Dear Anthony,
Can you please send us a sample subject directory (the mri dir is enough, i don't need the surfaces), so i can play with it and see if there's anything we can do?
Cheers
E

Sent from my phone, please excuse brevity and typos

From: Anthony Dick
Sent: Thursday, June 1, 16:40
Subject: [Freesurfer] running hippocampal segmentation on PING
To: Freesurfer support list

Hello,

Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not a part of v.4.5.

One option is to start from scratch with v6: recon-all -all -s bert -hippocampal-subfields-T1

However, this seems to be a bad option because the quality control on the ~1500 brains is already completed for the original FS run.

My question is, are there certain flags from –autorecon2 and –autorecon3 that we could run so we don’t have to re-freesurf everything, or would it be better to just run –all? In other words, what are the minimum files needed to get hippocampal-subfields-T1 to run?

Thanks for any suggestions!

Anthony

—

Anthony Steven Dick, Ph.D.  

Associate Professor

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