It can be done but only with the “hard” (discrete) segmentations, i.e., by counting voxels yourself (and multiplying by the voxel size in cubic mm, which is 1/27!)

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: Monday, March 17, 2025 at 10:12 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal Subfield Hierarchies

        External Email - Use Caution        

Thank you for your reply, Eugenio!

How do we get values described here:  "Molecular subregion added to nearest neighbor: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields. GC-ML-DG is absorbed by CA4, and the voxels in the molecular layer are assigned the label of the closest voxel that is neither molecular layer nor background (suffix: "CA")." Is it possible to get this information by extracting the volumes from the CA hierarchy mgz files?

Thank you!

Erin

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Date: Friday, March 14, 2025 at 5:44 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal Subfield Hierarchies

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

        External Email - Use Caution        

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