Brain Stem segmentation/visualization for nuclei and tracts

I want to visualize/segment the nuclei and tracts in the brainstem using images such as DWI and MRI. I read about this being done with MRtrix in a previous study, but unfortunately, I couldn’t find the study now.

Does anyone have information on this? My goal is to visualize/segment the nuclei and tracts (the important structures) in the brainstem. If it can be done with any other program, that would also work.

Kind Regards
Emre

I found the study I mentioned. It mentions the use of MRtrix, TORTOISE3, and ITKsnap, but it doesn’t explain how they were implemented.

Is there a specific article or code example regarding the implementation of this task?

https://cds.ismrm.org/protected/18MProceedings/PDFfiles/2061.html

Hi Emre,

This can probably be done in mrview using a combination of the volume render and tractography visualisation toolbars.

Also, check out the function mask2glass. mask2glass can be used for the whole-brain mask as well as sub-structures.

Streamlines can be viewed either by using the tractography visualisation toolbar, or, consider using tckmap to convert the .tck file to a .mif file, which can subsequently be used as a main image (or image overlay).

Hope this helps!

Cheers,
Arkiev

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Hi Arkiev,

The mask2glass function looks fun to try, but I do not see it in the most recent release. Do you know what version this is from?

Thanks!

Hi Erika,
I’m using version mrtrix3 version 3.0.4 (and mask2glass works) :slight_smile:

Cheers,
Arkiev

Hi again,

After reading this New command "mask2glass" by remikamito · Pull Request #2359 · MRtrix3/mrtrix3 · GitHub it might be worth giving the dev branch a go…

Cheers,
Arkiev

oh great, thanks for finding that in the dev branch, I didn’t see it at first pass. I am also on 3.0.4 but with the precompiled version.

I also found this from the archives if helpful to original post.

-e

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The problem is,

I dont understand how can I build the proper .tck file or .mif file which has nucleus and tracts in it (which are specific to brain stem such as DCML, Superior colliculus…).

I mean building a glass brain and putting the segmentation in it seems cool but as I said I could not understand the part which is creating those segmentations.

And also I am looking for a semi-automatic way to do it. If there is no other choice then manual way is an option.

Emre

Hi Emre,

There are a few options… TractSeg might be able to segment the pathways of interest.

Alternatively, the commands tckgen and tckedit might be worth exploring, along with options such as -include, -exclude and -seed_image. The ends_only in tck_edit might also be useful here. This will involve conducting manual segmentations to identify regions of interest that the streamlines must traverse or avoid :slight_smile:

Hope this helps!

Cheers,
Arkiev