(Note: This page is automatically generated. Please do not attempt to edit it!)
This script will re-run FreeSurfer after you have made various edits.

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

  All arguments after fsRerunAfterEdits.sh are FreeSurfer directories under the current directory.
  
Mandatory Arguments:

  -c              : If you edited control points
  -w              : If you edited white matter
  -b              : If you edited brain volume
  
Options are:

  -no-vents-fix           : Don't use our vents fix.        [ default is to use it ] 
  -start                  : Step to start at                [ default 2 ie. auto-recon2]
  -stop                   : Step to stop at                 [ default 3 ie. auto-recon3]
  -reconall " options "   : Any additiopnal options to pass to recon-all, in quotes.  
  -r2 " options "         : Any additional options to pass to autorecon2, in quotes.
  -r3 " options "         : Any additional options to pass to autorecon3, in quotes.
  -expert                 : Name of an expert options file
  -echo                   : Just echo the command, don't actually do it.
  

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