# Ukf tractography

**URL:** <https://discourse.slicer.org/t/ukf-tractography/2747>\
**Category:** Support\
**Tags:** diffusion\
**Created:** [May 1, 2018, 5:46pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747 "2018-05-01T17:46:49Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![Jin](https://avatars.discourse-cdn.com/v4/letter/j/4af34b/32.png) [@Jin](https://discourse.slicer.org/u/Jin)\
**Post date:** [May 1, 2018, 5:46pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747/1 "2018-05-01T17:46:49Z")

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Operating system:windows 10  
Slicer version:4.8.0  
Expected behavior: DTI Process  
Actual behavior: Standard error  
The current UKF Tractography is different from the tutorial(4.4)

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/d/3dd0ddea85b4f48d265b63253002d5e3c68220b1.png)  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/7/1788c1b1435d4cdb1ffaf9a1760205a74723f7d7.png)

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**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [May 1, 2018, 7:44pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747/2 "2018-05-01T19:44:38Z")

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Hi @Jin, thanks for the report. The `minGA` error has already been fixed in the 4.8.1 release, so please download that (or a more recent SlicerPreview build).

We will update the documentation.

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**Author:** ![ljod](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ljod/32/652_2.png) [@ljod](https://discourse.slicer.org/u/ljod)\
**Post date:** [May 1, 2018, 8:18pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747/3 "2018-05-01T20:18:33Z")

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Also, here’s an explanation of the change to UKF tractography. We have made this change (removing GA and adding the new parameter of normalized mean signal) to provide a measure that is suitable for both single-shell and multi-shell (multiple b-values) data.

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**Author:** ![Jin](https://avatars.discourse-cdn.com/v4/letter/j/4af34b/32.png) [@Jin](https://discourse.slicer.org/u/Jin)\
**Post date:** [May 2, 2018, 1:14am UTC](https://discourse.slicer.org/t/ukf-tractography/2747/4 "2018-05-02T01:14:54Z")

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I will try it, thanks very much!

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**Author:** ![mnrad22](https://avatars.discourse-cdn.com/v4/letter/m/b38774/32.png) [@mnrad22](https://discourse.slicer.org/u/mnrad22)\
**Post date:** [March 6, 2019, 3:42pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747/5 "2019-03-06T15:42:40Z")

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Operating system: Ubuntu 18.04  
Slicer version: 4.10

Is it possible to set waypoints or endpoints in the UKF tractography module?

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**Author:** ![ljod](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ljod/32/652_2.png) [@ljod](https://discourse.slicer.org/u/ljod)\
**Post date:** [March 6, 2019, 4:05pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747/6 "2019-03-06T16:05:57Z")

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Those mainly are used for probabilistic tractography. For UKF, the traditional processing is to seed tractography in a large area or in the whole brain, then select the tracts of interest. You can use regions of interest for selection, and these can correspond to the waypoints or endpoints you are interested in.

If you let us know your overall goal we may have more suggestions to help.

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**Author:** ![fpsiddiqui91](https://avatars.discourse-cdn.com/v4/letter/f/53a042/32.png) [@fpsiddiqui91](https://discourse.slicer.org/u/fpsiddiqui91)\
**Post date:** [June 1, 2020, 12:04pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747/7 "2020-06-01T12:04:29Z")

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Hello @ljod

I was wondering if it is possible to perform seeding tractography with seed and endpoint. I am quite aware that streamline tractography needs only the seeding region. However, in my case, I want to add some endpoints as well to explore the tracts starting from one region and end at the specific region. I do have the seeding label and end label.

I am just not sure how to perform region-based stratigraphy. Is ROI selection in the diffusion module helpful? Can you guide me to how to perform this tractography?

Thank you.

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**Author:** ![ljod](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ljod/32/652_2.png) [@ljod](https://discourse.slicer.org/u/ljod)\
**Post date:** [July 28, 2020, 1:19pm UTC](https://discourse.slicer.org/t/ukf-tractography/2747/8 "2020-07-28T13:19:00Z")

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I apologize for the late reply. We have tutorials about ROI selection here under Slicer Fiber Bundle Selection:  
[http://dmri.slicer.org/docs/](http://dmri.slicer.org/docs/)