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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of O'Dor, Sarah Louise SODOR@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