# \#tractography

**URL:** https://discourse.slicer.org/tag/tractography/13.md

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## [Tractography ROI selection via script](https://discourse.slicer.org/t/tractography-roi-selection-via-script/36466)

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**Author:** [@fcruz](https://discourse.slicer.org/u/fcruz)\
**Replies:** 1\
**Last updated:** [April 30, 2026, 1:14pm UTC](https://discourse.slicer.org/t/tractography-roi-selection-via-script/36466 "2026-04-30T13:14:02Z")

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Operating system: Ubutu 22.04 Slicer version: 5.6.2 I would like to automatically extract fiber bundles from a UKF tractography vtk file using the Tractography ROI selection module. I have a label map that contains Fre…

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## [Slicer doesn't open after installing SlicerWMA extension](https://discourse.slicer.org/t/slicer-doesnt-open-after-installing-slicerwma-extension/42356)

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**Author:** [@Dmytro\_Shyshlov](https://discourse.slicer.org/u/Dmytro_Shyshlov)\
**Replies:** 5\
**Last updated:** [April 3, 2025, 12:44am UTC](https://discourse.slicer.org/t/slicer-doesnt-open-after-installing-slicerwma-extension/42356 "2025-04-03T00:44:42Z")

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Hello! I’m trying to run Slicer 5.8.1 on CentOS 7.9 server with 3 extensions: SlicerDMRI, SlicerWMA, UKFTractography. Everything works fine with DMRI and UKFT, but every time I try to install SlicerWMA the program doesn…

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## [UKF Tractography extension missing in 3D Slicer 5.8.0](https://discourse.slicer.org/t/ukf-tractography-extension-missing-in-3d-slicer-5-8-0/41516)

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**Author:** [@TinaNant28](https://discourse.slicer.org/u/TinaNant28)\
**Replies:** 1\
**Last updated:** [February 5, 2025, 7:31pm UTC](https://discourse.slicer.org/t/ukf-tractography-extension-missing-in-3d-slicer-5-8-0/41516 "2025-02-05T19:31:33Z")

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Hello, the UKF Tractography extension is not available in the latest version of 3D Slicer 5.8.0. Is there any solution for that? Thank you

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## [Modul "Export Tractography to PLY (mesh)" doesn't work in Slicer 5.7.0](https://discourse.slicer.org/t/modul-export-tractography-to-ply-mesh-doesnt-work-in-slicer-5-7-0/40805)

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**Author:** [@Elisabeth](https://discourse.slicer.org/u/Elisabeth)\
**Replies:** 1\
**Last updated:** [December 19, 2024, 8:26pm UTC](https://discourse.slicer.org/t/modul-export-tractography-to-ply-mesh-doesnt-work-in-slicer-5-7-0/40805 "2024-12-19T20:26:06Z")

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Problem report for Slicer 5.7.0-2024-12-13 win-amd64: \[please describe expected and actual behavior\] Dear community, I’ve done tractography in the 3D Slicer 5.7.0 software and now I planned to export my fiber bundle as…

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## [Data format of the probabilistic segmentation map for UKF Tractography module?](https://discourse.slicer.org/t/data-format-of-the-probabilistic-segmentation-map-for-ukf-tractography-module/40730)

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**Author:** [@Ilya\_Pshenichnyy](https://discourse.slicer.org/u/Ilya_Pshenichnyy)\
**Replies:** 0\
**Last updated:** [December 17, 2024, 5:42pm UTC](https://discourse.slicer.org/t/data-format-of-the-probabilistic-segmentation-map-for-ukf-tractography-module/40730 "2024-12-17T17:42:46Z")

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I have been trying to use Option 2 in Seeding Options ( Documentation/Nightly/Modules/UKFTractography - Slicer Wiki). I used Tracula generated probability distribution volume, normalized it to have 0 to 1 values as the d…

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## [What kind of default colormap use in tractography seeding ](https://discourse.slicer.org/t/what-kind-of-default-colormap-use-in-tractography-seeding/37545)

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**Author:** [@xixi911](https://discourse.slicer.org/u/xixi911)\
**Replies:** 2\
**Last updated:** [July 25, 2024, 6:50am UTC](https://discourse.slicer.org/t/what-kind-of-default-colormap-use-in-tractography-seeding/37545 "2024-07-25T06:50:56Z")

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Operating system:win 11 Slicer version:5.4.0 Expected behavior: Actual behavior: I was wondering what type of colormap was used in tractography seeding, which was user-defined when I debuging use vs2019, but I couldn…

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## [Slicer 5.0.3 - UKF Tractography Resource Issue](https://discourse.slicer.org/t/slicer-5-0-3-ukf-tractography-resource-issue/25702)

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**Author:** [@cnot](https://discourse.slicer.org/u/cnot)\
**Replies:** 14\
**Last updated:** [July 18, 2024, 3:49am UTC](https://discourse.slicer.org/t/slicer-5-0-3-ukf-tractography-resource-issue/25702 "2024-07-18T03:49:16Z")

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Hi all, I am trying to run UKF Tractography on my DTI data, and am encountering problems that seem to be related to memory use. Note: this always worked with the same data and parameters on a previous release of Slicer…

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## [Tractography segmentation](https://discourse.slicer.org/t/tractography-segmentation/24161)

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**Author:** [@massimo](https://discourse.slicer.org/u/massimo)\
**Replies:** 2\
**Last updated:** [May 13, 2024, 4:11pm UTC](https://discourse.slicer.org/t/tractography-segmentation/24161 "2024-05-13T16:11:12Z")

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Dear Community, Starting from a tractography, where i can already see all the brain fibers (Using the DMRI module) I need to segment them in: In particular, I’d need to first identify the: Arcuate fascicle optic r…

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## [How to perform the UKFTractography via command line on ubuntu 20.04?](https://discourse.slicer.org/t/how-to-perform-the-ukftractography-via-command-line-on-ubuntu-20-04/30657)

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**Author:** [@dazhangge-666](https://discourse.slicer.org/u/dazhangge-666)\
**Replies:** 11\
**Last updated:** [October 16, 2023, 3:36am UTC](https://discourse.slicer.org/t/how-to-perform-the-ukftractography-via-command-line-on-ubuntu-20-04/30657 "2023-10-16T03:36:42Z")

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I want to use .sh to batch process my data via UKFTractography ,so maybe I must use the command line of it.How could I do?

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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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## [Adding an icon to identify an extension](https://discourse.slicer.org/t/adding-an-icon-to-identify-an-extension/30562)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 11\
**Last updated:** [July 25, 2023, 4:03pm UTC](https://discourse.slicer.org/t/adding-an-icon-to-identify-an-extension/30562 "2023-07-25T16:03:08Z")

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Hi, when having adding some of the diffusion-related extension to the favorites toolbar I see that all have the same default icon used for extensions, which makes it difficult to recognize them. What is the appropri…

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## [tractography single color tract not multi-color tract](https://discourse.slicer.org/t/tractography-single-color-tract-not-multi-color-tract/29952)

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**Author:** [@GunnarE](https://discourse.slicer.org/u/GunnarE)\
**Replies:** 2\
**Last updated:** [July 24, 2023, 10:43pm UTC](https://discourse.slicer.org/t/tractography-single-color-tract-not-multi-color-tract/29952 "2023-07-24T22:43:20Z")

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Hi Slicer community, We have been following multiple tutorials from Dr. Sonia Pujol on diffusion tractography including “Exploring Peritumoral White Matter Fibers for Neurosurgical Planning”, “Diffusion MRI Analsyis”, a…

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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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## [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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## [Multiple tractography file selection for visualization and 2D vs 3D visualization toggles](https://discourse.slicer.org/t/multiple-tractography-file-selection-for-visualization-and-2d-vs-3d-visualization-toggles/30314)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 3\
**Last updated:** [June 30, 2023, 3:33pm UTC](https://discourse.slicer.org/t/multiple-tractography-file-selection-for-visualization-and-2d-vs-3d-visualization-toggles/30314 "2023-06-30T15:33:43Z")

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Hi, when having multiple bundle data loaded onto Slicer, is there a way to select multiple files at the same time and to change the visualization type (under Diffusion/Tractography/Tractography Display) to Tubes instead…

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## [What's wrong with my DWI? Failed to convert from DWI to tensors](https://discourse.slicer.org/t/whats-wrong-with-my-dwi-failed-to-convert-from-dwi-to-tensors/26864)

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**Author:** [@peter\_adidharma](https://discourse.slicer.org/u/peter_adidharma)\
**Replies:** 3\
**Last updated:** [December 22, 2022, 1:40pm UTC](https://discourse.slicer.org/t/whats-wrong-with-my-dwi-failed-to-convert-from-dwi-to-tensors/26864 "2022-12-22T13:40:38Z")

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Hi all, I’ve been working to do some tractography using slicerDMRI, but seems to encounter the same problem with all DWI files that i have as i failed to convert it to tensors. Here, I attached the .nrrd file of our DWI…

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## [Which module can export the relevant data of the fiber bundle，which created using UKF tractography](https://discourse.slicer.org/t/which-module-can-export-the-relevant-data-of-the-fiber-bundle-which-created-using-ukf-tractography/26031)

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**Author:** [@Joshuazzzs](https://discourse.slicer.org/u/Joshuazzzs)\
**Replies:** 1\
**Last updated:** [November 2, 2022, 11:57pm UTC](https://discourse.slicer.org/t/which-module-can-export-the-relevant-data-of-the-fiber-bundle-which-created-using-ukf-tractography/26031 "2022-11-02T23:57:04Z")

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Hi! We use the UKF tractography module to creat the neural fibers. Which module can export the relevant data of the fiber bundle, as in the following image, generate a table directly…

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## [Tractography issue](https://discourse.slicer.org/t/tractography-issue/24093)

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**Author:** [@massimo](https://discourse.slicer.org/u/massimo)\
**Replies:** 4\
**Last updated:** [June 30, 2022, 6:21pm UTC](https://discourse.slicer.org/t/tractography-issue/24093 "2022-06-30T18:21:55Z")

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Operating system: Mac OSX Monterey Slicer version:5.0.2 Expected behavior: Tractography visualization Actual behavior: Errors in data import Dear Community, I’m trying to create a 3d model of a tractography to view …

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## [UKF tractography fails for large scans (~1.5mm iso)](https://discourse.slicer.org/t/ukf-tractography-fails-for-large-scans-1-5mm-iso/23863)

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**Author:** [@phoebeimms](https://discourse.slicer.org/u/phoebeimms)\
**Replies:** 1\
**Last updated:** [June 14, 2022, 3:46pm UTC](https://discourse.slicer.org/t/ukf-tractography-fails-for-large-scans-1-5mm-iso/23863 "2022-06-14T15:46:40Z")

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Hi! We are running whole brain 2-tensor UKF tractography, using 5 seeds ver voxel and otherwise default parameters, on a large range of scans (from various online repositories, e.g., HCP, UKBB, etc). Depending on the ac…

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## [Problem while processing DWI images in Slicer](https://discourse.slicer.org/t/problem-while-processing-dwi-images-in-slicer/17820)

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**Author:** [@benxa](https://discourse.slicer.org/u/benxa)\
**Replies:** 1\
**Last updated:** [May 27, 2021, 7:00pm UTC](https://discourse.slicer.org/t/problem-while-processing-dwi-images-in-slicer/17820 "2021-05-27T19:00:30Z")

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Dear experts, I am interested in learning how to use Slicer but I encounter a problem. When I have to indicate the inputs for the processes necessary to carry out the tractography (e.g create a brain mask), my images do …

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## [DWI to DTI Estimation Problem](https://discourse.slicer.org/t/dwi-to-dti-estimation-problem/719)

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**Author:** [@AsliBeriL](https://discourse.slicer.org/u/AsliBeriL)\
**Replies:** 19\
**Last updated:** [August 21, 2020, 6:12pm UTC](https://discourse.slicer.org/t/dwi-to-dti-estimation-problem/719 "2020-08-21T18:12:21Z")

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Operating system: Win 10 Pro Slicer version: 4.5.0-1 Hello everyone, I want DWI images convert to DTI and tractography. First step, i created .nrrd file, baseline and mask. Later, DWI to DTI estimation module is worki…

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## [Optic Nerve tractography](https://discourse.slicer.org/t/optic-nerve-tractography/9993)

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**Author:** [@HariES](https://discourse.slicer.org/u/HariES)\
**Replies:** 2\
**Last updated:** [January 29, 2020, 11:37pm UTC](https://discourse.slicer.org/t/optic-nerve-tractography/9993 "2020-01-29T23:37:20Z")

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Dear Sir, Optic nerve is mixing with noise of image in the mask. So tensor is not estimated in dti estimation for the optic nerve. How to do optic nerve tracts after installing fiducial in optic nerve.

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## [Tractography - bad quality](https://discourse.slicer.org/t/tractography-bad-quality/6191)

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**Author:** [@eNable\_Polska](https://discourse.slicer.org/u/eNable_Polska)\
**Replies:** 2\
**Last updated:** [April 2, 2019, 7:17pm UTC](https://discourse.slicer.org/t/tractography-bad-quality/6191 "2019-04-02T19:17:10Z")

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Id like to ask you about resolution of my images. Sorry about my English We take MRI with tractography, GE machine. I saw the tractography made of this research and it looked good. Id like to build it in slicer, but I ca…

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## [How to Split Up VTK Fiber Bundle Files](https://discourse.slicer.org/t/how-to-split-up-vtk-fiber-bundle-files/5856)

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**Author:** [@rpl6](https://discourse.slicer.org/u/rpl6)\
**Replies:** 11\
**Last updated:** [February 27, 2019, 3:47pm UTC](https://discourse.slicer.org/t/how-to-split-up-vtk-fiber-bundle-files/5856 "2019-02-27T15:47:55Z")

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Hello everyone, I was wondering if there was a way to split up a VTK fiber bundle file into smaller parts (or multiple smaller files) for more manageable processing. I am currently working with Slicer Python, but I woul…

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## [Refereces for Tractography ROI Seeding](https://discourse.slicer.org/t/refereces-for-tractography-roi-seeding/5550)

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**Author:** [@sim.zanoni](https://discourse.slicer.org/u/sim.zanoni)\
**Replies:** 2\
**Last updated:** [February 1, 2019, 1:34am UTC](https://discourse.slicer.org/t/refereces-for-tractography-roi-seeding/5550 "2019-02-01T01:34:00Z")

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Dear Authors/Contributors, I would be interested in using the Tractography ROI Seeding module provided as extension in Slicer (4.8.1). I started by reading the documentation (https://www.slicer.org/wiki/Documentation/Ni…

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## [Performing tractography with multiple ROIs](https://discourse.slicer.org/t/performing-tractography-with-multiple-rois/2525)

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**Author:** [@lsmith](https://discourse.slicer.org/u/lsmith)\
**Replies:** 3\
**Last updated:** [April 10, 2018, 6:28pm UTC](https://discourse.slicer.org/t/performing-tractography-with-multiple-rois/2525 "2018-04-10T18:28:53Z")

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Hi! I’m an RA and quite new to 3D slicer. My lab is working on using DTI data to map motor pathways in the brain. We are wanting to define regions of interest in the motor cortex and the brainstem and see the fibers that…

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## [vtkMRMLFiberBundleNode Transmission via OpenIGTLinkIF](https://discourse.slicer.org/t/vtkmrmlfiberbundlenode-transmission-via-openigtlinkif/1233)

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**Author:** [@leochan2009](https://discourse.slicer.org/u/leochan2009)\
**Replies:** 9\
**Last updated:** [October 17, 2017, 11:13pm UTC](https://discourse.slicer.org/t/vtkmrmlfiberbundlenode-transmission-via-openigtlinkif/1233 "2017-10-17T23:13:56Z")

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Dear Slicer Developers, I am trying to extend OpenIGTLinkIF module to transmit the tractography. The tracts are vtkMRMLFiberBundleNode data, which is a derived class from vtkMRMLModelNode. The OpenIGTLinkIF module is …

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## [Tractography color display from ASCII .vtk Polydata](https://discourse.slicer.org/t/tractography-color-display-from-ascii-vtk-polydata/871)

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**Author:** [@bartbols](https://discourse.slicer.org/u/bartbols)\
**Replies:** 7\
**Last updated:** [August 16, 2017, 5:44am UTC](https://discourse.slicer.org/t/tractography-color-display-from-ascii-vtk-polydata/871 "2017-08-16T05:44:05Z")

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Hi, I’m trying to visualize some fibre tracts in 3D slicer form a ASCII vtkPolydata file that I generate through Matlab. The file reads in well and displays the fibres in the correct position, however, I cannot assign c…

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## [Ukftractography](https://discourse.slicer.org/t/ukftractography/693)

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**Author:** [@ElvaChen](https://discourse.slicer.org/u/ElvaChen)\
**Replies:** 5\
**Last updated:** [July 22, 2017, 10:19am UTC](https://discourse.slicer.org/t/ukftractography/693 "2017-07-22T10:19:04Z")

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Operating system: Linux Slicer version: 4.5.0-1 Hi: I wonder if there is any way to view the saved output of free water fraction (free water imaging volume) in UKF? I use Slicer version 4.5.0-1. Thanks. Elva

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## [Tractography through ROIs from TMS-DICOM-Data - anyone experience?](https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502)

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**Author:** [@LGG](https://discourse.slicer.org/u/LGG)\
**Replies:** 4\
**Last updated:** [June 14, 2017, 7:37pm UTC](https://discourse.slicer.org/t/tractography-through-rois-from-tms-dicom-data-anyone-experience/502 "2017-06-14T19:37:26Z")

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Hi everyone, I would like to create ROIs out of DICOM-Data that has been acquired through TMS (with Slicer 4.6). The aim is to run tractography through these ROIs. I tried to do full brain tractography and use the TMS-…

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