Hi Jasmine,
This is tricky because the “absorption” happens at the discrete segmentation level (rather than using the soft probabilities).
At that point, you’re probably better off counting voxels and multiplying by their volume.
Doug: is there a way to do this with FreeSurfer programs, as opposed to using eg Matlab or Python?
If not, you could run something like this in Matlab:
addpath /path/to/freesurfer/matlab; mri = MRIread(segmentation_file); volume = sum(mri.vol(:)==label_of_interest) * det(mri.vox2ras0)
Cheers,
/E
http://www.jeiglesias.com
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yasmine Salman <yasmine.salman@uclouvain.be>
Date: Wednesday, October 18, 2023 at 5:22 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HBT/FS60/CA segmentation
External Email - Use Caution
Dear Freesurfer Developpers,
When I look at the FreeSurfer documentation on hippocampal segmentation, I see that it is possible to obtain different segmentations in addition to the 'traditionnal
' freesurfer 7 one:
- HBT: the hippocampus is subdivided into head, body and tail.
- FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e. there is no head/body subdivision for the hippocampus.
no head/body subdivision for hippocampal sub-regions.
- CA: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields.
When I run the command line: segmentHA_T1.sh bert
I get files: hipposubfields.lh.T1.v21.stats which contain the volumes of the freesurfer 7 segmentation but not the other segmentations. I would like to generate a
.stat file (one/subject) of segmentation type 'CA' , how can I do this?