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This script will import data into the standard FreeSurfer directory structure.
 
Usage: fsImport.sh dataFile [ options ]
 
Mandatory Arguments:

  dataFile      : A file containing your patient names and details, like this:

                  Patient ImageType Image         Mask                 WhichMask     
                  ALLFR   I         02979-002-1   Nic_02979_1140620563 002       
                  ALLHA   I         03920-002-1   Nic_03920_1351234123 002       

                  The ImageType column must have: 
                    "I" if the Image column contains an image name
                    "S" if the Image column contains a study number
                           
                  The Image column must be:
                    a study number                       - e.g. 02979
                    or proper image name.                - e.g. 03920-002-1
                                      
                  The WhichMask column should have:
                    If ImageType=S, then a series number - e.g. 002
                    If ImageType=I, then anything you like, as it's not used
                    
Options:

  -b beginRow   : is the start row in the dataFile.
  -e endRow     : is the end row in the dataFile.
  
  -o ax|cor|sag : re-orient the images as they are imported.
  
  -s directory  : is the scans directory [ default is <current_dir>/scans ]
  -m directory  : is the masks directory [ default is <current_dir>/masks ]