# SlicerDMRI

**URL:** https://discourse.slicer.org/c/community/slicerdmri/16.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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## [About the SlicerDMRI category](https://discourse.slicer.org/t/about-the-slicerdmri-category/374)

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**Author:** [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Replies:** 1\
**Last updated:** [May 25, 2017, 4:14am UTC](https://discourse.slicer.org/t/about-the-slicerdmri-category/374 "2017-05-25T04:14:18Z")

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The SlicerDMRI extension provides diffusion MRI tools including tensor estimation, tractography, and quantification. For more information, please visit: http://dmri.slicer.org

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## [Workflow Questions on SWM Analysis with UKFtractography and whitematteranalysis](https://discourse.slicer.org/t/workflow-questions-on-swm-analysis-with-ukftractography-and-whitematteranalysis/44753)

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**Author:** [@younghoo](https://discourse.slicer.org/u/younghoo)\
**Replies:** 12\
**Last updated:** [January 18, 2026, 3:50am UTC](https://discourse.slicer.org/t/workflow-questions-on-swm-analysis-with-ukftractography-and-whitematteranalysis/44753 "2026-01-18T03:50:11Z")

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Dear Experts, I am attempting to replicate the methodology described in the following paper and have a few questions that I hope you can help clarify: Wang, S., Zhang, F., Zeng, Q., Hong, H., Zhang, Y., Xie, L., Lin, M…

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## [Getting errors while building Slicer 5.6.2 using  Visual Studio 2022](https://discourse.slicer.org/t/getting-errors-while-building-slicer-5-6-2-using-visual-studio-2022/44548)

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**Author:** [@kiran](https://discourse.slicer.org/u/kiran)\
**Replies:** 0\
**Last updated:** [September 22, 2025, 8:52pm UTC](https://discourse.slicer.org/t/getting-errors-while-building-slicer-5-6-2-using-visual-studio-2022/44548 "2025-09-22T20:52:37Z")

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Hi all, I’m trying to build Slicer 5.6.2 from source on Windows 10 using Visual Studio 2022 (CMake 3.29.2, Ninja/VS generator). The CMake configure step completes successfully — all dependencies are found and I see Supe…

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## [Any help to do simple tractography by simple easy steps?@](https://discourse.slicer.org/t/any-help-to-do-simple-tractography-by-simple-easy-steps/44036)

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**Author:** [@ahmad\_elgamal](https://discourse.slicer.org/u/ahmad_elgamal)\
**Replies:** 5\
**Last updated:** [August 11, 2025, 7:23pm UTC](https://discourse.slicer.org/t/any-help-to-do-simple-tractography-by-simple-easy-steps/44036 "2025-08-11T19:23:58Z")

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Any help to do simple tractography by simple easy steps?@

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## ['Global' FW/FA Inquiry - whitematteranalysis](https://discourse.slicer.org/t/global-fw-fa-inquiry-whitematteranalysis/40989)

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**Author:** [@kvandeloo](https://discourse.slicer.org/u/kvandeloo)\
**Replies:** 1\
**Last updated:** [May 20, 2025, 3:56pm UTC](https://discourse.slicer.org/t/global-fw-fa-inquiry-whitematteranalysis/40989 "2025-05-20T15:56:02Z")

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I’m using whitematteranalysis for whole-brain tractography analysis (Tutorial - whitematteranalysis 0.4.0 documentation). Using this tutorial, I’m able to derive FA and FW from anatomical tracts and/or 800 fibre clusters…

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## [Exporting an MRI slice to a flat .obj with preserved coordinates](https://discourse.slicer.org/t/exporting-an-mri-slice-to-a-flat-obj-with-preserved-coordinates/42638)

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**Author:** [@Harman\_Osh](https://discourse.slicer.org/u/Harman_Osh)\
**Replies:** 0\
**Last updated:** [April 20, 2025, 7:57pm UTC](https://discourse.slicer.org/t/exporting-an-mri-slice-to-a-flat-obj-with-preserved-coordinates/42638 "2025-04-20T19:57:35Z")

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Hello, I am eternally grateful to you for your hard work. I have a question. I’m trying to collect all the patient’s digital data in one program. In Slicer, I’m trying to do this: I upload an MRI scan and want to get cer…

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## [How to import DSI Studio trk.gz files](https://discourse.slicer.org/t/how-to-import-dsi-studio-trk-gz-files/21052)

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**Author:** [@William\_McCuddy](https://discourse.slicer.org/u/William_McCuddy)\
**Replies:** 14\
**Last updated:** [October 19, 2024, 6:42pm UTC](https://discourse.slicer.org/t/how-to-import-dsi-studio-trk-gz-files/21052 "2024-10-19T18:42:14Z")

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Hello, Just checking in to see if anyone is working on a way to import tracts generated in DSI studio (.trk.gz) into 3d Slicer. I’ve tried converting to vtk via TrackVis, but the orientation was off and I could not figu…

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## [Getting error while trying to load tracts](https://discourse.slicer.org/t/getting-error-while-trying-to-load-tracts/37459)

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**Author:** [@egemen4552](https://discourse.slicer.org/u/egemen4552)\
**Replies:** 1\
**Last updated:** [October 19, 2024, 6:38pm UTC](https://discourse.slicer.org/t/getting-error-while-trying-to-load-tracts/37459 "2024-10-19T18:38:34Z")

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Dear SlicerDMRI forum, I am very new with Slicer and I have been using other MRI tools such as MRtrix, FreeSurfer, DSI studio etc. I couldnt find a visualization tool better than Slicer and I am trying to visualize a v…

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## [Failed to load segmentation in DentalSegmentator extension - nnUNet processing error](https://discourse.slicer.org/t/failed-to-load-segmentation-in-dentalsegmentator-extension-nnunet-processing-error/37448)

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**Author:** [@Adityanath\_Shiralkar](https://discourse.slicer.org/u/Adityanath_Shiralkar)\
**Replies:** 0\
**Last updated:** [July 18, 2024, 10:51am UTC](https://discourse.slicer.org/t/failed-to-load-segmentation-in-dentalsegmentator-extension-nnunet-processing-error/37448 "2024-07-18T10:51:43Z")

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Summary: I encountered an error while using the DentalSegmentator extension in 3D Slicer. When attempting to run the segmentation process, the following error message was displayed: “Failed to load the segmentation. So…

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## [Understanding FiberTractMeasurements output](https://discourse.slicer.org/t/understanding-fibertractmeasurements-output/37284)

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**Author:** [@Calth822](https://discourse.slicer.org/u/Calth822)\
**Replies:** 1\
**Last updated:** [July 9, 2024, 3:14pm UTC](https://discourse.slicer.org/t/understanding-fibertractmeasurements-output/37284 "2024-07-09T15:14:37Z")

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Hello, I following the WMA tutorial and I have understood all steps except for the last step of tutorial, " 8. Fiber tract diffusion measurements". I have been able to follow the tutorial and extract the diffusion measu…

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## [DTI\_ALPS x,y,z-projection of mean diffusivity](https://discourse.slicer.org/t/dti-alps-x-y-z-projection-of-mean-diffusivity/29578)

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**Author:** [@JSteinJ](https://discourse.slicer.org/u/JSteinJ)\
**Replies:** 10\
**Last updated:** [March 4, 2024, 3:02pm UTC](https://discourse.slicer.org/t/dti-alps-x-y-z-projection-of-mean-diffusivity/29578 "2024-03-04T15:02:09Z")

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terribly sorry me again, I forgot that I need x,y,z projections of MeanDiffusivity to. How can I calculate it from the maps in DiffusionTensorScalarMeasurement provided…? thank you, jürgen

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## [Call a widget's methods in Python](https://discourse.slicer.org/t/call-a-widgets-methods-in-python/33416)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 3\
**Last updated:** [December 17, 2023, 11:57am UTC](https://discourse.slicer.org/t/call-a-widgets-methods-in-python/33416 "2023-12-17T11:57:15Z")

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Hello, For the purposes of building a test, I am wondering whether there is a way to instantiate and call the methods from a class that inherits from qSlicerWidget​ (e.g. qSlicerTractographyDisplayWidget​, which lives i…

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## [ UKF tractography vs MRtrix CSD in my data ](https://discourse.slicer.org/t/ukf-tractography-vs-mrtrix-csd-in-my-data/33165)

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**Author:** [@gaunny](https://discourse.slicer.org/u/gaunny)\
**Replies:** 4\
**Last updated:** [December 6, 2023, 9:18am UTC](https://discourse.slicer.org/t/ukf-tractography-vs-mrtrix-csd-in-my-data/33165 "2023-12-06T09:18:55Z")

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Hi! I meet problem when I use UKF tractography in my data. I used the default parameters in Slicer 3D, but the traced out fibres are very discontinuous and even in the wrong direction. For example, the corticospinal tra…

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## [Docker container with 3D Slicer build to build and test an extension](https://discourse.slicer.org/t/docker-container-with-3d-slicer-build-to-build-and-test-an-extension/32461)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 0\
**Last updated:** [October 29, 2023, 9:03pm UTC](https://discourse.slicer.org/t/docker-container-with-3d-slicer-build-to-build-and-test-an-extension/32461 "2023-10-29T21:03:37Z")

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Hi, related to Adding a CI build to a Slicer extension, I am willing to add an additional GitHub Actions workflow to check building and testing an extension this time using a Slicer Docker image, so that I can know earl…

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## [Running Python tests automatically](https://discourse.slicer.org/t/running-python-tests-automatically/32426)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 0\
**Last updated:** [October 26, 2023, 4:12pm UTC](https://discourse.slicer.org/t/running-python-tests-automatically/32426 "2023-10-26T16:12:56Z")

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Hi, I am trying to figure out why some of the Python tests in an extension are not being executed following: COMP: Update GHA workflow ensuring Slicer is built with NumPy support by jcfr · Pull Request #179 · SlicerDMR…

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## [UKF Tractography fiber orientation function](https://discourse.slicer.org/t/ukf-tractography-fiber-orientation-function/32173)

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**Author:** [@gaunny](https://discourse.slicer.org/u/gaunny)\
**Replies:** 0\
**Last updated:** [October 12, 2023, 3:06am UTC](https://discourse.slicer.org/t/ukf-tractography-fiber-orientation-function/32173 "2023-10-12T03:06:50Z")

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Hi, I meet problem when I read the UKF Tractography paper (Malcolm J G, Shenton M E, Rathi Y. Filtered multitensor tractography\[J\]. IEEE transactions on medical imaging, 2010, 29(9): 1664-1675.) and use it in Slicer. I …

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## [How to show fiber bundles with appropreate brain volume?](https://discourse.slicer.org/t/how-to-show-fiber-bundles-with-appropreate-brain-volume/31798)

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**Author:** [@Fumi](https://discourse.slicer.org/u/Fumi)\
**Replies:** 8\
**Last updated:** [September 21, 2023, 1:06pm UTC](https://discourse.slicer.org/t/how-to-show-fiber-bundles-with-appropreate-brain-volume/31798 "2023-09-21T13:06:33Z")

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Hi, I am using WMA for DTI tractography and have got anatomical tracts. I just wondering how to show fiber bundles with 3D brain image which is anatomically appropriate. I f I use the own case’s 3D-T1 brain image, the lo…

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## [Load scene into Slicer with empty vtk errors](https://discourse.slicer.org/t/load-scene-into-slicer-with-empty-vtk-errors/31615)

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**Author:** [@Kening\_Zhang](https://discourse.slicer.org/u/Kening_Zhang)\
**Replies:** 0\
**Last updated:** [September 8, 2023, 7:20am UTC](https://discourse.slicer.org/t/load-scene-into-slicer-with-empty-vtk-errors/31615 "2023-09-08T07:20:56Z")

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Dear developers, When I try to load a scene in Slicer, error happened, VTK may report it as an error when I attempt to read or write an empty file, while it may be normal that a fiber is empty. According to Iasso…

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## [Adding a CI build to a Slicer extension](https://discourse.slicer.org/t/adding-a-ci-build-to-a-slicer-extension/30857)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 28\
**Last updated:** [August 1, 2023, 12:51pm UTC](https://discourse.slicer.org/t/adding-a-ci-build-to-a-slicer-extension/30857 "2023-08-01T12:51:44Z")

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Hi, I am trying to set up a GHA workflow for CI of the SlicerdMRI module: ENH: Add GitHub actions build, test workflow file for CI by jhlegarreta · Pull Request #172 · SlicerDMRI/SlicerDMRI · GitHub The CI is timing o…

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## [Displaying a colorbar across viewers for diffusion scalar maps on tractography data](https://discourse.slicer.org/t/displaying-a-colorbar-across-viewers-for-diffusion-scalar-maps-on-tractography-data/30564)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 7\
**Last updated:** [July 24, 2023, 5:42pm UTC](https://discourse.slicer.org/t/displaying-a-colorbar-across-viewers-for-diffusion-scalar-maps-on-tractography-data/30564 "2023-07-24T17:42:36Z")

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Hi, is it possible to add a colorbar across the Slicer viewers (just as shown in the image in this post for another type of data) when we load some tractography data and load an associated scalar map, e.g. FA? If yes, h…

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## [No CSV file in DiffusionMessurements folder in WMA](https://discourse.slicer.org/t/no-csv-file-in-diffusionmessurements-folder-in-wma/28439)

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**Author:** [@Fumi](https://discourse.slicer.org/u/Fumi)\
**Replies:** 14\
**Last updated:** [July 18, 2023, 8:53pm UTC](https://discourse.slicer.org/t/no-csv-file-in-diffusionmessurements-folder-in-wma/28439 "2023-07-18T20:53:44Z")

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Hi there, I am doing whitematteranalysis along with WMA tutorial: https://github.com/SlicerDMRI/whitematteranalysis/blob/master/doc/subject-specific-tractography-parcellation.md. In the last step of tutorial, " 8. Fiber …

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## [Slicer FiberTractMeasurements unable to find libSlicerBaseLogic](https://discourse.slicer.org/t/slicer-fibertractmeasurements-unable-to-find-libslicerbaselogic/30357)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 11\
**Last updated:** [July 6, 2023, 2:35pm UTC](https://discourse.slicer.org/t/slicer-fibertractmeasurements-unable-to-find-libslicerbaselogic/30357 "2023-07-06T14:35:33Z")

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Hi, I am trying to run WMA on a given dataset. The process runs fine until the moment where the FiberTractMeasurements module in Slicer is called. The tool writes the following to the std output: \<wm\_apply\_ORG\_atlas\_to…

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## [Custom Colormap Lookup Table for 'ColorOrientation' of DTI Volume?](https://discourse.slicer.org/t/custom-colormap-lookup-table-for-colororientation-of-dti-volume/30174)

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**Author:** [@ste](https://discourse.slicer.org/u/ste)\
**Replies:** 1\
**Last updated:** [June 21, 2023, 6:47pm UTC](https://discourse.slicer.org/t/custom-colormap-lookup-table-for-colororientation-of-dti-volume/30174 "2023-06-21T18:47:20Z")

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Operating system: Ubuntu 20.04.6 LTS Slicer version: 4.10.2 Would it be possible to import a custom colormap for the ‘ColorOrientation’ of a DTI volume? Currently that option is locked to the conventional color-code: …

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## [DTI maxEigenValueProjectionX ,Y ,Z in Slicer 5.0.3 or (4.11)](https://discourse.slicer.org/t/dti-maxeigenvalueprojectionx-y-z-in-slicer-5-0-3-or-4-11/29580)

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**Author:** [@JSteinJ](https://discourse.slicer.org/u/JSteinJ)\
**Replies:** 0\
**Last updated:** [May 22, 2023, 1:36pm UTC](https://discourse.slicer.org/t/dti-maxeigenvalueprojectionx-y-z-in-slicer-5-0-3-or-4-11/29580 "2023-05-22T13:36:29Z")

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Operating system: Ubuntu 22.04 Slicer version: 5.0.3 Expected behavior: calculation of maxEigenValueProjectionX ,Y ,Z Actual behavior: none… Hello Community, I want to calculate ALPS index from a DTI-MRI sequence… …

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## [Cannot install the whitematteranalysis for SlicerWMA](https://discourse.slicer.org/t/cannot-install-the-whitematteranalysis-for-slicerwma/28243)

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**Author:** [@Fumi](https://discourse.slicer.org/u/Fumi)\
**Replies:** 2\
**Last updated:** [March 15, 2023, 3:51am UTC](https://discourse.slicer.org/t/cannot-install-the-whitematteranalysis-for-slicerwma/28243 "2023-03-15T03:51:55Z")

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Hi all, I am having a problem in installing whitematteranalysis with pip as follows; (base) C:\\Users\\kidokoro\_win\> pip install git+https://github.com/SlicerDMRI/whitematteranalysis.git Collecting git+https://github.c…

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## [Some errors when install the whitematteranalysis](https://discourse.slicer.org/t/some-errors-when-install-the-whitematteranalysis/26574)

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**Author:** [@Joshuazzzs](https://discourse.slicer.org/u/Joshuazzzs)\
**Replies:** 2\
**Last updated:** [December 7, 2022, 2:38am UTC](https://discourse.slicer.org/t/some-errors-when-install-the-whitematteranalysis/26574 "2022-12-07T02:38:21Z")

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Hi, all When I install the whitematteranalysis on Windows 64bit with python 3.7, there are some errors as show in the picture. What should I do? Any help would be appreciated.

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## [motion and eddy currents correction](https://discourse.slicer.org/t/motion-and-eddy-currents-correction/26097)

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**Author:** [@batel](https://discourse.slicer.org/u/batel)\
**Replies:** 1\
**Last updated:** [November 7, 2022, 9:40pm UTC](https://discourse.slicer.org/t/motion-and-eddy-currents-correction/26097 "2022-11-07T21:40:17Z")

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Hi all, How can I correct for motion and eddy currents in slicer? Any help would be appreciated!

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## [B-matrix rotation](https://discourse.slicer.org/t/b-matrix-rotation/26050)

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**Author:** [@batel](https://discourse.slicer.org/u/batel)\
**Replies:** 1\
**Last updated:** [November 3, 2022, 12:36pm UTC](https://discourse.slicer.org/t/b-matrix-rotation/26050 "2022-11-03T12:36:18Z")

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Hi all, I wonder if there is a way of doing B-matrix rotation on slicer. I want to change my gradient directions according to the changes that were done in the registration of motion and deddy currents corrections. is …

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## [having difficulty saving a segmentation as nii.gz format](https://discourse.slicer.org/t/having-difficulty-saving-a-segmentation-as-nii-gz-format/25317)

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**Author:** [@eleanor](https://discourse.slicer.org/u/eleanor)\
**Replies:** 0\
**Last updated:** [September 18, 2022, 5:08am UTC](https://discourse.slicer.org/t/having-difficulty-saving-a-segmentation-as-nii-gz-format/25317 "2022-09-18T05:08:35Z")

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having difficulty saving a segmentation as nii.gz format

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## [Load DSI Studio (\*.trk.gz) or TrackVis (\*.trk) tracks in Slicer](https://discourse.slicer.org/t/load-dsi-studio-trk-gz-or-trackvis-trk-tracks-in-slicer/1356)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 16\
**Last updated:** [July 28, 2022, 11:05am UTC](https://discourse.slicer.org/t/load-dsi-studio-trk-gz-or-trackvis-trk-tracks-in-slicer/1356 "2022-07-28T11:05:13Z")

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Does anyone have experience converting and then loading fibertrack generated by these software into 3D Slicer ? Is there any recommended pathway to export tracts and import them into Slicer ? We are thinking of these …

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