External Email - Use Caution
Hi Andreas,
If you want to run recon-all on Bert, I would suggest to copy him to some place where you have write access and use that as the SUBJECTS_DIR.
Running FreeSurfer as root is a bad idea and usually leads to trouble later (e.g., the output will also be owned by root instead of your user).
Something like this if you use the bash shell:
mkdir -p ~/data/bert_only/ cp -r /usr/local/freesurfer/subjects/bert ~/data/bert_only/ export SUBJECTS_DIR=~/data/bert_only # now run recon-all
Best,
Tim
On February 19, 2020 at 11:25 AM Andreas Vitikan andreas.vitikan@gmail.com wrote:
External Email - Use CautionHello,
I am trying to get the examples running as per the FreeSurfer installation guide. I initially got a recon-all not found error which turned out to be due to the lack of tcsh/csh, which I installed (I found this fix in the mailing list) and now get a different error.
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c /usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or directory.
I thought it might be related to permissions but running under sudo gives a different error. How do I fix this?
- Andreas V.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer