Hi Eric

I think if FREESURFER_HOME is set properly recon-all will create the symlinks it needs so you won't have to do it yourself (including the fsaverage one - I just checked).

cheers Bruce

On Mon, 23 Nov 2015, Eric Cunningham wrote:

Other than fsaverage, are there any other files that need to be linked for recon-all to work?

Thanks

On Mon, Nov 23, 2015 at 4:57 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Eric No, you can just symlink fsaverage and such Cheers Bruce

  > On Nov 23, 2015, at 9:40 PM, Eric Cunningham
  <etc42@hawaii.edu> wrote:
  >
  > Greetings Freesurfer experts,
  >
  > The README file in the $SUBJECTS_DIR says that a different
  directory can be specified by setting the env var SUBJECTS_DIR
  prior to the 'source $FREESURFER_HOME/FreeSurferEnv.csh'
  statement.
  >
  > Do the original contents of SUBJECTS_DIR (such as fsaverage)
  need to be moved into the newly specified SUBJECTS_DIR?
  >
  > Thanks,
  > -Eric
  >

...

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