# \#elastix

**URL:** https://discourse.slicer.org/tag/elastix/127.md

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

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## [How can I use GPU to accelerate General Registration (Elastix) module?](https://discourse.slicer.org/t/how-can-i-use-gpu-to-accelerate-general-registration-elastix-module/43129)

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**Author:** [@LanceDuan](https://discourse.slicer.org/u/LanceDuan)\
**Replies:** 1\
**Last updated:** [May 28, 2025, 8:17am UTC](https://discourse.slicer.org/t/how-can-i-use-gpu-to-accelerate-general-registration-elastix-module/43129 "2025-05-28T08:17:38Z")

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Hi all, I’m using General Registration (Elastix) to align two different time DICOM CT of one patient, and it works very well! However it takes such a long time, about 5min. I checked the CPU and GPU usage status. As yo…

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## [Register MRI with CT by Elastix](https://discourse.slicer.org/t/register-mri-with-ct-by-elastix/42624)

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**Author:** [@Asparagine](https://discourse.slicer.org/u/Asparagine)\
**Replies:** 2\
**Last updated:** [April 21, 2025, 5:36am UTC](https://discourse.slicer.org/t/register-mri-with-ct-by-elastix/42624 "2025-04-21T05:36:12Z")

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Hello everyone. I’m new to slicer and now using elastix to register the MRI to CT (about temporomandibular joint), but I found it is not that accurate using presets generic (all) and generic rigid (all). I read the pape…

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## [How to generate transform at Elastix rigid registration](https://discourse.slicer.org/t/how-to-generate-transform-at-elastix-rigid-registration/40955)

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**Author:** [@Jason\_chen](https://discourse.slicer.org/u/Jason_chen)\
**Replies:** 4\
**Last updated:** [March 6, 2025, 8:07pm UTC](https://discourse.slicer.org/t/how-to-generate-transform-at-elastix-rigid-registration/40955 "2025-03-06T20:07:16Z")

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Hi, I am using 3D slicer to register a CT volume into MR volume and transform node labels on CT into MR coordinates. Through Elastix in 3D slicer I can do the registration and output the transform to do the job, which i…

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## [Output transform from Elastix Registration](https://discourse.slicer.org/t/output-transform-from-elastix-registration/41936)

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**Author:** [@Jason\_chen](https://discourse.slicer.org/u/Jason_chen)\
**Replies:** 0\
**Last updated:** [March 3, 2025, 2:26am UTC](https://discourse.slicer.org/t/output-transform-from-elastix-registration/41936 "2025-03-03T02:26:27Z")

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Hi, I am using Elastix extension in Slicer to register two medical volumes. During this process, I found that the transform output by Elastix which can be used to transfrom other volumes from moving field to fixed field…

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## [Not able to select masks for registration in elastix](https://discourse.slicer.org/t/not-able-to-select-masks-for-registration-in-elastix/35871)

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**Author:** [@Chih-Ying-Huang](https://discourse.slicer.org/u/Chih-Ying-Huang)\
**Replies:** 2\
**Last updated:** [May 2, 2024, 1:10pm UTC](https://discourse.slicer.org/t/not-able-to-select-masks-for-registration-in-elastix/35871 "2024-05-02T13:10:26Z")

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Operating system: Windows10 Slicer version: 5.6.2 Expected behavior: Registration between 2 abdominal CT image with masks Actual behavior: After import my binary mask as segmentations in slicer, I was not able to fin…

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## [Not able to select masks for registration in elastix](https://discourse.slicer.org/t/not-able-to-select-masks-for-registration-in-elastix/35870)

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**Author:** [@Chih-Ying-Huang](https://discourse.slicer.org/u/Chih-Ying-Huang)\
**Replies:** 0\
**Last updated:** [May 2, 2024, 12:48pm UTC](https://discourse.slicer.org/t/not-able-to-select-masks-for-registration-in-elastix/35870 "2024-05-02T12:48:34Z")

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Operating system: Windows10 Slicer version: 5.6.2 Expected behavior: Registration between 2 abdominal CT image with masks Actual behavior: After import my binary mask as segmentations in slicer, I was not able to fin…

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## [Lung deformable image registration](https://discourse.slicer.org/t/lung-deformable-image-registration/35627)

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**Author:** [@Wpy\_K](https://discourse.slicer.org/u/Wpy_K)\
**Replies:** 2\
**Last updated:** [April 22, 2024, 6:11am UTC](https://discourse.slicer.org/t/lung-deformable-image-registration/35627 "2024-04-22T06:11:16Z")

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Hi everyone, I’m a Medical physics student, I’m new for using 3DSlicer. I has problem that I want to deformable image (DIR) organ at risk nearby lung for check about breathing motion effected to other organ nearby lung,…

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## [Cleaning elastix results](https://discourse.slicer.org/t/cleaning-elastix-results/34784)

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**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 7\
**Last updated:** [March 15, 2024, 1:59pm UTC](https://discourse.slicer.org/t/cleaning-elastix-results/34784 "2024-03-15T13:59:26Z")

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Hello, I’ve been trying to use elastix to register some organs but I have a few issue. After registration, the results need “cleaning” (see picture where I registered a liver onto itself) I can fix it by doing some…

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## [Elastix Registration 3D CT monomodal lung](https://discourse.slicer.org/t/elastix-registration-3d-ct-monomodal-lung/34394)

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**Author:** [@Alice\_Durante](https://discourse.slicer.org/u/Alice_Durante)\
**Replies:** 4\
**Last updated:** [February 19, 2024, 4:23pm UTC](https://discourse.slicer.org/t/elastix-registration-3d-ct-monomodal-lung/34394 "2024-02-19T16:23:50Z")

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Hello to all I’ve been using the toolbox “registration” of 3d Slicer, especially “elastix”. Trying with a registration with “generic (all)” preset I get a discreet result, but not great. My goal is to get the best possi…

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## [Theory of elastix registration](https://discourse.slicer.org/t/theory-of-elastix-registration/34298)

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**Author:** [@Alice\_Durante](https://discourse.slicer.org/u/Alice_Durante)\
**Replies:** 2\
**Last updated:** [February 13, 2024, 5:09pm UTC](https://discourse.slicer.org/t/theory-of-elastix-registration/34298 "2024-02-13T17:09:35Z")

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Hi everyone I used the 3d slicer extension called “Registration- general registration-elastix”, and I managed to get a very good recording result, but I need some information for my thesis. Can you confirm me first of…

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## [Elastix: generated output image doesn't align with applied and hardend transform ](https://discourse.slicer.org/t/elastix-generated-output-image-doesnt-align-with-applied-and-hardend-transform/33147)

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**Author:** [@ekls](https://discourse.slicer.org/u/ekls)\
**Replies:** 1\
**Last updated:** [December 6, 2023, 6:07pm UTC](https://discourse.slicer.org/t/elastix-generated-output-image-doesnt-align-with-applied-and-hardend-transform/33147 "2023-12-06T18:07:35Z")

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Hi, I’m quite new to slicer so maybe there‘s a very simple answer to my problem. I’m currently using Elastix to registrate brain MRIs. The genereated output volume looks perfectly fine but applying the transform to th…

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## [DSA 3D reconstruction](https://discourse.slicer.org/t/dsa-3d-reconstruction/31549)

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**Author:** [@Murillo\_Cunegatto\_Br](https://discourse.slicer.org/u/Murillo_Cunegatto_Br)\
**Replies:** 2\
**Last updated:** [September 5, 2023, 4:31pm UTC](https://discourse.slicer.org/t/dsa-3d-reconstruction/31549 "2023-09-05T16:31:59Z")

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Hi I wonder how to reconstruct a rotational cerebral angiography run to 3D with Slicer. The DICOM file contains 120 frames but loads in Slicer in the same position. I tried to transform each frame position but did not s…

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## [Elastix, why applying a transform on image does not produce same image as the generated output at registration time?](https://discourse.slicer.org/t/elastix-why-applying-a-transform-on-image-does-not-produce-same-image-as-the-generated-output-at-registration-time/28179)

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**Author:** [@S\_Arbabi](https://discourse.slicer.org/u/S_Arbabi)\
**Replies:** 1\
**Last updated:** [March 6, 2023, 4:13am UTC](https://discourse.slicer.org/t/elastix-why-applying-a-transform-on-image-does-not-produce-same-image-as-the-generated-output-at-registration-time/28179 "2023-03-06T04:13:37Z")

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Hi, I have two MR images (fixed, moving) and do the Elastix “rigid” registration in Slicer (5.0.2): after this process finishes, I have a generated (registered) moving image (called Volume\_7) and a transformation (c…

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## [Elastix registration fails: Too many samples map outside moving image buffer](https://discourse.slicer.org/t/elastix-registration-fails-too-many-samples-map-outside-moving-image-buffer/15798)

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**Author:** [@DAT\_Minh](https://discourse.slicer.org/u/DAT_Minh)\
**Replies:** 18\
**Last updated:** [December 10, 2022, 12:00am UTC](https://discourse.slicer.org/t/elastix-registration-fails-too-many-samples-map-outside-moving-image-buffer/15798 "2022-12-10T00:00:15Z")

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Dear Andras @lassoan . I’m segmenting temporal bone using ABL Temporal Bone Segmentation. I stuck at step 2: Rigid registration. When I apply Rigid registration, the process stopped at 14% and it said: “command ‘elastix…

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## [Elastix returned non-zero exit status 1](https://discourse.slicer.org/t/elastix-returned-non-zero-exit-status-1/26521)

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**Author:** [@Kaczor69xd](https://discourse.slicer.org/u/Kaczor69xd)\
**Replies:** 9\
**Last updated:** [December 5, 2022, 2:33am UTC](https://discourse.slicer.org/t/elastix-returned-non-zero-exit-status-1/26521 "2022-12-05T02:33:56Z")

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Hello I also have some problem with this extension. Tried it yesterday twice on different CTs. I’m pasting whole code from python interaction. I think the problem is with elastix, it can’t get the measurements right. I…

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## [How to get a linear or affine transform from Elastix?](https://discourse.slicer.org/t/how-to-get-a-linear-or-affine-transform-from-elastix/25791)

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**Author:** [@tdchen](https://discourse.slicer.org/u/tdchen)\
**Replies:** 1\
**Last updated:** [October 20, 2022, 5:22am UTC](https://discourse.slicer.org/t/how-to-get-a-linear-or-affine-transform-from-elastix/25791 "2022-10-20T05:22:51Z")

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It works fine but always output a b-spline transform even I selected the generic rigid (all) preset. What else should be done? I use Slicer 5.0.3 Thx.

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## [Problem with Elastix](https://discourse.slicer.org/t/problem-with-elastix/25762)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 13\
**Last updated:** [October 19, 2022, 10:39pm UTC](https://discourse.slicer.org/t/problem-with-elastix/25762 "2022-10-19T22:39:05Z")

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I have a problem lately with elastix, it doesn’t execute anything. Traceback (most recent call last): File "/home/alex/GIT/opendose3d/OpenDose3D/OpenDose3D.py", line 944, in onRunTestButton self.test.FullTest\_posi…

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## [Bounding box correction](https://discourse.slicer.org/t/bounding-box-correction/22251)

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**Author:** [@Kalman](https://discourse.slicer.org/u/Kalman)\
**Replies:** 1\
**Last updated:** [March 5, 2022, 7:33pm UTC](https://discourse.slicer.org/t/bounding-box-correction/22251 "2022-03-05T19:33:41Z")

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Hi, I would like to ask you regarding the size of the transformation result. The brief summary: I use the Elastix modul for non-linear normalization to get the transformation matrix (on a mean volume), which is then app…

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## [Elastix Registration Problem by registration of two CT Scans with completely different Gray Values and artifacts](https://discourse.slicer.org/t/elastix-registration-problem-by-registration-of-two-ct-scans-with-completely-different-gray-values-and-artifacts/18910)

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**Author:** [@Solli](https://discourse.slicer.org/u/Solli)\
**Replies:** 5\
**Last updated:** [July 25, 2021, 6:08pm UTC](https://discourse.slicer.org/t/elastix-registration-problem-by-registration-of-two-ct-scans-with-completely-different-gray-values-and-artifacts/18910 "2021-07-25T18:08:30Z")

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Hello, I have two CT Datasets of a 3D Printed Skull Phantom. One CT Scan is from a clinical CT scanner and the second scan is from an industrial CT scanner. The scan from the clinical CT has Hounsfield values between -1…

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## [Incompatible Elastix transformation parameters with Transforms module](https://discourse.slicer.org/t/incompatible-elastix-transformation-parameters-with-transforms-module/18151)

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**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 2\
**Last updated:** [June 16, 2021, 6:03pm UTC](https://discourse.slicer.org/t/incompatible-elastix-transformation-parameters-with-transforms-module/18151 "2021-06-16T18:03:09Z")

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Hi, The resulting transform parameters from parameters file or elastix log are different from what I see in the transforms module and this is happening for all my registrations. For example this is in the transform par…

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## [Elastix non-rigid transform displaying in the wrong area?](https://discourse.slicer.org/t/elastix-non-rigid-transform-displaying-in-the-wrong-area/17426)

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**Author:** [@Teresa\_Gadda](https://discourse.slicer.org/u/Teresa_Gadda)\
**Replies:** 1\
**Last updated:** [May 21, 2021, 6:42pm UTC](https://discourse.slicer.org/t/elastix-non-rigid-transform-displaying-in-the-wrong-area/17426 "2021-05-21T18:42:45Z")

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Hello Slicer team - I have performed a rigid registration using elastix of two spine images and thought I would try doing a non-rigid registration on the same images to see if it improves my result further. I hardened …

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## [Plotting Registration Results from Elastix](https://discourse.slicer.org/t/plotting-registration-results-from-elastix/15959)

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**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 0\
**Last updated:** [February 11, 2021, 9:04pm UTC](https://discourse.slicer.org/t/plotting-registration-results-from-elastix/15959 "2021-02-11T21:04:50Z")

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Hello, I want to plot my registration results to compare different metric values and also the amount of translation in x, y, z direction. I found some code from SimpleITK here: SimpleITK-Notebooks/60\_Registration\_Introd…

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## [Elastix AND Python Scripting](https://discourse.slicer.org/t/elastix-and-python-scripting/15923)

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**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 3\
**Last updated:** [April 26, 2021, 10:23pm UTC](https://discourse.slicer.org/t/elastix-and-python-scripting/15923 "2021-04-26T22:23:36Z")

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Hi all, I want to perform groupwise registration as described here https://simpleelastix.readthedocs.io/GroupwiseRegistration.html with python scripting. Should I build Elastix from scratch or is there a way to do it wi…

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## [Elastix registration error](https://discourse.slicer.org/t/elastix-registration-error/17335)

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**Author:** [@Bence\_Horvath](https://discourse.slicer.org/u/Bence_Horvath)\
**Replies:** 4\
**Last updated:** [April 26, 2021, 4:58pm UTC](https://discourse.slicer.org/t/elastix-registration-error/17335 "2021-04-26T16:58:21Z")

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Hi, I want to registrate preoperative CT with postoperative CT , but Elastix always give me this error, when try to generate output: Failed to load output transform from C:/Users/HORVIR~1/AppData/Local/Temp/Slicer/E…

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## [Slicer Elastix extension not available for newest Slicer 13.0. 2021.03.19](https://discourse.slicer.org/t/slicer-elastix-extension-not-available-for-newest-slicer-13-0-2021-03-19/16688)

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**Author:** [@PalkoD](https://discourse.slicer.org/u/PalkoD)\
**Replies:** 2\
**Last updated:** [March 25, 2021, 1:25pm UTC](https://discourse.slicer.org/t/slicer-elastix-extension-not-available-for-newest-slicer-13-0-2021-03-19/16688 "2021-03-25T13:25:37Z")

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Dear All! I just downloaded the newest version of slicer, and I was trying to restore extensions, and few of the extensions including Elastix, are unfortunately not available for the newest version. This is very unfortu…

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## [Elastix in 3dslicer](https://discourse.slicer.org/t/elastix-in-3dslicer/16425)

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**Author:** [@sara\_sharifi](https://discourse.slicer.org/u/sara_sharifi)\
**Replies:** 2\
**Last updated:** [March 8, 2021, 8:02pm UTC](https://discourse.slicer.org/t/elastix-in-3dslicer/16425 "2021-03-08T20:02:56Z")

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hi 3D slicer 4.11 has general registration (Brains) , Is this the same as Elastix? I do not find exactly Elastix and is this module also used for NiTFI format CT images? Thank you

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## [Invert transform (Elastix)](https://discourse.slicer.org/t/invert-transform-elastix/14754)

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**Author:** [@janneke\_slicer](https://discourse.slicer.org/u/janneke_slicer)\
**Replies:** 3\
**Last updated:** [November 25, 2020, 2:58pm UTC](https://discourse.slicer.org/t/invert-transform-elastix/14754 "2020-11-25T14:58:35Z")

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Hello, I used Elastix (in Matlab) to register two images and to get the displacement field. I can import this displacement field in Slicer as a Transform. Now I have two questions: It seems that Slicer then automatica…

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## [Elastix components not installed](https://discourse.slicer.org/t/elastix-components-not-installed/13660)

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**Author:** [@janneke\_slicer](https://discourse.slicer.org/u/janneke_slicer)\
**Replies:** 1\
**Last updated:** [September 23, 2020, 3:23pm UTC](https://discourse.slicer.org/t/elastix-components-not-installed/13660 "2020-09-23T15:23:33Z")

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Hello, I am using Elastix in 3DSlicer. I also used it in Matlab, but Slicer is better for visualization. I’m for example interested in visualizing the deformation field. However, I noticed that in 3D Slicer Elastix is …

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## [Accessing SlicerElastix from within python module](https://discourse.slicer.org/t/accessing-slicerelastix-from-within-python-module/9410)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 7\
**Last updated:** [April 28, 2020, 3:17pm UTC](https://discourse.slicer.org/t/accessing-slicerelastix-from-within-python-module/9410 "2020-04-28T15:17:41Z")

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I am trying to use SlicerElastix module from my module as a cli call. However, all these fails slicer.cli.run(module=slicer.modules.slicerelastix, None, parameters, wait\_for\_completion=Tr…

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## [Elastix fails to build](https://discourse.slicer.org/t/elastix-fails-to-build/11077)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 4\
**Last updated:** [April 13, 2020, 3:43pm UTC](https://discourse.slicer.org/t/elastix-fails-to-build/11077 "2020-04-13T15:43:18Z")

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As seen here http://slicer.cdash.org/buildSummary.php?buildid=1880612 Elastix is failing to build. I can follow the current errors up to 13/03/2020 build. I see nobody has reported this

[Next page](https://discourse.slicer.org/tag/elastix/127.md?match_all_tags=true&page=1&tags%5B%5D=elastix)