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Dear Free Surfer team,
Surely this is a basic question but I am having a trouble setting the subjects_dir in my terminal and, as a result, any of the commands work.
This is how I have my Free Surfer configurated in my computer:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 --------------------------------------------------------------------------------------------------------
As it is, I cannot work in the SUBJECTS_DIR, as it is protected. I tried to set a new subjects_dir: export SUBJECTS_DIR=/home/rosalia/Desktop
Then I try to run the first step (autorecon1) with one subject, and it appears the following error: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s 001 -autorecon1 *ERROR: cannot find /usr/local/freesurfer/subjects/001* rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $
I have even changed my .bashrc file...but it seems I am doing something wrong as my terminal keeps pointing to the same subject_dir. I have tried to use sudo so in order to move my folder and subfolders to the subjects_dir set by default, and I am experiencing problems as well.
I would much appreciate any help with this basic question. Kind regards, Rosalia