External Email - Use Caution I simply put the desired brains in SUBJECTS_DIR, and then with SUBJECTS_DIR as the pwd, type quantifyThalamicSubnuclei.sh thal.txt T1
and that works. Perhaps drop mentioning the parent directories? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of O'Dor, Sarah Louise <so...@mgh.harvard.edu> Sent: Tuesday, May 10, 2022 12:37 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [External] [Freesurfer] Compiling thalamic nuclei segmentation volumes Good morning, I apologize in advance that my background is not in coding. I have run the freesurfer thalamic segmentation tool on over 100 subjects. I am now trying to compile the data. I know that the instructions for this command are: quantifyThalamicNuclei.sh <output_file> <analysisID> <OPTIONAL_SUBJECTS_DIR> For <output_file>, I have specified the name and location for the text file it will generate. For <analysisID>, I’m using the T1 that was processed through freesurfer, so I simply put T1. For <OPTIONAL_SUBJECTS_DIR>, I specify the subject directory. When I run the script above as: quantifyThalamicNuclei.sh [complete path]/ThalamicSegSheet.txt T1 [complete path]/Subjects/ The response is: Gathering results from subjects in: [complete path]/Subjects And writing them to: [complete path]/ThalamicSegSheet.txt …but nothing is generated. Any advice? I’d hate to compile the date individually for over 100 subjects. Many thanks, Sarah
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