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