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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

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