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It looks like you have an extra slash in front of the output file name, so you're trying to write in the root directory...
On Tuesday, March 8, 2022, daedalus39@aol.com wrote:
External Email - Use CautionDear experts,
Having installed Freesurfer on WSL2, I was able to get the basic FS segmentation to run without error. However, when I tried to run_samseg on a single T1 image, I received the following error message (permissions denied creating the "output folder")
Is there anything in the trace (below) that provides a clue?
daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg --input o_ADNI_002_S_4654__MRI-m072.nii --output /T1-only -samsegOutput/ Traceback (most recent call last): File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 67, in <module> os.makedirs(args.outputDirectory, exist_ok=True) File "/usr/local/freesurfer/7-dev/python/lib/python3.6/os.py", line 220, in makedirs mkdir(name, mode) PermissionError: [Errno 13] Permission denied: '/T1-only-samsegOutput/'