Hi Hao - The simplest way to get around this is to create under $SUBJECTS_DIR/ symbolic links to the subjects' recon-all directories, wherever those may be in your own hierarchy.

Best,
a.y

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hao wen [hao.freesurfer@hotmail.com]
Sent: Friday, January 06, 2017 5:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula, adapt Freesurfer structure into other stucture hieraachy

Hello, Tracula expert:

I am here again, I want to know right now, the 5.3 version tracula seems to only support Freesurfer recon-alled structure, so in the config file, it works like this:

set subjlist = ( sub-PREVDEMALS0010001BE_ses-M0 )

because i want to apply tracula also into my own recon-alled structure, lets call it CAPS, and I define the sublist like this:

set subjlist = ( sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0 )

So this gives me some error when running trac-all -priors:


#@# Priors Thu Jan  5 15:19:27 CET 2017

Standard error:
/tmp/subj33.sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0.3193.txt: No such file or directory.

Return code: 1
Interface CommandLine failed to run.
Interface Function failed to run. 

So my question is trac-all is only compatible with FS structure??? if I want to adapt it to other hierarchy, i have to touch the trac-all.tcsh source code, right??


Thanks in advance


Hao