Hi Annie,
It looks like ‘/packages/freesurfer-5.0.0/’ is your system Freesurfer install
directory.
It is a good idea to keep your SUBJECTS_DIR separate from Freesurfer install
directory. Create your SUBJECTS_DIR where you have write permissions will solve
the problem.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Annie Cooper
Sent: Wednesday, March 15, 2023 2:19 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Unable to Run Recon-all on T1 Image
External Email - Use Caution
Hi there,
I am trying to run recon-all using the Agave Supercomputer at ASU. When I try
to run recon-all, these error messages pop up prohibiting me from running
recon-all on my T1 image. Here is the error message I received:
[asurite@agave2:~/Desktop/T1_IMAGE]$ recon-all -s ATN001v1 -i
T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz -all
mkdir: cannot create directory '/packages/freesurfer-5.0.0/subjects/ATN001v1':
Permission denied
mkdir: cannot create directory '/packages/freesurfer-5.0.0/subjects/ATN001v1':
Permission denied
cp: cannot create regular file
'/packages/freesurfer-5.0.0/subjects/ATN001v1/scripts/build-stamp.txt': No such
file or directory
cat: /packages/freesurfer-5.0.0/subjects/ATN001v1/scripts/build-stamp.txt: No
such file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
INFO: SUBJECTS_DIR is /packages/freesurfer-5.0.0/subjects
Actual FREESURFER_HOME /packages/freesurfer-5.0.0
/packages/freesurfer-5.0.0/subjects/ATN001v1: No such file or directory.
I’m curious if the issue is that in order to run recon all and put subject
“ATN001v1” into the subjects folder, I have to have the necessary permissions
to edit a folder that isn’t under my username in the supercomputer. Please let
me know if there are any solutions to this problem. Thanks!
Best,
Annie
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