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This script takes an image and two MIDAS regions, a ground truth and a segmented example, 
and calculates segmentation statistics, such as Dice and Jaccard.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/propogationCheck.sh baseline.img truth.roi segmented.roi

Mandatory Arguments:

  baseline.img     : An image that has been segmented
  truth.roi        : Ground truth MIDAS segmentation
  segmented.roi    : A segmentation that you want to assess.
                        
Options:

  -output file.txt : Text file to hold output
  -tmpdir dir      : Set temporary workspace directory (If not set, will
                     use environment variable $TMPDIR, and then allocate
                     one in /tmp (e.g., /tmp/propReg.20650) if $TMPDIR not set

  -keeptmp         : Keep temporary workspace directory (default = remove)