Dear Jamie,

Sorry for the late response; I was on vacation.

If I’m understanding correctly, the file without “surnames” is what you need: [lr]h.hippoAmygLabels-T1.v2x.mgz.

Cheers,

/Eugenio

-- 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jamie Hanson <jamielarshanson@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 15 August 2019 at 16:24
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Question re: hippocampal & amygdala subdivision files.

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Dear Freesurfer List,

I had a (hopefully) quick question re: output files from the hippocampal and amygdala subdivision routines. I know that there are multiple parcel schemes for the hippocampus (HBT, FS60, and CA), and per this thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57898.html), the final subfield segments are "computed from none of those volumes, but the parent of all of them".

I wondered however if there was an MGZ file that corresponded to the final/combined sub-divisions? Or if there was a way to output this? My group was interested in doing some spatial and surface analyses of sub-divisions (using Spherical Harmonics or some other related techniques). 

And I understand what the different MGZ files were in the mri directory (e.g., CA.FSvoxelSpace.mgz, FS60.FSvoxelSpace.mgz, HBT.FSvoxelSpace.mgz), but what was the file without any suffix (e.g., lh.hippoAmygLabels-T1.long.v21.mgz)? Or is that the file I'm looking for? Any information is deeply appreciated!

Thanks much,
Jamie.

--
Jamie Hanson
Assistant Professor, Psychology
Research Scientist, Learning Research and Development Center
University of Pittsburgh
Personal website: jamiehanson.org