Hi Carl,
the use of quantifyHippocampalSubfields.sh is:
quantifyHippocampalSubfields.sh suffix outputFile [subjectsDirectory]
Simply run
quantifyHippocampalSubfields.sh T1 test_no-T1.txt
or
quantifyHippocampalSubfields.sh T1 test_no-T1.txt
/Applications/freesurfer/subjects/RBrain
and everything should work
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Carl Anderson remfr...@gmail.com
To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, June 10, 2015 6:54:55 PM
Subject: [Freesurfer] quantifyHippocampalSubfields.sh fails in the current
version of freesurfer-Darwin-snowleopard-i686-dev.tar.gz
Hi All,
I have been using the quantifyHippocampalSubfields.sh from build 20150507 with
no problems.
However when I try to run the script in the new build (20150610) it fails if I
run with the T1 flag or without.
here is the result with T1:
vermisii:RBrain carlanderson$
Gathering results from subjects in:
test_T1.txt
Using the suffix name:
T1
And writing them to:
subfieldAnalysis_T1_v1.0
/Applications/freesurfer/bin/quantifyHippocampalSubfields.sh: line 8: cd:
test_T1.txt: No such file or directory
failed to do cd test_T1.txt
vermisii:RBrain carlanderson$
if I omit the T1 flag:
vermisii:RBrain carlanderson$ quantifyHippocampalSubfields.sh
subfieldAnalysis_T1_v1.0 test_no-T1.txt
Gathering results from subjects in:
/Applications/freesurfer/subjects/RBrain
Using the suffix name:
subfieldAnalysis_T1_v1.0
And writing them to:
test_no-T1.txt
vermisii:RBrain carlanderson$
Hope this helps,
Carl
--
•~~•~~•~~•~~•~~•~~•~~•
Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Harvard Medical School
The Neuroimaging Center,
McLean Hospital 115 Mill St. Belmont, MA 02478
Ph: 617-855-2972; Fax: 617-855-2770
e-mail: remfr...@gmail.com ; carl_ander...@hms.harvard.edu
•~~•~~•~~•~~•~~•~~•~~•
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