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

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