Hi Jasmin
you need to create a directory where you have write permission and room for the subject reconstruction to be written to, then set the SUBJECTS_DIR environment variable to point to it. At the moment you are trying to use the subject directory we distribute, which is in some system (and read-only) location. You can do this on the command line of recon-all via:
recon-all -sd <path to directory> ...
cheers Bruce
On Sun, 24 Jan 2016, Jasmin Alves wrote:
Hello Freesurfer,
I am trying to learn freesurfer and ran into the following issues below running the recon -all command.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.5.0 x86_64
1)
joya
2)
Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i T1_original_joya.nii -subject joya -all &
[1] 12300
Jasmins-MacBook-Pro:subjects jasminalves$ mkdir: /Applications/freesurfer/subjects/joya: Permission denied
mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied
cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such file or directory
cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
/Applications/freesurfer/subjects/joya: No such file or directory.
[1]+ Exit 1 recon-all -i T1_original_joya.nii -subject joya -a
Thank you,Jasmin
Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu