Hi Andrew,
Thanks for pointing this out, it looks like the permissions of our fsaverage
subjects have all changed since yesterday! Will fix this now
Best,
Andrew
From: on behalf of "Russo, Andrew
William"
Reply-To: FS Help
Date: Monday, February 24, 2020 at 10:51 AM
To: FS Help
Subject: [Freesurfer] samseg permissions error
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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