CAT12 - cerebellum extraction

1

Hello

I have recently been interested in nirs and cerebellum and wanted to try our optimal montage on the cerebellum :slight_smile:

I just saw that cerebellum extraction was deactivated by default when using cat12? Is there any reason for that? I was wondering if you were having any suggestions to extract the cerebellar surface similarly to the cortical surface?

Regards,
Edouuard

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I added initially the option to compute the cerebellum surface when looking at the CAT12 options.
Then decided to hide it because @CGaser explained it was an experimental feature, too unstable to be used in production at that moment. But this was a while ago, maybe there were improvements on this front.

@CGaser: Is it safer now to use this option?
matlabbatch{1}.spm.tools.cat.estwrite.output.surface = 2; % 2: lh+rh+cerebellum

@edelaire
If you want to try it, select the process "Import anatomy > Segment MRI with CAT12", generate the Matlab script, and change the option cerebellum to 1. You should get something like this:

% Process: Segment MRI with CAT12
sFiles = bst_process('CallProcess', 'process_segment_cat12', sFiles, [], ...
    'subjectname', SubjectNames{1}, ...
    'nvertices',   15000, ...
    'tpmnii',      {'', 'Nifti1'}, ...
    'sphreg',      1, ...
    'vol',         1, ...
    'extramaps',   0, ...
    'cerebellum',  1);

Please let us know how this goes, and post screen captures of the result.

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Hello Francois,

I just tried on an MRI; the result isn't really convincing :smiley: I tried with 'CAT12.8-Beta'. I am going to update it and try again:

Capture d’écran 2021-11-17 à 14.29.47
Capture d’écran 2021-11-17 à 14.29.47647×506 41.6 KB
Capture d’écran 2021-11-17 à 14.28.57
Capture d’écran 2021-11-17 à 14.28.57647×506 61.7 KB

Edit: in case that's helpful, here is the report provided by CAT12 (I modified the code so it doesn't delete the Cat12 output at the end)

catreportj_Subject03
catreportj_Subject032480×3508 1.08 MB

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@edelaire
The extraction of the cerebellum is still experimental and should currently not be used. However, our results never looked so poor like yours....

Regards

Christian

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Interestingly, if we overlay the cerebellum with the MRI it seems that it's capturing well the bottom of the cerebellum but the algorithm is having a hard time closing the surface :
I can share the MRI file with you if you want.

cerebelum
cerebelum1407×1057 137 KB

Here is the surface produced by Freesurfer:

Screenshot from 2021-11-25 09-30-15
Screenshot from 2021-11-25 09-30-151404×1054 113 KB

Edouard

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Here is the surface produced by Freesurfer:

Note that this very smooth cerebellum surface is not produced by FreeSurfer, it is meshed from the ASEG volume parcellation by Brainstorm using Matlab function isosurface.m, called in function in_tess_mrimask.m.

https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Subcortical_structures:_aseg_atlas

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