Re: [Freesurfer] Running Freesurfer in the Desktop

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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

mailto:T.Auer@surrey.ac.uk T.Auer@surrey.ac.uk

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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