what is your command line and terminal output?
On 2/24/2020 10:50 AM, Russo, Andrew William wrote:
Hello Freesurfer Developers,
I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory?
ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist ERROR: fs_time run_samseg
I did not find any related issues with samseg on the archive and I have had it work in the past. Before running samseg I sourced the freesurfer environment: export FREESURFER_HOME=/usr/local/freesurfer/dev source $FREESURFER_HOME/SetUpFreeSurfer.sh (Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
Thank you in advance, Andrew /____________ /Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer