# Latest

**URL:** https://discourse.itk.org/latest.md?page=34

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

**Page:** 35

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## [C order or F order？](https://discourse.itk.org/t/c-order-or-f-order/5287)

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**Author:** [@liguangops](https://discourse.itk.org/u/liguangops)\
**Replies:** 7\
**Last updated:** [August 26, 2022, 1:09pm UTC](https://discourse.itk.org/t/c-order-or-f-order/5287 "2022-08-26T13:09:21Z")

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I have a 3d dicom nii.gz file with shape \[900,900,500\]. And I read it by using itk::ImageReader. Then I want to split it into 6480 with shapes \[50,50,25\] by moving ImageBufferPointer. But I don’t know if the order in me…

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## [How to understand the coordinate system of dicom](https://discourse.itk.org/t/how-to-understand-the-coordinate-system-of-dicom/5180)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 11\
**Last updated:** [August 26, 2022, 2:25am UTC](https://discourse.itk.org/t/how-to-understand-the-coordinate-system-of-dicom/5180 "2022-08-26T02:25:15Z")

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I am confuzed in the understanding of dicom coordinate system. I display dicom information with SimpleITK: import SimpleITK as sitk path1 = 'C:\\\\Users\\\\Administrator\\\\Desktop\\\\medspro\\\\Data\\\\dce1\\\\IMG-0001-00001.dcm' …

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## [Doxygen with Github Actions and Pages.](https://discourse.itk.org/t/doxygen-with-github-actions-and-pages/4790)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 23\
**Last updated:** [August 24, 2022, 6:52pm UTC](https://discourse.itk.org/t/doxygen-with-github-actions-and-pages/4790 "2022-08-24T18:52:49Z")

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I recently made some changes with the ITK Doxygen configuration to minimize the about of changes from night to night in the HTML generated by Doxygen. Minimizing the number of files modified each day enabled regular web …

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## [Is instance number used to collect dicom series?](https://discourse.itk.org/t/is-instance-number-used-to-collect-dicom-series/5283)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 5\
**Last updated:** [August 24, 2022, 1:54am UTC](https://discourse.itk.org/t/is-instance-number-used-to-collect-dicom-series/5283 "2022-08-24T01:54:52Z")

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Usually, I use Instance Number to collect dicom series, just like: imgs\[ key \] = dicomImg where key is the Instance Number, and dicomImg is the dicom information (header/pixel array). However, sometimes, I find that t…

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## [ITK 5.3 Release Candidate 4 available for testing](https://discourse.itk.org/t/itk-5-3-release-candidate-4-available-for-testing/5290)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [August 23, 2022, 7:11pm UTC](https://discourse.itk.org/t/itk-5-3-release-candidate-4-available-for-testing/5290 "2022-08-23T19:11:38Z")

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We are happy to announce the Insight Toolkit (ITK) 5.3 Release Candidate 4 is available for testing! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and r…

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## [Thanks](https://discourse.itk.org/t/thanks/5284)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 3\
**Last updated:** [August 23, 2022, 1:51pm UTC](https://discourse.itk.org/t/thanks/5284 "2022-08-23T13:51:12Z")

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Hello, dear users and developers, I just want to thank the ITK team, because I was just able to calculate the displacement field of a non-rigid deformation (simple 3D registration). Then applied that displacement to the…

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## [4D and 3D + t images](https://discourse.itk.org/t/4d-and-3d-t-images/5288)

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**Author:** [@Farah](https://discourse.itk.org/u/Farah)\
**Replies:** 1\
**Last updated:** [August 23, 2022, 12:47pm UTC](https://discourse.itk.org/t/4d-and-3d-t-images/5288 "2022-08-23T12:47:13Z")

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Hi, I have 4D CT dataset that is basically lots of DCM files (DICOM), each group of DCMs present a 3D volume phase in the cardiac cycle, so I ended up with 10 3D volumes, I don’t know if this is assumed as 3D + t or 4D …

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## [pythonic api: issue calling filter with two input types](https://discourse.itk.org/t/pythonic-api-issue-calling-filter-with-two-input-types/5280)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 2\
**Last updated:** [August 23, 2022, 1:14am UTC](https://discourse.itk.org/t/pythonic-api-issue-calling-filter-with-two-input-types/5280 "2022-08-23T01:14:39Z")

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I created a new ITK external module to benefit from the nice packaging and pypi distribution. My filter is templated over the input image types (a scalar image and a mask image). The wrapping instructions looks like: …

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## [links on pypi for itkwidgets need update](https://discourse.itk.org/t/links-on-pypi-for-itkwidgets-need-update/5273)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 3\
**Last updated:** [August 23, 2022, 1:02am UTC](https://discourse.itk.org/t/links-on-pypi-for-itkwidgets-need-update/5273 "2022-08-23T01:02:20Z")

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Hello! I just noticed that itkwidgets · PyPI may need an update, because the mybinder.org links are kind of broken. For the interested reader, one can turn, for example: https://mybinder.org/v2/gh/InsightSoftwareConsor…

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## [calling itk from javascript in nodejs (without using C++)](https://discourse.itk.org/t/calling-itk-from-javascript-in-nodejs-without-using-c/4783)

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**Author:** [@vincenzoml](https://discourse.itk.org/u/vincenzoml)\
**Replies:** 2\
**Last updated:** [August 23, 2022, 12:20am UTC](https://discourse.itk.org/t/calling-itk-from-javascript-in-nodejs-without-using-c/4783 "2022-08-23T00:20:52Z")

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I would like to use some itk filters server-side from nodejs. I would like if possible to avoid writing bits of the code in C++. The web site of itk-wasm seems to only document the process of using C++. Is there a javasc…

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## [Problem realated to ITK.JS WebWorkers/ImageIO.worker.js](https://discourse.itk.org/t/problem-realated-to-itk-js-webworkers-imageio-worker-js/5216)

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**Author:** [@Yuvi-416](https://discourse.itk.org/u/Yuvi-416)\
**Replies:** 2\
**Last updated:** [August 23, 2022, 12:15am UTC](https://discourse.itk.org/t/problem-realated-to-itk-js-webworkers-imageio-worker-js/5216 "2022-08-23T00:15:11Z")

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Hello everyone, I am trying to run the below code to read a series of DICOM images and convert them into VTK objects before I send them for visualization. Problem is that, sometimes, itk.js read the image but most of t…

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## [Turning on the log for ITKElastix](https://discourse.itk.org/t/turning-on-the-log-for-itkelastix/5281)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 0\
**Last updated:** [August 21, 2022, 4:30pm UTC](https://discourse.itk.org/t/turning-on-the-log-for-itkelastix/5281 "2022-08-21T16:30:00Z")

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Hi! I just want to share a tip. If you get something like Internal elastix error: See elastix log (use LogToConsoleOn() or LogToFileOn()) try to use this option log\_to\_console=True (from help(itk.elastix\_registr…

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## [Ordering of 4D DICOM images while writing](https://discourse.itk.org/t/ordering-of-4d-dicom-images-while-writing/5277)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 5\
**Last updated:** [August 19, 2022, 11:31am UTC](https://discourse.itk.org/t/ordering-of-4d-dicom-images-while-writing/5277 "2022-08-19T11:31:07Z")

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Hello everyone! I am currently trying to write a 4D series of DICOM images (with Python and SimpleITK). Can anyone tell me which tag identifies the location of a volume in the fourth/time dimension (if there even is one…

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## [itk::JSONImageIO](https://discourse.itk.org/t/itk-jsonimageio/5276)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 2\
**Last updated:** [August 18, 2022, 5:09pm UTC](https://discourse.itk.org/t/itk-jsonimageio/5276 "2022-08-18T17:09:20Z")

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Hi @dzenanz , I have problem finding class itk::JSONImageIO, i wanna convert png images to png.json files. I know we can use itk::JSONImageIO class. thank you @sag

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## [Backwards incompatibility with (pip) itk-5.3rc4.post2 and itk-elastix-0.14.1](https://discourse.itk.org/t/backwards-incompatibility-with-pip-itk-5-3rc4-post2-and-itk-elastix-0-14-1/5272)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 2\
**Last updated:** [August 18, 2022, 3:25pm UTC](https://discourse.itk.org/t/backwards-incompatibility-with-pip-itk-5-3rc4-post2-and-itk-elastix-0-14-1/5272 "2022-08-18T15:25:24Z")

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Hi! I just want to report that if I install: pip uninstall -y itk{,-{,elastix,tubetk,strain,core,filtering,io,minimalpathextraction,numerics,registration,segmentation}} && pip install -U pip && pip cache purge && pip i…

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## [How to perform change of basis from a non-orthogonal 3D array to an orthogonal 3D array ?](https://discourse.itk.org/t/how-to-perform-change-of-basis-from-a-non-orthogonal-3d-array-to-an-orthogonal-3d-array/5266)

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**Author:** [@pranoy-ray](https://discourse.itk.org/u/pranoy-ray)\
**Replies:** 6\
**Last updated:** [August 17, 2022, 8:07pm UTC](https://discourse.itk.org/t/how-to-perform-change-of-basis-from-a-non-orthogonal-3d-array-to-an-orthogonal-3d-array/5266 "2022-08-17T20:07:15Z")

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I am trying to understand how to code the resampling of the voxels from a non-orthogonal basis as shown in the image below (taken from SimpleITK’s homepage) to an orthogonal grid. My input is say a 3D grayscale image…

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## [download javascript index.js, access denied](https://discourse.itk.org/t/download-javascript-index-js-access-denied/5270)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 2\
**Last updated:** [August 17, 2022, 7:25pm UTC](https://discourse.itk.org/t/download-javascript-index-js-access-denied/5270 "2022-08-17T19:25:51Z")

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Hi @dzenanz , do you know why i cannot download javascript file upploaded by ITK member, I click on the download symbol in my message and access denied pops up, there are two screen shots to make the issue clear. …

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## [How to \`itk.resample\_image\_filter\` with a \`BSplineTransform\` with 3D images?](https://discourse.itk.org/t/how-to-itk-resample-image-filter-with-a-bsplinetransform-with-3d-images/4987)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 11\
**Last updated:** [August 16, 2022, 9:06am UTC](https://discourse.itk.org/t/how-to-itk-resample-image-filter-with-a-bsplinetransform-with-3d-images/4987 "2022-08-16T09:06:57Z")

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Table of Contents 1. How to itk.resample\_image\_filter with a BSplineTransform with 3D images? 1.1. What I have tried 1.1.1. Inputs (data) 1.1.2. Failed attempt with resample\_image\_filter 1.1.3. Useless result wit…

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## [how to read a multi-frame DICOM with itk-wasm](https://discourse.itk.org/t/how-to-read-a-multi-frame-dicom-with-itk-wasm/5029)

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**Author:** [@maoweihang1995](https://discourse.itk.org/u/maoweihang1995)\
**Replies:** 6\
**Last updated:** [August 15, 2022, 9:06pm UTC](https://discourse.itk.org/t/how-to-read-a-multi-frame-dicom-with-itk-wasm/5029 "2022-08-15T21:06:42Z")

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I want to read a multi frame DICOM file with the API of readImageFile，but it doesn’t work。And it is normal to read a single frame file. And using the demo also doesn’t work.I wonder if itk-wasm does not support multi f…

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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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## [GetMatrix from SimpleITK ImageRegistrationMethod.Execute transform result](https://discourse.itk.org/t/getmatrix-from-simpleitk-imageregistrationmethod-execute-transform-result/5256)

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**Author:** [@ktdiedrich](https://discourse.itk.org/u/ktdiedrich)\
**Replies:** 2\
**Last updated:** [August 15, 2022, 2:51pm UTC](https://discourse.itk.org/t/getmatrix-from-simpleitk-imageregistrationmethod-execute-transform-result/5256 "2022-08-15T14:51:32Z")

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Is there a way to GetMatrix from the base transform returned from ImageRegistrationMethod.Execute(…)? final\_transform = registration\_method.Execute(fixed\_image, moving\_image) Final\_transform doesn’t have access to GetM…

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## [domain issues with bspline and inverse bspline](https://discourse.itk.org/t/domain-issues-with-bspline-and-inverse-bspline/5253)

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**Author:** [@Ilay\_Kamai](https://discourse.itk.org/u/Ilay_Kamai)\
**Replies:** 5\
**Last updated:** [August 15, 2022, 2:10pm UTC](https://discourse.itk.org/t/domain-issues-with-bspline-and-inverse-bspline/5253 "2022-08-15T14:10:20Z")

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Hi, I have the following issue - I’m registering two images with different physical domains using bspline. afterwards, im transforming some points from images. since the points needs to be at the same frame of reference…

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## [Exception occured during image io error](https://discourse.itk.org/t/exception-occured-during-image-io-error/5259)

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**Author:** [@mahesh\_bhosale](https://discourse.itk.org/u/mahesh_bhosale)\
**Replies:** 1\
**Last updated:** [August 15, 2022, 12:50pm UTC](https://discourse.itk.org/t/exception-occured-during-image-io-error/5259 "2022-08-15T12:50:25Z")

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Hi, I have been trying to load the predicted segmentation mask, which is a 3d PyTorch tensor saved as a nifty file, but I am getting below error. I am actually able to load the image volumes stored in a similar manner b…

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## [The image is full of zero after using resample filter.](https://discourse.itk.org/t/the-image-is-full-of-zero-after-using-resample-filter/5232)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 10\
**Last updated:** [August 12, 2022, 12:55pm UTC](https://discourse.itk.org/t/the-image-is-full-of-zero-after-using-resample-filter/5232 "2022-08-12T12:55:00Z")

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Hi, I am sorry for troubling you so many times. I am trying to resize my image from (530,530,604) -\>(512,512,604), then i use ResampleImageFilter, ScaleTransform and BSplineInterpolateImageFunction to do it. The conve…

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## [Confocal imaging alignment](https://discourse.itk.org/t/confocal-imaging-alignment/5252)

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**Author:** [@mixail\_orfanakis](https://discourse.itk.org/u/mixail_orfanakis)\
**Replies:** 1\
**Last updated:** [August 10, 2022, 2:10am UTC](https://discourse.itk.org/t/confocal-imaging-alignment/5252 "2022-08-10T02:10:36Z")

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Hallo everyone, I am trying to align different images obtained either from confocal microscopy or from vectra polaris. I am using the Simple ITK imaris python extension, but since I do not have any idea of how the algor…

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## [transform point with inverse bspline](https://discourse.itk.org/t/transform-point-with-inverse-bspline/5248)

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**Author:** [@Ilay\_Kamai](https://discourse.itk.org/u/Ilay_Kamai)\
**Replies:** 2\
**Last updated:** [August 9, 2022, 8:00am UTC](https://discourse.itk.org/t/transform-point-with-inverse-bspline/5248 "2022-08-09T08:00:18Z")

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Hi, i’m trying to transform 3D points using inverse displacement field of Bspline transformation. after calculating the transformation i’m creating the inverse as suggested here : Inverse of BSpline transform this is …

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## [Quick Test for "are images in the same space" aka "overalpping" (SimpleITK)?](https://discourse.itk.org/t/quick-test-for-are-images-in-the-same-space-aka-overalpping-simpleitk/5249)

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**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 7\
**Last updated:** [August 8, 2022, 9:10pm UTC](https://discourse.itk.org/t/quick-test-for-are-images-in-the-same-space-aka-overalpping-simpleitk/5249 "2022-08-08T21:10:49Z")

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If I have a collection of images and I’d like to quickly check that they’re “overlapping”, that is, have the same origin, pixel dimensions and direction cosines, is there a filter/test which does this other than comparin…

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## [SimpleITK, numpy, scipy, and voxel ordering](https://discourse.itk.org/t/simpleitk-numpy-scipy-and-voxel-ordering/5250)

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**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 0\
**Last updated:** [August 8, 2022, 7:14pm UTC](https://discourse.itk.org/t/simpleitk-numpy-scipy-and-voxel-ordering/5250 "2022-08-08T19:14:26Z")

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Following up on Images in physical space in Python Was it decided how x,y,z in SimpleITK, is represented? I can’t find a complete description of the voxel dimension ordering in Fundamental Concepts — SimpleITK 2.0rc2 do…

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## [changing origin bspline registration](https://discourse.itk.org/t/changing-origin-bspline-registration/5246)

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**Author:** [@Ilay\_Kamai](https://discourse.itk.org/u/Ilay_Kamai)\
**Replies:** 1\
**Last updated:** [August 8, 2022, 4:16am UTC](https://discourse.itk.org/t/changing-origin-bspline-registration/5246 "2022-08-08T04:16:55Z")

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hi, i’m trying to change the domain origin of a bspline registration, but it seems to have no effect. this is part of the code: def bspline\_registration(fixed\_image, moving\_image, out\_path, params): """ bspline…

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## [Python wrapping for 64-bit double \`itk::Mesh\` coordinates?](https://discourse.itk.org/t/python-wrapping-for-64-bit-double-itk-mesh-coordinates/5241)

<div class="topic-metadata">

**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 4\
**Last updated:** [August 5, 2022, 9:12pm UTC](https://discourse.itk.org/t/python-wrapping-for-64-bit-double-itk-mesh-coordinates/5241 "2022-08-05T21:12:21Z")

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Is there a Python wrapping of itk::Mesh for 64-bit floating point (double) coordinates of its points? In C++, an itk::Mesh has 32-bit float coordinates by default, but it can be set to 64-bit double by some “mesh trait…

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