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This script will run the standard FreeSurfer process.

Usage: fsRunCrossSectionals.sh [ options ] ALLFR ALLHA CCCCC DDDDD etc.

  All arguments after the options are FreeSurfer directories under the current directory.
  
Options:

  -not-our-mask           : Don't use our brain mask           [ default is to use it]
  -not-our-vents-fix      : Don't use our vents fix            [ default is to use it] 
  -start                  : Step to start at                   [ default 1 ie. auto-recon1]
  -stop                   : Step to stop at                    [ default 3 ie. auto-recon3]
  -reconall " options "   : Any additiopnal options to pass to recon-all, in quotes.
  -r1 " -notal-check "    : Any additional options to pass to autorecon1, in quotes.
  -r2 " options "         : Any additional options to pass to autorecon2, in quotes.
  -r3 " options "         : Any additional options to pass to autorecon3, in quotes.
  -echo                   : Just echo the command, don't actually do it.
  -expert                 : Name of an expert options file
      

Hints:
  1. You must set the environment variable $SUBJECTS_DIR
  
     For example, go to the right directory and:
     
       In bash type:export SUBJECTS_DIR=`pwd`
       In csh  type:setenv SUBJECTS_DIR `pwd`
  
  2. If you are re-running after a failed attempt, be sure to 
     clear out the IsRunning* files.
     
     fsCheckJob.sh which will display the location of these files.
     
     or setup the following environment variable
       FREESURFER_IGNORE_ISRUNNING=1