# Latest

**URL:** https://discourse.itk.org/latest.md?page=28

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

**Page:** 29

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## [PhyCV](https://discourse.itk.org/t/phycv/5662)

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**Author:** [@Jon](https://discourse.itk.org/u/Jon)\
**Replies:** 2\
**Last updated:** [February 2, 2023, 11:42am UTC](https://discourse.itk.org/t/phycv/5662 "2023-02-02T11:42:20Z")

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PhyCV is a physics-based public domain package for computer vision recently released. See https://github.com/JalaliLabUCLA/phycv/blob/main/README.md I’m now using the VEViD routine to preprocess under-stained H&E histo…

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## [Squeeze dicom ITK image from 4D to 3D](https://discourse.itk.org/t/squeeze-dicom-itk-image-from-4d-to-3d/4300)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 4\
**Last updated:** [July 30, 2021, 4:53pm UTC](https://discourse.itk.org/t/squeeze-dicom-itk-image-from-4d-to-3d/4300 "2021-07-30T16:53:02Z")

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I have Dicom images in an unusual format. For example, usually, Dicom images are saved in a casepath/folder in multiple slices. IM-0001-0240-0001.dcm I use the following helper function to read the dicom images: def d…

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## [Status of ITK Logger classes?](https://discourse.itk.org/t/status-of-itk-logger-classes/5664)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 5\
**Last updated:** [February 1, 2023, 5:27pm UTC](https://discourse.itk.org/t/status-of-itk-logger-classes/5664 "2023-02-01T17:27:44Z")

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ITK has this group of Logger and LogOutput classes, originally by Hee-Su Kim, and included with ITK in 2005: Are they still recommended to be used within a new application? Because they look rather old, and there are …

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## [How to separate layers from a NRRD file?](https://discourse.itk.org/t/how-to-separate-layers-from-a-nrrd-file/5661)

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**Author:** [@Sterben\_01](https://discourse.itk.org/u/Sterben_01)\
**Replies:** 2\
**Last updated:** [February 1, 2023, 12:18am UTC](https://discourse.itk.org/t/how-to-separate-layers-from-a-nrrd-file/5661 "2023-02-01T00:18:21Z")

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Hi! I am a beginner of ITK/VTK. Currently, I have an NRRD file, and it has three layers. If I want to separate it and write it to three files, which class should I use? I know how to read and write, but I don’t know how…

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## [itk-wasm PipelineFunctor with 2 input image types](https://discourse.itk.org/t/itk-wasm-pipelinefunctor-with-2-input-image-types/5657)

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**Author:** [@PaulHax](https://discourse.itk.org/u/PaulHax)\
**Replies:** 1\
**Last updated:** [January 31, 2023, 12:07pm UTC](https://discourse.itk.org/t/itk-wasm-pipelinefunctor-with-2-input-image-types/5657 "2023-01-31T12:07:36Z")

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Hello! I am making a checkerboard itk-wasm pipeline that takes 2 images, with possibly different component types. Using a itk::wasm::SupportInputImageTypes with a PipelineFunctor would be perfect. But I don’t know how …

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## [registration of histological hne image on segmentation label.](https://discourse.itk.org/t/registration-of-histological-hne-image-on-segmentation-label/5659)

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**Author:** [@banikr](https://discourse.itk.org/u/banikr)\
**Replies:** 2\
**Last updated:** [January 30, 2023, 9:10pm UTC](https://discourse.itk.org/t/registration-of-histological-hne-image-on-segmentation-label/5659 "2023-01-30T21:10:11Z")

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Hello, I am trying to register a high resolution H & E stained image(RGB) on a segmentation image. The RGB image size is: (620, 734, 3) and label image is: (96, 73) The problems are: Is it possible to register 3 ch…

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## [Sitk AffineTransform vs Pytorch grid sample](https://discourse.itk.org/t/sitk-affinetransform-vs-pytorch-grid-sample/3603)

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**Author:** [@prms](https://discourse.itk.org/u/prms)\
**Replies:** 11\
**Last updated:** [January 26, 2023, 6:45pm UTC](https://discourse.itk.org/t/sitk-affinetransform-vs-pytorch-grid-sample/3603 "2023-01-26T18:45:28Z")

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I’m comparing the result of SITK AffineTransform and Pytorch grid\_sample. The difference between them is that sitk treats origin as the centre of rotation while Pytorch treats the centre of the image as the centre of rot…

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## [Wrong header when reading a NIFTI file](https://discourse.itk.org/t/wrong-header-when-reading-a-nifti-file/5520)

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**Author:** [@niruta](https://discourse.itk.org/u/niruta)\
**Replies:** 12\
**Last updated:** [January 25, 2023, 7:35am UTC](https://discourse.itk.org/t/wrong-header-when-reading-a-nifti-file/5520 "2023-01-25T07:35:26Z")

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Hi, I am a beginner in SimpleITK. I used SimpleITK to load a nifti image and view its header information. The pixdim\[0\] header is changed from -1 to 0. I used ITKsnap, nifti-tool and nibabel to see the header informatio…

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## [False Positive value](https://discourse.itk.org/t/false-positive-value/5640)

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**Author:** [@Moha\_data](https://discourse.itk.org/u/Moha_data)\
**Replies:** 2\
**Last updated:** [January 24, 2023, 4:41pm UTC](https://discourse.itk.org/t/false-positive-value/5640 "2023-01-24T16:41:52Z")

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I have a binary image (background = 0) and to see how False positive works, I applied the dilation to the image (as a test image) and calculated the False Positive. The left image is the reference and the right one is…

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## [05 Basic Registration tutorial error](https://discourse.itk.org/t/05-basic-registration-tutorial-error/5649)

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**Author:** [@Priscilla](https://discourse.itk.org/u/Priscilla)\
**Replies:** 4\
**Last updated:** [January 24, 2023, 3:44pm UTC](https://discourse.itk.org/t/05-basic-registration-tutorial-error/5649 "2023-01-24T15:44:38Z")

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Hello, I’m following the SimpeITK MICCAI tutorial (2020), and I can’t reproduce the results in the Initialisation section of the notebook 05\_basic\_registration, because I get the following error: AttributeError: module…

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## [cmake\_minimum\_required ITK\_NEWEST\_VALIDATED\_POLICIES\_VERSION 3.19.7?](https://discourse.itk.org/t/cmake-minimum-required-itk-newest-validated-policies-version-3-19-7/5644)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 10\
**Last updated:** [January 23, 2023, 8:52pm UTC](https://discourse.itk.org/t/cmake-minimum-required-itk-newest-validated-policies-version-3-19-7/5644 "2023-01-23T20:52:37Z")

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ITK’s root CMakeLists starts with cmake\_minimum\_required(VERSION 3.16.3...3.19.7), or more precisely: Using the VERSION \<min\>...\<max\> parameters, as documented at https://cmake.org/cmake/help/v3.19/command/cmake\_minimu…

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## [Multimodal Registration of Dicom file in physical space (mm space)](https://discourse.itk.org/t/multimodal-registration-of-dicom-file-in-physical-space-mm-space/5639)

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**Author:** [@gaurav\_patel](https://discourse.itk.org/u/gaurav_patel)\
**Replies:** 2\
**Last updated:** [January 23, 2023, 5:13am UTC](https://discourse.itk.org/t/multimodal-registration-of-dicom-file-in-physical-space-mm-space/5639 "2023-01-23T05:13:28Z")

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I am new to simpleITK. My task is to register MR volume with CT volume. The CT volume is entire body while MR volume is abdomen only. Moreover MR volume is rotated i.e. direction cosines are not (1,0,0,1) from dicom IOP …

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## [Suitability of registration algorithms for a specific image type](https://discourse.itk.org/t/suitability-of-registration-algorithms-for-a-specific-image-type/5636)

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**Author:** [@ericrhenry](https://discourse.itk.org/u/ericrhenry)\
**Replies:** 4\
**Last updated:** [January 20, 2023, 3:58pm UTC](https://discourse.itk.org/t/suitability-of-registration-algorithms-for-a-specific-image-type/5636 "2023-01-20T15:58:02Z")

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I am new to ITK, and have been exploring the different registration algorithms available. (Kudos on the breadth and depth of examples provided, BTW.) Most of the illustrations I have seen deal with biomedical images, of …

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## [Need guidance to address the regression error ?](https://discourse.itk.org/t/need-guidance-to-address-the-regression-error/5569)

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**Author:** [@parth721](https://discourse.itk.org/u/parth721)\
**Replies:** 14\
**Last updated:** [January 20, 2023, 2:48pm UTC](https://discourse.itk.org/t/need-guidance-to-address-the-regression-error/5569 "2023-01-20T14:48:41Z")

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As a beginner I take up an issue, where I need to perform regression testing. In order to understand the code, I had read the ItkSoftwareGuide pdf, google about it, watch lectures on youtube about regression testing, as…

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## [Is there a way to get the dicom slice index number of the slice which contains the ROI?](https://discourse.itk.org/t/is-there-a-way-to-get-the-dicom-slice-index-number-of-the-slice-which-contains-the-roi/5637)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 1\
**Last updated:** [January 20, 2023, 2:27pm UTC](https://discourse.itk.org/t/is-there-a-way-to-get-the-dicom-slice-index-number-of-the-slice-which-contains-the-roi/5637 "2023-01-20T14:27:30Z")

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Hello, I am working with 3D Dicom images. I would like to get the index of the slices which contains the liver region (ROI) as some slices do not show liver or full black. Is it possible to do it in sitk?

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## [Can I look at label intensity histograms with SimpleITK?](https://discourse.itk.org/t/can-i-look-at-label-intensity-histograms-with-simpleitk/5634)

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**Author:** [@Toby-Jackson](https://discourse.itk.org/u/Toby-Jackson)\
**Replies:** 1\
**Last updated:** [January 20, 2023, 2:16pm UTC](https://discourse.itk.org/t/can-i-look-at-label-intensity-histograms-with-simpleitk/5634 "2023-01-20T14:16:36Z")

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I have a label map and and corresponding image and would like to look at the intensity histograms for each or each label, I know that there is an intensity histogram being calculated behind the scenes, for example in sit…

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## [Resampling along the z-axis of binary segmentation stack](https://discourse.itk.org/t/resampling-along-the-z-axis-of-binary-segmentation-stack/4286)

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**Author:** [@caniko](https://discourse.itk.org/u/caniko)\
**Replies:** 8\
**Last updated:** [January 18, 2023, 3:15pm UTC](https://discourse.itk.org/t/resampling-along-the-z-axis-of-binary-segmentation-stack/4286 "2023-01-18T15:15:20Z")

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I have a binary image stack or space of binarized voxels (either black or white voxels). Since my data is from electron microscopy the spacing of the pixels are (1, 1, Z) where (x, y, z), and Z is an arbitrary value def…

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## [Placing a ball in a CT volume](https://discourse.itk.org/t/placing-a-ball-in-a-ct-volume/5632)

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**Author:** [@User0](https://discourse.itk.org/u/User0)\
**Replies:** 4\
**Last updated:** [January 18, 2023, 8:09am UTC](https://discourse.itk.org/t/placing-a-ball-in-a-ct-volume/5632 "2023-01-18T08:09:42Z")

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I’m trying to place a 25mm reference ball within a CT. I think I have a function that can create a ball in a volume that has the same shape and spacing as the CT. However, I tried adding, pasting and masking but the ball…

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## [Compute TRE after image registration for 4DCT lung images](https://discourse.itk.org/t/compute-tre-after-image-registration-for-4dct-lung-images/5558)

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**Author:** [@VHK](https://discourse.itk.org/u/VHK)\
**Replies:** 3\
**Last updated:** [January 17, 2023, 2:26pm UTC](https://discourse.itk.org/t/compute-tre-after-image-registration-for-4dct-lung-images/5558 "2023-01-17T14:26:46Z")

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Hello, I am doing a deformable image registration for 4DCT lung images. I want to evaluate the registration accuracy by calculating the TRE in SITK. I did Elastix registration in 3D-Slicer and got the transformation as …

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## [Any example or implement for image registration with cuda](https://discourse.itk.org/t/any-example-or-implement-for-image-registration-with-cuda/5107)

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**Author:** [@busyyang](https://discourse.itk.org/u/busyyang)\
**Replies:** 3\
**Last updated:** [January 17, 2023, 9:30am UTC](https://discourse.itk.org/t/any-example-or-implement-for-image-registration-with-cuda/5107 "2023-01-17T09:30:10Z")

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Hi all, we have implemented a demo for 2D/3D image registration with help by this article. But it cost too much time when registration even over 5 minites. We’d like to speed up the process. And cuda may help it, but we…

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## [Gradient magnitude (0) in registration.](https://discourse.itk.org/t/gradient-magnitude-0-in-registration/2266)

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**Author:** [@spic](https://discourse.itk.org/u/spic)\
**Replies:** 7\
**Last updated:** [January 17, 2023, 8:24am UTC](https://discourse.itk.org/t/gradient-magnitude-0-in-registration/2266 "2023-01-17T08:24:38Z")

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I am trying to register 2 3D volumes. I know that there is significant (rigid) shift between the two images, but registration keep stopping after first iteration. The gradient value is zero at the first iteration! The me…

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## [Testing with ctest fails when testing ITK5.2 with VTK9.2 with the itkVkGlue module in MSVC release mode](https://discourse.itk.org/t/testing-with-ctest-fails-when-testing-itk5-2-with-vtk9-2-with-the-itkvkglue-module-in-msvc-release-mode/5622)

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**Author:** [@fab672000](https://discourse.itk.org/u/fab672000)\
**Replies:** 10\
**Last updated:** [January 16, 2023, 7:30pm UTC](https://discourse.itk.org/t/testing-with-ctest-fails-when-testing-itk5-2-with-vtk9-2-with-the-itkvkglue-module-in-msvc-release-mode/5622 "2023-01-16T19:30:56Z")

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All tests passed but those: The following tests FAILED: 2538 - itkImageToVTKImageFilterTest (Failed) 2540 - itkVTKImageToImageFilterTest (Failed) Trace shows very similar root causes for the failing tests: Debug: …

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## [Gradient magnitude (0) at the first iteration](https://discourse.itk.org/t/gradient-magnitude-0-at-the-first-iteration/5628)

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**Author:** [@suzume](https://discourse.itk.org/u/suzume)\
**Replies:** 0\
**Last updated:** [January 14, 2023, 2:27pm UTC](https://discourse.itk.org/t/gradient-magnitude-0-at-the-first-iteration/5628 "2023-01-14T14:27:49Z")

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Hi, the iteration stopped at the first iteration no matter what the initial transform parameters are and the stop reason is " RegularStepGradientDescentOptimizer: Gradient magnitude tolerance met after 0 iterations. Grad…

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## [Using ITK + Eigen](https://discourse.itk.org/t/using-itk-eigen/5627)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 2\
**Last updated:** [January 13, 2023, 9:42pm UTC](https://discourse.itk.org/t/using-itk-eigen/5627 "2023-01-13T21:42:37Z")

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Hello, I am trying to use ITK with an external Eigen build. ITK was installed first in our server by the system analyst. Then I asked him if he could install Eigen. I am making an application that uses ITK for reading…

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## [Resampling results in an all black images](https://discourse.itk.org/t/resampling-results-in-an-all-black-images/5624)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 6\
**Last updated:** [January 12, 2023, 9:57pm UTC](https://discourse.itk.org/t/resampling-results-in-an-all-black-images/5624 "2023-01-12T21:57:46Z")

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I have two CT volumetric scans for the same patient (for arterial and venous) with different number of slices. e.g. arterial scan has ~146 dicom images whereas venous scan has ~156 dicom images. I want to resample one p…

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## [Welcome and guide first-time contributors with a GitHub Action](https://discourse.itk.org/t/welcome-and-guide-first-time-contributors-with-a-github-action/5625)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [January 12, 2023, 4:37pm UTC](https://discourse.itk.org/t/welcome-and-guide-first-time-contributors-with-a-github-action/5625 "2023-01-12T16:37:41Z")

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By: Matt McCormick , Mary Elise Dedicke , Jon Haitz Legarreta Gorroño , Stephen Aylward , Will Schroeder Back in the day, before open source won the Closed vs. Open Wars (especially in scientific computing), RTFM. w…

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## [Resampling two volumes with different number of slices.](https://discourse.itk.org/t/resampling-two-volumes-with-different-number-of-slices/5051)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 10\
**Last updated:** [January 11, 2023, 4:45pm UTC](https://discourse.itk.org/t/resampling-two-volumes-with-different-number-of-slices/5051 "2023-01-11T16:45:29Z")

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I have two CT volumetric scans for the same patient (for arterial and venous) with different number of slices. e.g. arterial scan has ~146 dicom images whereas venous scan has ~156 dicom images. I want to resample one p…

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## [Missing header files in ITK package I built](https://discourse.itk.org/t/missing-header-files-in-itk-package-i-built/5620)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 3\
**Last updated:** [January 10, 2023, 10:42pm UTC](https://discourse.itk.org/t/missing-header-files-in-itk-package-i-built/5620 "2023-01-10T22:42:05Z")

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I am maintaining dcmqi, which is a library that uses ITK for a handful of operations, including IO and some basic filtering. For quite some time I used an older version of ITK, which I customized manually to take out as …

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## [about dicom regesition](https://discourse.itk.org/t/about-dicom-regesition/5618)

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**Author:** [@ma1282029525](https://discourse.itk.org/u/ma1282029525)\
**Replies:** 2\
**Last updated:** [January 10, 2023, 9:58am UTC](https://discourse.itk.org/t/about-dicom-regesition/5618 "2023-01-10T09:58:32Z")

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When using 3Dslicer, I found that some plug-ins will transfer dicom images to other formats for registration. I want to know what is the advantage of this?

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## [Name mangling for the Eigen library](https://discourse.itk.org/t/name-mangling-for-the-eigen-library/5562)

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**Author:** [@Fijoy\_Vadakkumpadan](https://discourse.itk.org/u/Fijoy_Vadakkumpadan)\
**Replies:** 2\
**Last updated:** [January 9, 2023, 9:51am UTC](https://discourse.itk.org/t/name-mangling-for-the-eigen-library/5562 "2023-01-09T09:51:04Z")

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Does ITK mangle the symbols in the Eigen 3rd party library it includes? The initial paragraph in this file states that it does the mangling to avoid conflicts with other copies of the Eigen library in the same process: …

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