on medical image processing , ITK is a great tool to help me in the implementation. But I have got the exception when the OrImageFilter was using. Here is my example code segment: using OrImageFi…

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## [Resampling images - LinearInterpolateImageFunction](https://discourse.itk.org/t/resampling-images-linearinterpolateimagefunction/4887)

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**Author:** [@tabro](https://discourse.itk.org/u/tabro)\
**Replies:** 1\
**Last updated:** [March 28, 2022, 3:14pm UTC](https://discourse.itk.org/t/resampling-images-linearinterpolateimagefunction/4887 "2022-03-28T15:14:45Z")

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Hi, I’m trying to resample a CT (nifti) of non-isotropic spacing to have isotropic spacing of (0.5, 0.5, 0.5), no rescaling. I’m using the code below. The output is an array of the desired size but consists of almost on…

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## [itk::LabelGeometryImageFilter GetMajorAxisLength() return type](https://discourse.itk.org/t/itk-labelgeometryimagefilter-getmajoraxislength-return-type/4876)

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**Author:** [@anillspawar](https://discourse.itk.org/u/anillspawar)\
**Replies:** 4\
**Last updated:** [March 26, 2022, 8:51pm UTC](https://discourse.itk.org/t/itk-labelgeometryimagefilter-getmajoraxislength-return-type/4876 "2022-03-26T20:51:48Z")

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I am using itk::LabelGeometryImageFilter to GetMajorAxisLength() of an object. I want to know the return unit of length given, is it in millimeter or pixel? If it is in pixel how to convert it into millimeter? Thanks i…

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## [Registration repeatability](https://discourse.itk.org/t/registration-repeatability/4883)

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**Author:** [@Kyoto\_Love](https://discourse.itk.org/u/Kyoto_Love)\
**Replies:** 3\
**Last updated:** [March 26, 2022, 3:59pm UTC](https://discourse.itk.org/t/registration-repeatability/4883 "2022-03-26T15:59:27Z")

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Hello everyone! I am stuck on one task, I need to register 2 identical images and do: 1.Write a loop for initializing the transformation with different parameters, and start the registration from different places. 2.St…

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## [Centerline extraction](https://discourse.itk.org/t/centerline-extraction/4885)

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**Author:** [@ekmungi](https://discourse.itk.org/u/ekmungi)\
**Replies:** 7\
**Last updated:** [March 25, 2022, 5:46pm UTC](https://discourse.itk.org/t/centerline-extraction/4885 "2022-03-25T17:46:42Z")

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I am new to ITK. I have a 3D model of a tubular structure and I am looking for a way to extract the centerline for it. Could someone help? So far, I have tried using VMTK but it requires a closed model (end points are c…

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## [itk.js readImageDICOMFileSeries](https://discourse.itk.org/t/itk-js-readimagedicomfileseries/2086)

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**Author:** [@aliu4](https://discourse.itk.org/u/aliu4)\
**Replies:** 2\
**Last updated:** [March 24, 2022, 4:12pm UTC](https://discourse.itk.org/t/itk-js-readimagedicomfileseries/2086 "2022-03-24T16:12:08Z")

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hello, I am developing an application in vue-js and im having issues with the readImageDICOMFileSeries method. I’m currently not using a web-worker and it keeps returning this error. “ImageIO.worker.js:1 Uncaught Syntax…

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## [Read, manipulate tags and write dicom series](https://discourse.itk.org/t/read-manipulate-tags-and-write-dicom-series/4863)

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**Author:** [@csad6517](https://discourse.itk.org/u/csad6517)\
**Replies:** 6\
**Last updated:** [March 24, 2022, 12:29pm UTC](https://discourse.itk.org/t/read-manipulate-tags-and-write-dicom-series/4863 "2022-03-24T12:29:26Z")

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I am reading dicom series and manipulate some tags from it. Finally write the new series. I can change any dicom tag without any problems. They are correcly changed. But the new dataset is visualized wrongly. The axial s…

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## [Resampling image](https://discourse.itk.org/t/resampling-image/4793)

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**Author:** [@tutti](https://discourse.itk.org/u/tutti)\
**Replies:** 7\
**Last updated:** [March 23, 2022, 3:30am UTC](https://discourse.itk.org/t/resampling-image/4793 "2022-03-23T03:30:33Z")

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Hello everyone, I try to resample image 1 (nii) \[128,128,128\], spacing \[1,1,1\] to image2 \[512,512,476\], spacing2 \[0.6,0.6,0.6\], but I got image as following. def resample\_img(itk\_image1, itk\_image2, out\_spacing=\[0.6…

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## [Is it easy to change the level set function ?](https://discourse.itk.org/t/is-it-easy-to-change-the-level-set-function/4871)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 0\
**Last updated:** [March 18, 2022, 9:33pm UTC](https://discourse.itk.org/t/is-it-easy-to-change-the-level-set-function/4871 "2022-03-18T21:33:37Z")

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Level set methods solve the diferencial equation with the level set function: I am using geodesic active contour: But I wished that A was the solution of the gradient vector flow ( Using anatomical knowledge expres…

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## [Segmentation fault in geodesic active contour](https://discourse.itk.org/t/segmentation-fault-in-geodesic-active-contour/4865)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 2\
**Last updated:** [March 18, 2022, 6:16pm UTC](https://discourse.itk.org/t/segmentation-fault-in-geodesic-active-contour/4865 "2022-03-18T18:16:02Z")

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I am segmentation fault with geodesic active contour. my code: using SmoothingFilterType\_Heart\_Seg = itk::CurvatureAnisotropicDiffusionImageFilter\<InternalImageType, InternalImageType\>; auto Smoothi…

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## [Inverting Resample Filter Execute operation](https://discourse.itk.org/t/inverting-resample-filter-execute-operation/4856)

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**Author:** [@BraveDistribution](https://discourse.itk.org/u/BraveDistribution)\
**Replies:** 16\
**Last updated:** [March 16, 2022, 7:28pm UTC](https://discourse.itk.org/t/inverting-resample-filter-execute-operation/4856 "2022-03-16T19:28:10Z")

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Hello, The problem that I am trying to solve with SimpleITK: 1/ I have a temporal sequence of volumes from the same patient 2/ I have one segmentation mask of the organ under observation. 3/ I want to get segmentatio…

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