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
No, fsaverage will be linked in by recon-all if needed
On 1/2/18 10:09 PM, zuxfoucault Wong 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
correct, it will not
On 1/3/18 7:23 PM, zuxfoucault Wong wrote:
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 mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
zuxfoucault Wong