External Email - Use Caution        


Hello Padma,

The freesurfer installation under /Applications on MacOS, like most applications installed there, does not expect users to write their own data into what is installed there.  Or the example subjects that  are part of the freesurfer installation - pointed to by the environment variable SUBJECTS_DIR - is not meant to be written to with user data.

So just change SUBJECTS_DIR to point to a directory where you have normal write permissions.  One location would be your home directory, e.g.,

$ echo $HOME

/Users/padma

$ cd $HOME

$ mkdir subjects

$ export SUBJECTS_DIR=$HOME/subjects

$ echo $SUBJECTS_DIR

/Users/padma/subjects

Then put your subjects data there to process, etc.

Here are some links with some additional info,

https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer

https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_03_ReconAll.html

- R.

On 10/9/22 01:40, priya padma (priya@phenomx..ai) wrote:

        External Email - Use Caution        

Hello Team,

Thanks for the help before I successfully opened freeview. now i am trying to run recon-all for a nifti file. After setting the path 

export FREESURFER_HOME=/Applications/freesurfer/7.3.2

export SUBJECTS_DIR=$FREESURFER_HOME/subjects

source $FREESURFER_HOME/SetUpFreeSurfer.sh


My data is in downloads so I navigated to Downloads and then gave 


$ recon-all -s sub01 -i sub-AD003S1059S61129_0000.nii.gz -all


but I always get permission error


mkdir: /Applications/freesurfer/7.3.2/subjects/sub01: Permission denied

fs-check-version --s sub01 --o /var/folders/j3/plp0z25j1j969hgspftsz2fm0000gp/T//tmp.gqzblo

ERROR: cannot find sub01

recon-all: version check failed

fs-check-version --s sub01 --o /var/folders/j3/plp0z25j1j969hgspftsz2fm0000gp/T//tmp.gqzblo


so I did it with sudo then also I get error which I learnt that the environment changes with sudo so we shouldn't use sudo.


I tried keeping the data in the subjects folder and still the same error 


Could you help me with this?


Thank you 




--
Best Regards
Padma Priya
AI Developer 

PhenoMx, Inc.
priya@phenomx.ai | (+82)10-5405-2685



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