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This script will run the brain cropping algorithm (ask Jo or Nicky) on a whole set of images.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/flCrop.sh fileContainingListOfFiles [ options ] 

Mandatory Arguments:
  fileContainingListOfFiles : is a text file containing 3 columns, containing the full path of your region, baseline image and repeat image.
                            : optional 4th column to contain the repeat mask. 
  
Options:
  -f firstRoundOfDilations     : is an integer number of dilations.             [Default 3   ]
  -s secondRoundOfDilations    : is an integer number of dilations.             [Default 2   ]
  -g gaussianFWHM              : is a decimal FWHM in mm for Gaussian blurring. [Default 2mm.]