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 &


3)

[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 

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