# \#registration

**URL:** https://discourse.itk.org/tag/registration/33.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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## [elastix 5.3.0 released!](https://discourse.itk.org/t/elastix-5-3-0-released/7707)

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**Author:** [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)\
**Replies:** 2\
**Last updated:** [April 6, 2026, 1:00pm UTC](https://discourse.itk.org/t/elastix-5-3-0-released/7707 "2026-04-06T13:00:03Z")

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:tada: I’m very pleased to announce that we have just released version 5.3.0 of our image registration toolbox elastix, at https://github.com/SuperElastix/elastix/releases Binaries of elastix executables are provided f…

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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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## [Running optimizer in parallel](https://discourse.itk.org/t/running-optimizer-in-parallel/1421)

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**Author:** [@Gordian](https://discourse.itk.org/u/Gordian)\
**Replies:** 6\
**Last updated:** [December 3, 2025, 8:42pm UTC](https://discourse.itk.org/t/running-optimizer-in-parallel/1421 "2025-12-03T20:42:34Z")

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Hello, i have a question regarding parallel optimization. The actual setup is more cpmplex. Therefore I try to simplify. I have a reference image and multiple other images. I want to register the other images onto the …

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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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## [The effect of mutual information rigid registration is extremely poor.](https://discourse.itk.org/t/the-effect-of-mutual-information-rigid-registration-is-extremely-poor/7600)

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**Author:** [@wen](https://discourse.itk.org/u/wen)\
**Replies:** 1\
**Last updated:** [July 23, 2025, 8:03am UTC](https://discourse.itk.org/t/the-effect-of-mutual-information-rigid-registration-is-extremely-poor/7600 "2025-07-23T08:03:52Z")

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Using the Mattes Mutual Information Image-to-Image Metric v4 as the similarity measurement for three-dimensional rigid registration, their initial gradient is not equal to zero and the registration results of two comple…

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## [Multi-resolution registration anomaly](https://discourse.itk.org/t/multi-resolution-registration-anomaly/7591)

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**Author:** [@wen](https://discourse.itk.org/u/wen)\
**Replies:** 2\
**Last updated:** [July 23, 2025, 7:18am UTC](https://discourse.itk.org/t/multi-resolution-registration-anomaly/7591 "2025-07-23T07:18:18Z")

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When utilizing the ImageRegistrationMethodv4 for multi-resolution registration, I encountered the following unusual behavior: In cases where the initial positions of the images to be registered were significantly misal…

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## [MRI-CT phantom registration](https://discourse.itk.org/t/mri-ct-phantom-registration/7598)

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**Author:** [@rohit\_inippully](https://discourse.itk.org/u/rohit_inippully)\
**Replies:** 3\
**Last updated:** [July 22, 2025, 1:46pm UTC](https://discourse.itk.org/t/mri-ct-phantom-registration/7598 "2025-07-22T13:46:00Z")

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I am trying to register (rigid) a MRI image of a phantom to its CT image. However, I am not getting the results I need. I am using MattesMutual Metric, and regularstepgradient, Euler3DTransform, etc. Has anyone encoun…

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## [Elastix WeightedCombinationTransform](https://discourse.itk.org/t/elastix-weightedcombinationtransform/7568)

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**Author:** [@Sylvester\_Wu](https://discourse.itk.org/u/Sylvester_Wu)\
**Replies:** 2\
**Last updated:** [June 23, 2025, 4:14pm UTC](https://discourse.itk.org/t/elastix-weightedcombinationtransform/7568 "2025-06-23T16:14:45Z")

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Hi Everyone, I’m very new to ITK and elastix. I have a set of 2-channel images of Tetraspeck fiducial beads in green and far red fluorescence and would like to register the two channels relative to each other for subseq…

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## [SetOptimizerWeights in parameter file in SimpleElastix](https://discourse.itk.org/t/setoptimizerweights-in-parameter-file-in-simpleelastix/7488)

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**Author:** [@Brynolf](https://discourse.itk.org/u/Brynolf)\
**Replies:** 0\
**Last updated:** [April 1, 2025, 9:37am UTC](https://discourse.itk.org/t/setoptimizerweights-in-parameter-file-in-simpleelastix/7488 "2025-04-01T09:37:53Z")

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Hello! I would like to restrict the registration to some dimensions, and found that you can use SetOptimizerWeights() in python. How can I define this if I setup my registration using a parameter file? I would like to r…

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## [Points are not transformed correctly when using BSplineTransform](https://discourse.itk.org/t/points-are-not-transformed-correctly-when-using-bsplinetransform/7483)

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**Author:** [@lukasz-migas](https://discourse.itk.org/u/lukasz-migas)\
**Replies:** 4\
**Last updated:** [March 31, 2025, 8:38am UTC](https://discourse.itk.org/t/points-are-not-transformed-correctly-when-using-bsplinetransform/7483 "2025-03-31T08:38:35Z")

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Hi, I am looking for a bit of advice (or information on where I am going wrong) with regard to applying transformation to an image and coordinating points from GeoJSON. I have a composite transform consisting of 5 tran…

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## [1st Get Your Brain Straight Hackathon!](https://discourse.itk.org/t/1st-get-your-brain-straight-hackathon/4896)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 1\
**Last updated:** [March 17, 2025, 2:42pm UTC](https://discourse.itk.org/t/1st-get-your-brain-straight-hackathon/4896 "2025-03-17T14:42:38Z")

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What? The Get Your Brain Straight hackathons bring together neuroimage data generators, image registration researchers, and neurodata compute infrastructure providers for a hands-on, collaborative event. This community c…

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## [ImageRegistrationMethodv4 crashes Unexpectedly](https://discourse.itk.org/t/imageregistrationmethodv4-crashes-unexpectedly/5268)

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**Author:** [@autobuyer](https://discourse.itk.org/u/autobuyer)\
**Replies:** 1\
**Last updated:** [March 12, 2025, 4:12pm UTC](https://discourse.itk.org/t/imageregistrationmethodv4-crashes-unexpectedly/5268 "2025-03-12T16:12:01Z")

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Hello, I am relatively new ITK user and I am trying to implement affine registration in C++. After going through examples, I was able to put together a reasonable solution. However, when I run it it crashes unexpectedly…

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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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## [Registration on subregions using DEMONS](https://discourse.itk.org/t/registration-on-subregions-using-demons/7321)

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**Author:** [@ignaciobartol](https://discourse.itk.org/u/ignaciobartol)\
**Replies:** 2\
**Last updated:** [November 21, 2024, 9:41pm UTC](https://discourse.itk.org/t/registration-on-subregions-using-demons/7321 "2024-11-21T21:41:01Z")

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Hi all, Long-time reader, first-time poster here! I’m not sure if this is the right category, but as it’s my first question, I’ll post it here. I am performing deformable image registration using DEMONS in a 3D domain …

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## [How to synthesize the 2D image after each layer correction back into 3D？](https://discourse.itk.org/t/how-to-synthesize-the-2d-image-after-each-layer-correction-back-into-3d/7273)

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**Author:** [@Breeze-Zero](https://discourse.itk.org/u/Breeze-Zero)\
**Replies:** 2\
**Last updated:** [October 21, 2024, 2:01pm UTC](https://discourse.itk.org/t/how-to-synthesize-the-2d-image-after-each-layer-correction-back-into-3d/7273 "2024-10-21T14:01:19Z")

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I have a cardiac MRI motion correction code that splits the original 4D nii into multiple slices for correction, which is actually modifying the saved affine matrix, but this code saves the corrected results as separate …

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## [Need help understanding codes from sitk notebook](https://discourse.itk.org/t/need-help-understanding-codes-from-sitk-notebook/7228)

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**Author:** [@Learner](https://discourse.itk.org/u/Learner)\
**Replies:** 1\
**Last updated:** [September 19, 2024, 5:56pm UTC](https://discourse.itk.org/t/need-help-understanding-codes-from-sitk-notebook/7228 "2024-09-19T17:56:02Z")

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I need help understanding some codes lines from sitk notebook (63\_Registration\_Initialization), link here. I will (1) show the codes that I am using, (2) then ask my specific questions. I have so many questions (I apolo…

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## [3rd Get Your Brain Together Hackathon - OME-Zarr Coordinate Transforms](https://discourse.itk.org/t/3rd-get-your-brain-together-hackathon-ome-zarr-coordinate-transforms/7119)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 4\
**Last updated:** [July 29, 2024, 4:06am UTC](https://discourse.itk.org/t/3rd-get-your-brain-together-hackathon-ome-zarr-coordinate-transforms/7119 "2024-07-29T04:06:00Z")

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Join us for the 3rd Get Your Brain Together Hackathon ! Register now! What? Purpose The Get Your Brain Together hackathons bring together neuroimage data generators, image registration researchers, and neurodata comp…

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## [Difference between SimpleElastix and ITKElastix](https://discourse.itk.org/t/difference-between-simpleelastix-and-itkelastix/6658)

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**Author:** [@l.mejivar](https://discourse.itk.org/u/l.mejivar)\
**Replies:** 3\
**Last updated:** [July 19, 2024, 6:47pm UTC](https://discourse.itk.org/t/difference-between-simpleelastix-and-itkelastix/6658 "2024-07-19T18:47:15Z")

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Hello, I am writing a script to register (non-rigid) several thousands of images. I noticed that SimpleElastix is integrated and ITK, but the original repository was archived. I also noticed that there is a different op…

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## [Registering with only one slice of 3d image](https://discourse.itk.org/t/registering-with-only-one-slice-of-3d-image/7028)

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**Author:** [@cadaei](https://discourse.itk.org/u/cadaei)\
**Replies:** 4\
**Last updated:** [July 15, 2024, 9:30am UTC](https://discourse.itk.org/t/registering-with-only-one-slice-of-3d-image/7028 "2024-07-15T09:30:14Z")

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Hi, I want to register 2 dicom images which are of the same examination, but with a slightly different FOV. Each image stack consists of three slices, but their distance is too large, so each slice has to be registered …

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## [Motion correction for 4D brain image (DTI and fMRI)](https://discourse.itk.org/t/motion-correction-for-4d-brain-image-dti-and-fmri/7048)

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**Author:** [@Sunita\_Patel](https://discourse.itk.org/u/Sunita_Patel)\
**Replies:** 1\
**Last updated:** [July 11, 2024, 12:44pm UTC](https://discourse.itk.org/t/motion-correction-for-4d-brain-image-dti-and-fmri/7048 "2024-07-11T12:44:38Z")

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Dear ITK members, We want to perform motion correction in 4D brain image such as DTI and fMRI. Is it fine to register the series of 3D brain volume on the first 3D image or b0 (baseline) MRI image in case DTI? or Any ad…

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## [Convert .nii.gz warp to .h5 (with proper header)](https://discourse.itk.org/t/convert-nii-gz-warp-to-h5-with-proper-header/6673)

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**Author:** [@smeisler](https://discourse.itk.org/u/smeisler)\
**Replies:** 10\
**Last updated:** [July 10, 2024, 8:08pm UTC](https://discourse.itk.org/t/convert-nii-gz-warp-to-h5-with-proper-header/6673 "2024-07-10T20:08:11Z")

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Hi! I have been modifying an anatomical processing workflow that largely uses ANTs. I have been trying to incorporate FreeSurfer’s synthmorph to calculate a registration, which outputs in RAS convention. I have been abl…

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## [A Colour filter error: ITK Montage Module](https://discourse.itk.org/t/a-colour-filter-error-itk-montage-module/6737)

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**Author:** [@sleepingcat4](https://discourse.itk.org/u/sleepingcat4)\
**Replies:** 4\
**Last updated:** [July 1, 2024, 5:59pm UTC](https://discourse.itk.org/t/a-colour-filter-error-itk-montage-module/6737 "2024-07-01T17:59:29Z")

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I encountered a similar problem like before mentioned in this thread (Stacking Z dimension images using SimpleITK - #22 by sleepingcat4) I tried to wrap and the error were persistent. Any help would be amazing : ) CODE: …

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## [Change of tumor location during registration with different templates](https://discourse.itk.org/t/change-of-tumor-location-during-registration-with-different-templates/6726)

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**Author:** [@Sunita\_Patel](https://discourse.itk.org/u/Sunita_Patel)\
**Replies:** 1\
**Last updated:** [June 28, 2024, 6:40am UTC](https://discourse.itk.org/t/change-of-tumor-location-during-registration-with-different-templates/6726 "2024-06-28T06:40:52Z")

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Dear ITK forum Members, All our registrations are performed using Simple ITK. T1 weighted image is registered with SRI24 atlas (240,240,155) as a template (1st image) and with MNI152 (197,233,189) atlas (2nd image). 2n…

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## [3D Registration of Anatomical and functional MRI of Brain Images](https://discourse.itk.org/t/3d-registration-of-anatomical-and-functional-mri-of-brain-images/6612)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 25\
**Last updated:** [June 13, 2024, 5:13am UTC](https://discourse.itk.org/t/3d-registration-of-anatomical-and-functional-mri-of-brain-images/6612 "2024-06-13T05:13:32Z")

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Hello, I have anatomical MR and functional MR images of a patient with tumor in the brain. I want to transform the low resolution functional MR image in such a way that it matches in shape with the anatomical MR image. …

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## [Marker registration does not follow image registration](https://discourse.itk.org/t/marker-registration-does-not-follow-image-registration/6691)

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**Author:** [@sebquet](https://discourse.itk.org/u/sebquet)\
**Replies:** 4\
**Last updated:** [June 11, 2024, 8:57pm UTC](https://discourse.itk.org/t/marker-registration-does-not-follow-image-registration/6691 "2024-06-11T20:57:02Z")

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Hello, I registered an MRI scan to a CT scan as follows: tx = sitk.AffineTransform(fixed\_image.GetDimension()) init\_pos = sitk.CenteredTransformInitializerFilter.MOMENTS initial\_transform = sitk.CenteredTransformIniti…

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## [Is it possible to create a user-defined cost function for registration?](https://discourse.itk.org/t/is-it-possible-to-create-a-user-defined-cost-function-for-registration/6677)

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**Author:** [@Vidya](https://discourse.itk.org/u/Vidya)\
**Replies:** 0\
**Last updated:** [June 6, 2024, 7:35am UTC](https://discourse.itk.org/t/is-it-possible-to-create-a-user-defined-cost-function-for-registration/6677 "2024-06-06T07:35:45Z")

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Hi, I am trying register two images with Bspline. I tried with itk::MeanSquaresImageToImageMetricv4 and itk::MattesMutualInformationImageToImageMetricv4. Both doesn’t give the correct registration for all the images. I w…

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## [SimpleElastix, do not store intermediate transform file](https://discourse.itk.org/t/simpleelastix-do-not-store-intermediate-transform-file/6664)

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**Author:** [@l.mejivar](https://discourse.itk.org/u/l.mejivar)\
**Replies:** 0\
**Last updated:** [May 28, 2024, 11:23am UTC](https://discourse.itk.org/t/simpleelastix-do-not-store-intermediate-transform-file/6664 "2024-05-28T11:23:46Z")

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Hello, I am registering some images using the method below. Everything works fine, except that for some reason, there is a file called TransformParameters.0.txt that is being created in the same directory where I run my…

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## [Registration Algorithm or Evolution Optimizer Not Deterministic](https://discourse.itk.org/t/registration-algorithm-or-evolution-optimizer-not-deterministic/6597)

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**Author:** [@Michael\_M](https://discourse.itk.org/u/Michael_M)\
**Replies:** 7\
**Last updated:** [May 3, 2024, 1:18pm UTC](https://discourse.itk.org/t/registration-algorithm-or-evolution-optimizer-not-deterministic/6597 "2024-05-03T13:18:03Z")

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Hi, I am following the example registration11 found here: ITK: Examples/RegistrationITKv3/ImageRegistration11.cxx Everything works, except the results are not deterministic. When I run it multiple times, I am getting …

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