External Email - Use Caution        

Hi Rosie,

 

You need to specify the SUBJECTS_DIR variable to tell FreeSurfer where to create the subject’s directory with the processed data.

 

If you use BASH:

export SUBJECTS_DIR=/home/rosalia/Desktop/ARTICO

will result in creation of /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii

 

BWT, I recommend leaving the “.nii” from the subject name. I.e.:

                recon-all -s sub-003_ses-BSL -i /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii -T2 /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all

 

Kind regards,

Tibor

 

Auer, Tibor M.D. Ph.D.

Research Fellow

School of Psychology, Faculty of Health and Medical Sciences

University of Surrey, Guildford GU2 7XH

T.Auer@surrey.ac.uk

@TiborAuer

 

Feladó: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> E személy nevében: Rosalia Dacosta Aguayo
Küldve: 19 June 2021 12:36
Címzett: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Tárgy: [Freesurfer] Running Freesurfer in the Desktop

 

        External Email - Use Caution        

Dear Freesurfer's team,

 

I am trying to run FreeSurfer recon-all -all in a folder placed on my Desktop and I am having some trouble.

 

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -subject sub-003_ses-BSL_T1w.nii -i /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T1w.nii -T2 /home/rosalia/Desktop/ARTICO/sub-003_ses-BSL_T2w.nii -T2pial -all
mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii': Permission denied
cp: cannot create regular file '/usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/scripts/build-stamp.txt': No such file or directory
cat: /usr/local/freesurfer/subjects/sub-003_ses-BSL_T1w.nii/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/sub-003_ses-BSL_T1w.nii/scripts/patchdir.txt: No such file or directory.

 

 

I would greatly appreciate your help.

Kind regards,

Rosie