You cannot have multiple SUBJECTS_DIR's. It is supposed to be the base directory under which all subjects' dirs are saved. You could have a different configuration file for each subject if you want each of them to have a different SUBJECTS_DIR, but this hack won't work for longitudinal analyses as all the time points from the same subject have to be defined in the same config file. If you must have subjects saved in different locations, you can create a "mock" SUBJECTS_DIR and in it create symlinks to the dirs of every individual subject (this includes both *.long.* and base dirs).

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edu>
Sent: Thursday, April 30, 2020 3:40 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal dmrirc script error with the baselist

External Email - Use Caution

Hi,

I have my trac-all up and running with no error with individual subjects when I set the subject directory to individual subjects.

as follow:

set SUBJECTS_DIR=/*/subjects/SUBJ1

set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2)
set baselist = (SUBJ1_base SUBJ1_base)

However, when I put subjects together and set the directory to multiple subjects as follow:

set SUBJECTS_DIR=/*/subjects

set subjlist = (SUBJ1/SUBJ1_ses-1 \

SUBJ1/SUBJ1_ses-2 \

SUBJ2/SUBJ2_ses-1 \

SUBJ2/SUBJ2_ses-2 \

etc. )

set baselist = (SUBJ1/SUBJ1_base \

SUBJ1/SUBJ1_base \

SUBJ2/SUBJ2_base \

etc.)

It has a problem finding the baselist file:

"cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it not happening with the subject individual?

Best,

Ph.D. candidate

Icahn School of Medicine at Mount Sinai