As I recommended earlier, you should put that variable in the ".bash_profile" file. Your problem likely occurs because ".bashrc" is loaded before ".bash_profile", and if you then source the Freesurfer scripts following the instructions on their wiki (placing it in ".bash_profile"), it overwrites the SUBJECTS_DIR variable. So place your SUBJECTS_DIR specification *after* you source SetUpFreesurfer.sh (or whatever it's called).

In any case, you can always set this variable yourself in a terminal, or in some other script. As long as you keep the terminal, the variable persists.

On Sun, Nov 12, 2017 at 2:08 AM, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:

Dear FLS experts,

I am having a problem with trying to change the path of SUBJECTS_DIR directory. I now this is something about FreeSurfer but I believe that changing a directory it is a very simple question and that I could ask to you as well.

My path to subject directory is set to usr/...It is a very bad place because I have no permissions to generate any directory in this place. What I have done to solve it is:

1. Change the path to another place in the .bashrc file.

Save and restart the computer.

Well, when I try to run recon-all, FreeSurfer keeps going to the same path usr/...to create the SUBJECTS_DIR diectory and it cannot be created because I have no permission.

2. Set a new path directory for SUBJECTS_DIR manually...PATH=....in the shell.

I tried to run recon-all again and FreeSurfer still keeps going to usr/... to create the SUBJECT_DIR directory and I have the same warning about permission...

I do not know what more I can do.

I would really much appreciate your helping in this because nothing of what I am doing seems to work.

Kind regards,

Rosalia