# \#simpleitk

**URL:** https://discourse.itk.org/tag/simpleitk/10.md

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

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## [Registation of two vascular images using Python Simple ITK](https://discourse.itk.org/t/registation-of-two-vascular-images-using-python-simple-itk/7766)

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**Author:** [@anatolejimenez](https://discourse.itk.org/u/anatolejimenez)\
**Replies:** 1\
**Last updated:** [May 22, 2026, 12:51pm UTC](https://discourse.itk.org/t/registation-of-two-vascular-images-using-python-simple-itk/7766 "2026-05-22T12:51:09Z")

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Hi, I would like to register two vascular images of the same modality but with different dynamics. I played a lot with the image registration metrics (correlation, mutual information and correlation) with optimizer grad…

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## [SimpleITK 3.0.0 Beta 1](https://discourse.itk.org/t/simpleitk-3-0-0-beta-1/7767)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 0\
**Last updated:** [May 22, 2026, 12:45pm UTC](https://discourse.itk.org/t/simpleitk-3-0-0-beta-1/7767 "2026-05-22T12:45:41Z")

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Announcing the SimpleITK 3.0.0b1 Beta Release! This beta release is a major milestone for SimpleITK 3.0, featuring new functionality and improvements including experimental integration of SimpleElastix into the binary d…

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## [SimpleITK 2.5.5 Release](https://discourse.itk.org/t/simpleitk-2-5-5-release/7765)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 0\
**Last updated:** [May 14, 2026, 6:10pm UTC](https://discourse.itk.org/t/simpleitk-2-5-5-release/7765 "2026-05-14T18:10:51Z")

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Announcing the SimpleITK 2.5.5 Release! Release Highlights SimpleITK in R on the Windows operating system is available! SimpleITK 2.5.5 is the first official release to support building SimpleITK with R wrapping for a…

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## [SimpleITK 3.0.0 Alpha 3](https://discourse.itk.org/t/simpleitk-3-0-0-alpha-3/7733)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 5\
**Last updated:** [March 19, 2026, 10:10am UTC](https://discourse.itk.org/t/simpleitk-3-0-0-alpha-3/7733 "2026-03-19T10:10:54Z")

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Release Notes for SimpleITK v3.0.0 Alpha Release 3 This is the third Alpha Release of SimpleITK 3.0. It covers changes since v3.0.0a1 (September 2025), including v3.0.0a2. Significant work has been done on the Python pa…

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## [Intermittent SIGSEGV in SignedMaurerDistanceMap](https://discourse.itk.org/t/intermittent-sigsegv-in-signedmaurerdistancemap/7714)

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**Author:** [@e\_s](https://discourse.itk.org/u/e_s)\
**Replies:** 8\
**Last updated:** [February 25, 2026, 5:54pm UTC](https://discourse.itk.org/t/intermittent-sigsegv-in-signedmaurerdistancemap/7714 "2026-02-25T17:54:01Z")

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Hello Everyone. I am experiencing an intermittent Segmentation Fault while using the itk::simple::SignedMaurerDistanceMap() function. Environment SimpleITK 2.4 (ITK 5.4), Ubuntu 24 with intel oneAPI 2025.1 (icpx) comp…

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## [python SimpleITK and parallelism](https://discourse.itk.org/t/python-simpleitk-and-parallelism/7678)

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**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 4\
**Last updated:** [January 30, 2026, 3:15pm UTC](https://discourse.itk.org/t/python-simpleitk-and-parallelism/7678 "2026-01-30T15:15:28Z")

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Following up on Running optimizer in parallel - #7 by blowekamp I wanted to ask ask about the interaction between python parallelism and SimpleITK. I’ve successfully wrapped the calls I need from SimpleITK in concurrent…

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## [Groupwise registration in SimpleITK or ITKElastix flipping images?](https://discourse.itk.org/t/groupwise-registration-in-simpleitk-or-itkelastix-flipping-images/7694)

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**Author:** [@Rock](https://discourse.itk.org/u/Rock)\
**Replies:** 1\
**Last updated:** [January 7, 2026, 7:59pm UTC](https://discourse.itk.org/t/groupwise-registration-in-simpleitk-or-itkelastix-flipping-images/7694 "2026-01-07T19:59:05Z")

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Hello, I am trying to run groupwise registrations in SimpleITK and ITKElastix, but with either the resulting images just seem to be flipped vertically. My original images are .tifs; I converted them to grayscale and the…

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## [Query on Regularization with BSplineTransform and GradientDescent in SimpleITK](https://discourse.itk.org/t/query-on-regularization-with-bsplinetransform-and-gradientdescent-in-simpleitk/7690)

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**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\
**Replies:** 4\
**Last updated:** [January 5, 2026, 4:17pm UTC](https://discourse.itk.org/t/query-on-regularization-with-bsplinetransform-and-gradientdescent-in-simpleitk/7690 "2026-01-05T16:17:06Z")

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Hello everyone, I am currently working with SimpleITK for image registration, specifically employing sitk.BSplineTransform and the SetOptimizerAsGradientDescent optimizer. I’ve been reviewing a Python example that demo…

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## [Different Rotation Matrices between Euler3DTransform and Scipy Rotation](https://discourse.itk.org/t/different-rotation-matrices-between-euler3dtransform-and-scipy-rotation/4273)

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**Author:** [@Floowey](https://discourse.itk.org/u/Floowey)\
**Replies:** 6\
**Last updated:** [December 25, 2025, 7:20am UTC](https://discourse.itk.org/t/different-rotation-matrices-between-euler3dtransform-and-scipy-rotation/4273 "2025-12-25T07:20:45Z")

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Hello, I’m trying to rotate sections of my images according to certain orientations. However, I noticed some discrepancies between the rotations of the Euler3DTransform object and scipy.spatial.transform.Rotation when g…

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## [Overlaying Structures on CT Images in Axial, Coronal, and Sagittal Views](https://discourse.itk.org/t/overlaying-structures-on-ct-images-in-axial-coronal-and-sagittal-views/7647)

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**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\
**Replies:** 3\
**Last updated:** [October 21, 2025, 1:40pm UTC](https://discourse.itk.org/t/overlaying-structures-on-ct-images-in-axial-coronal-and-sagittal-views/7647 "2025-10-21T13:40:45Z")

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Hello everyone, I am working on displaying CT images in the axial, coronal, and sagittal planes, along with dose maps and RTSTRUCT contours. While the CT and dose images are displayed correctly, I am having trouble over…

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## [SimpleITK 3.0.0 Alpha 1](https://discourse.itk.org/t/simpleitk-3-0-0-alpha-1/7637)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 0\
**Last updated:** [September 19, 2025, 4:10pm UTC](https://discourse.itk.org/t/simpleitk-3-0-0-alpha-1/7637 "2025-09-19T16:10:44Z")

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Release Notes for SimpleITK v3.0.0 Alpha Release 1 This is an initial Alpha Release of a major version change of SimpleITK. Please test the new building infrastructure, the package binaries, and report and issues encount…

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## [Dice Coefficient Calculation in Python](https://discourse.itk.org/t/dice-coefficient-calculation-in-python/7628)

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**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\
**Replies:** 2\
**Last updated:** [September 11, 2025, 9:01am UTC](https://discourse.itk.org/t/dice-coefficient-calculation-in-python/7628 "2025-09-11T09:01:10Z")

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Hello everyone, I’m trying to compute the Dice coefficient using a Python script. To implement this, I have used ideas and code from the following links: “SimpleITK-Notebooks/Python/34\_Segmentation\_Evaluation.ipynb at…

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## [Registration of CT Images with Large Organ Deformations](https://discourse.itk.org/t/registration-of-ct-images-with-large-organ-deformations/7627)

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**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\
**Replies:** 1\
**Last updated:** [September 2, 2025, 7:49pm UTC](https://discourse.itk.org/t/registration-of-ct-images-with-large-organ-deformations/7627 "2025-09-02T19:49:17Z")

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Hello everyone, I have two CT images that I want to register together. One is from external beam radiotherapy (EBRT), and the other is from brachytherapy. Before registration, I harmonized both images by making their Or…

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## [Unifying CT Images Geometry and Cropping to Common ROI](https://discourse.itk.org/t/unifying-ct-images-geometry-and-cropping-to-common-roi/7614)

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**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\
**Replies:** 3\
**Last updated:** [August 25, 2025, 5:11pm UTC](https://discourse.itk.org/t/unifying-ct-images-geometry-and-cropping-to-common-roi/7614 "2025-08-25T17:11:31Z")

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Hi everyone, I am currently working on a medical image processing task that involves the registration of five CT image series for a single patient. My dataset consists of: One CT scan acquired during an External Radiot…

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## [Faster interpolation using sitkLabelGaussian](https://discourse.itk.org/t/faster-interpolation-using-sitklabelgaussian/6183)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 11\
**Last updated:** [August 1, 2025, 10:13pm UTC](https://discourse.itk.org/t/faster-interpolation-using-sitklabelgaussian/6183 "2025-08-01T22:13:22Z")

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Hi I am working on a MONAI-based whole head segmentation tool, which predicts close to 30 tissue labels. Currently all post-processing is implemented in Python using SimpleITK. Once we have done some clean-up operation…

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## [reading and writng a dicom image](https://discourse.itk.org/t/reading-and-writng-a-dicom-image/3992)

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**Author:** [@sarbabi](https://discourse.itk.org/u/sarbabi)\
**Replies:** 7\
**Last updated:** [June 26, 2025, 9:59pm UTC](https://discourse.itk.org/t/reading-and-writng-a-dicom-image/3992 "2025-06-26T21:59:06Z")

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Hi, In the following simple piece of code I’m trying to read a DICOM image as sitkImage and its tags as a python dictionary. then I call another function to write that image in another location with the same tags readin…

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## [Vector type single channel image](https://discourse.itk.org/t/vector-type-single-channel-image/7575)

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**Author:** [@Franciska](https://discourse.itk.org/u/Franciska)\
**Replies:** 2\
**Last updated:** [June 25, 2025, 1:09pm UTC](https://discourse.itk.org/t/vector-type-single-channel-image/7575 "2025-06-25T13:09:54Z")

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I have a dicom image thats shape is (1136, 852, 1) and PixelID is ‘vector of 8-bit unsigned integer’ . I want to cast this to float32 but as I can not cast vector type to simple float, following online advice I tried: …

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## [Edge cases of DICOMOrient](https://discourse.itk.org/t/edge-cases-of-dicomorient/7559)

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**Author:** [@ahulist](https://discourse.itk.org/u/ahulist)\
**Replies:** 2\
**Last updated:** [June 5, 2025, 11:22pm UTC](https://discourse.itk.org/t/edge-cases-of-dicomorient/7559 "2025-06-05T23:22:39Z")

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I’m using SimpleITK’s DICOMOrient to reorient a stack of DICOM slices. When I read files as a simple list (instead of using ImageSeriesReader), SITK only uses the first slice’s Origin/Spacing and infers the rest on the f…

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## [ITK-snap cannot load DICOM](https://discourse.itk.org/t/itk-snap-cannot-load-dicom/4351)

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**Author:** [@Won\_Chul\_Chung](https://discourse.itk.org/u/Won_Chul_Chung)\
**Replies:** 9\
**Last updated:** [May 21, 2025, 6:25pm UTC](https://discourse.itk.org/t/itk-snap-cannot-load-dicom/4351 "2025-05-21T18:25:02Z")

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Hello, I am relatively new to python and itk. I originally started with MicroCT scan images with .tif extension. (single series, about 500 “slices”) I then transformed the slices into DICOM series using simpleitk func…

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## [Use an external SPM Displacement Field in SimpleITK to translate a point from the source MRI to the output MRI: Annotations not matching](https://discourse.itk.org/t/use-an-external-spm-displacement-field-in-simpleitk-to-translate-a-point-from-the-source-mri-to-the-output-mri-annotations-not-matching/7518)

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**Author:** [@miaomiaomiao](https://discourse.itk.org/u/miaomiaomiao)\
**Replies:** 2\
**Last updated:** [May 13, 2025, 1:22pm UTC](https://discourse.itk.org/t/use-an-external-spm-displacement-field-in-simpleitk-to-translate-a-point-from-the-source-mri-to-the-output-mri-annotations-not-matching/7518 "2025-05-13T13:22:57Z")

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Hello community, I have made point annotations in original MRIs and used SPM CAT12 to register the MRIs. Now I want to transform the points into the registered MRIs using SimpleITK. SPM CAT12 gives me a DisplacementFiel…

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## [DICOMOrient Voxel Data Permutations/Flips in SimpleITK](https://discourse.itk.org/t/dicomorient-voxel-data-permutations-flips-in-simpleitk/7516)

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**Author:** [@ahulist](https://discourse.itk.org/u/ahulist)\
**Replies:** 2\
**Last updated:** [May 12, 2025, 4:03am UTC](https://discourse.itk.org/t/dicomorient-voxel-data-permutations-flips-in-simpleitk/7516 "2025-05-12T04:03:52Z")

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Hi all, I’m working with a DICOM processing pipeline where I use sitk.DICOMOrient(image, "LPS") to reorient an original series. Later, I need to revert this lps\_oriented\_image back to match the exact voxel data order an…

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## [Get \`numpy\` to \`SimpleITK\` data type mapping](https://discourse.itk.org/t/get-numpy-to-simpleitk-data-type-mapping/7479)

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**Author:** [@jhlegarreta](https://discourse.itk.org/u/jhlegarreta)\
**Replies:** 13\
**Last updated:** [March 27, 2025, 4:04pm UTC](https://discourse.itk.org/t/get-numpy-to-simpleitk-data-type-mapping/7479 "2025-03-27T16:04:28Z")

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Hi, is there a way to get the mapping of numpy data types to the SimpleITK data types? I have seen this, but it is a method variable, and it requires an input image. I am wondering whether I cant get the SimpleITK ty…

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## [ElastixImageFilter() vs ImageRegistrationMethod()](https://discourse.itk.org/t/elastiximagefilter-vs-imageregistrationmethod/7416)

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**Author:** [@Weng\_Yann\_Seow](https://discourse.itk.org/u/Weng_Yann_Seow)\
**Replies:** 3\
**Last updated:** [February 10, 2025, 2:36pm UTC](https://discourse.itk.org/t/elastiximagefilter-vs-imageregistrationmethod/7416 "2025-02-10T14:36:24Z")

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I would like to replace deprecated ElastixImageFilter method with the ImageRegistrationMethod method for registration. I am expecting both of these method can derive a similar resampled images, but in fact, ElastixImageF…

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## [\[SOLVED\] Difficulty getting registration to work with mask on moving image](https://discourse.itk.org/t/solved-difficulty-getting-registration-to-work-with-mask-on-moving-image/7423)

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**Author:** [@ebaudrez](https://discourse.itk.org/u/ebaudrez)\
**Replies:** 5\
**Last updated:** [February 6, 2025, 1:37pm UTC](https://discourse.itk.org/t/solved-difficulty-getting-registration-to-work-with-mask-on-moving-image/7423 "2025-02-06T13:37:06Z")

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Update 6 February: I got this to work. I confirm the mask on the moving image works. Hello! I am having difficulty to get a registration with a mask on the moving image to work. I have attached the full code below, as w…

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## [SimpleITK 2.4.1 Release](https://discourse.itk.org/t/simpleitk-2-4-1-release/7382)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 0\
**Last updated:** [January 15, 2025, 3:45pm UTC](https://discourse.itk.org/t/simpleitk-2-4-1-release/7382 "2025-01-15T15:45:06Z")

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Announcing the SimpleITK 2.4.1 Release! The release includes critical bug fixes and compilation issues including an update to ITK v5.4.2. Installing SimpleITK Complete instructions on getting started with SimpleITK inc…

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## [Could Someone Give me Advice on Optimizing Image Resampling in ITK for Large Datasets?](https://discourse.itk.org/t/could-someone-give-me-advice-on-optimizing-image-resampling-in-itk-for-large-datasets/7354)

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**Author:** [@roberrttt](https://discourse.itk.org/u/roberrttt)\
**Replies:** 3\
**Last updated:** [December 17, 2024, 8:03pm UTC](https://discourse.itk.org/t/could-someone-give-me-advice-on-optimizing-image-resampling-in-itk-for-large-datasets/7354 "2024-12-17T20:03:57Z")

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Hello there, I am currently working on a project involving the processing of high resolution medical images; and I have run into some performance concerns when resampling large datasets using ITK. Specifically; I am usi…

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## [How should one set the output origin when resampling an image?](https://discourse.itk.org/t/how-should-one-set-the-output-origin-when-resampling-an-image/7307)

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**Author:** [@sebquet](https://discourse.itk.org/u/sebquet)\
**Replies:** 4\
**Last updated:** [November 14, 2024, 5:56am UTC](https://discourse.itk.org/t/how-should-one-set-the-output-origin-when-resampling-an-image/7307 "2024-11-14T05:56:38Z")

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Hello, I would like to know how to set the output origin when resampling a volume to a different spacing. I understand from Fundamental Concepts — SimpleITK 2.4.0 documentation that in SITK the origin is in the middle o…

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## [Resampling mask to avoid 0s](https://discourse.itk.org/t/resampling-mask-to-avoid-0s/7304)

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**Author:** [@rtlim](https://discourse.itk.org/u/rtlim)\
**Replies:** 6\
**Last updated:** [November 11, 2024, 10:54pm UTC](https://discourse.itk.org/t/resampling-mask-to-avoid-0s/7304 "2024-11-11T22:54:44Z")

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I have a 3D map of values that I need to resample, and the map is positive in one region and the rest of the image has zeros. The data format is float 64. However, I only want to resample the non-zero values and avoid in…

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## [Unable to save dicom metadata](https://discourse.itk.org/t/unable-to-save-dicom-metadata/7291)

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**Author:** [@alrut](https://discourse.itk.org/u/alrut)\
**Replies:** 3\
**Last updated:** [November 4, 2024, 2:07pm UTC](https://discourse.itk.org/t/unable-to-save-dicom-metadata/7291 "2024-11-04T14:07:42Z")

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I had to save images into dicoms. I did it with a help of example from docs. I wasn’t able to save modified metadata - most importantly uids. To prove it I prepared simplest script generating zero-filled dicoms and it d…

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## [Limit Threads for the whole host for the execution of multiple ITK processes](https://discourse.itk.org/t/limit-threads-for-the-whole-host-for-the-execution-of-multiple-itk-processes/7276)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 4\
**Last updated:** [October 22, 2024, 2:57pm UTC](https://discourse.itk.org/t/limit-threads-for-the-whole-host-for-the-execution-of-multiple-itk-processes/7276 "2024-10-22T14:57:42Z")

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I have a tool written in Python and SimpleITK and start multiple instances of it at the same time. I have limited the number of threads per process via the environment variable ITK\_GLOBAL\_DEFAULT\_NUMBER\_OF\_THREADS . How…

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