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
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) 
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
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
Hope this helps!
Cheers,
Arkiev
I have trouble with mask2glass,
How did you make it available for your system? I am also on 3.0.4 but I dont know how to make it available
