# Diffusion module in 4.13 version cannot complete the reconstruction of fiber bundle

**URL:** <https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896>\
**Category:** SlicerDMRI\
**Tags:** segmentation, diffusion\
**Created:** [September 28, 2021, 1:36pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896 "2021-09-28T13:36:35Z")\
**Posts on this page:** 11\
**Page:** 1

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [September 28, 2021, 1:36pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/1 "2021-09-28T13:36:35Z")

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Win10 64

I don’t know if this is a mistake

My friend and I have tried multiple versions of 4.13 Slicer

But in the last step, when setting the seed to display the fiber bundle, it can’t be displayed.

The same data, the same steps, the fiber bundle can be displayed normally in version 4.11.

Can the developer test whether the fiber bundle can be rebuilt in the latest 4.13 version？

 ![捕获.PNG](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/0/406c0f226d4a90f8732cf1ca6cd246c98f4a0637.jpeg)

**This is the same mrb file in 4.11 Version**

 ![捕获](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/5/e54c3aa3a74e514688afed31169a31bc93a372d0.png)

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**Author:** ![zhangfanmark](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/zhangfanmark/32/4451_2.png) [@zhangfanmark](https://discourse.slicer.org/u/zhangfanmark)\
**Post date:** [September 30, 2021, 6:01pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/2 "2021-09-30T18:01:13Z")

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Hi!

Thank you for reporting this. We are able to reproduce this issue.

For my initial test, I guess there is an issue in the tract VTK writer. I can see point data is being output but not the cell data. Thank you @pieper

 ![PastedGraphic-1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/d/fd9bcf839c38d6ccb9a2d6e9b69c183c3af52c72.png)

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [September 30, 2021, 10:59pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/3 "2021-09-30T22:59:35Z")

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This problem will be solved, right？ 👍

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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:** [October 1, 2021, 1:07am UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/4 "2021-10-01T01:07:59Z")

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Hi yes we are looking into it and it will be solved. Thank you for letting us know! In the meantime please use the release version of Slicer if that is possible.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [October 11, 2021, 10:39pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/5 "2021-10-11T22:39:34Z")

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@slicer365 thanks for reporting this. There was an API change in the version of VTK we use. The change below fixes it and will be available in the next preview build of Slicer tomorrow.

> <https://github.com/SlicerDMRI/SlicerDMRI/pull/151>
>
> The behavior of vtkCellArray::GetData changed with vtk9 such
> that is now return…s a copy of the data rather than the actual
> array, so manipulating it has no effect.
> 
> Instead now we must have the cell array import the legacy format.
> 
> This operation is no doubt slower but is a minimal change to restore
> funcationality. This code should really be threaded and reworked to
> use the new API if performance is critical.

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [October 11, 2021, 10:53pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/6 "2021-10-11T22:53:50Z")

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Thank you very much for your work！ 👍 👍

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [October 14, 2021, 1:29pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/7 "2021-10-14T13:29:18Z")

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A new question is, when a new fiber bundle is created, after clicking update, it takes a long time to show the fiber bundle. Can the speed be increased?

There is a open software called DSI-studio, it can quickly show the fiber bundle, can it be integrated into Slicer?  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/9/2957eeed993f305179e6e3dd347cfcc0bc37a46b.png)

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [October 14, 2021, 7:59pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/8 "2021-10-14T19:59:41Z")

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You might be able to load DSI-studio data into Slicer, but I’ve never tried.

The built-in tractography seeding in Slicer only uses a single CPU core. You may get better results and better performance using the UKF tractography extension which uses multiple threads.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 17, 2021, 9:27pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/9 "2021-10-17T21:27:39Z")

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You can also tune the UKF tractography parameters to get results faster. I can get nice results in a fraction of a second. Of course the speed depends on the size and quality of your input data and your accuracy requirements.

I don’t know why DSI Studio developers chose to maintain their own application. It should be no problem at all to use Slicer as a frontend for their algorithms and they would save a lot of time that they could then spend on improving their computational methods.

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [March 13, 2022, 2:45pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/10 "2022-03-13T14:45:54Z")

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Hello ,Mr Pieper,I fond the module SlicerDMRI still doesn’t work in the Slicer 4.13 0312 win10.  
Problem is after I install it through the extention manager，but it doesn‘t appear in the slicer Module’s menu,can you help check it ! thank you very much！

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [March 13, 2022, 4:29pm UTC](https://discourse.slicer.org/t/diffusion-module-in-4-13-version-cannot-complete-the-reconstruction-of-fiber-bundle/19896/11 "2022-03-13T16:29:56Z")

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Yes, a lot of extensions need to be updated to work with the current preview (upcoming Slicer5 version), so for now we need to use the older release 4.11 for DMRI.

> **[Slicer5-failing-extensions](https://docs.google.com/spreadsheets/d/1GC4DWDpOXhuDYdfYOjJ6PmjHTeMM3-K7SoiC5ZR1GYg/edit#gid=29807248)**
>
> Sheet1
> 
> Name,Operating system,Build error root cause,Last successful build,Action
> 1=remove, 2=remove?
> 3=would be nice to fix
> 4=should be fixed
> 5=must fix,Responsive maintainers,Comments
> SlicerIGSIO,Windows,long...