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 <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer