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Hi Chris, So I should change the path in the .bash_profile, right? Because doing this in the terminal does not work.... Have I understood you well? Kind regards, Rosalia El 12 nov. 2017 17:35, "Chris Watson" <[log in to unmask]> escribió: 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 > > >