Dear list,

I did a test on the aforementioned procedure. It turns out the fsaverage symbolic link will be automatically generated by FreeSurfer in the new SUBJECTS_DIRS location.

So far, under my limited experience on FreeSurfer, I think that changing the location of subjects_dir after `source $FREESURFER_HOME/FreeSurferEnv.sh` should not introduce any unexpected events for the analysis?

Best,

Foucault

On Wed, Jan 3, 2018 at 11:09 AM zuxfoucault Wong <zuxfoucault@gmail.com> wrote:

Dear list,

If I changed the location of subjects_dir (via `export SUBJECTS_DIRS=/new_location/) after `source $FREESURFER_HOME/FreeSurferEnv.sh`, could I still completely run the `recon-all -all`? I mean some folders in the default location of subjects_dir, such as fsaverage, would not be included in the new subjects_dir. Would this cause trouble to the subsequent freesurfer routine?

Thanks for your time!

Best,
Foucault