Dear Erin,

I would recommend taking the spreadsheet with the fine-grained volumes, and simply combine the volumes (columns) as follows:

CA1 = CA1-head  +  CA1-body

CA3 = CA3-head  +  CA3-body

CA4 = CA4-head  +  CA4-body

GC-ML-DG = GC-ML-DG -head  +  GC-ML-DG -body

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Erin L Ratliff <eratlif2@umd.edu>
Date: Thursday, March 13, 2025 at 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal Subfield Hierarchies

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Hi FS experts,

We are running the segmentHA_T2.sh script, and we get the .mgz files for the 3 hierarchies (CA, FS60, and HBT), but when we run either concatenatesubregions or asegstats2table, we get the fine grain hippocampal subfield volumes. Is it possible to extract the volumes (as .txt) from the hierarchy .mgz files? We are interested in using the CA hierarchy, and we are not sure how to calculate this with the output we receive from either concatenatesubregions/asegstats2table.

Any help is appreciated!

Erin