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This script is a wrapper which calls ffdareg.sh, which calls ITK++ areg.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/regAREG.sh imageDir regionDir fileContainingImageNames outputDir parameterFile [options ]

Mandatory Arguments:
 
  imageDir                 : is the directory containing your images
  regionDir                : is the directory containing your regions
  fileContainingImageNames : is a file containing:
  
                             baselineImage baselineMask repeatImage repeatMask
                             eg.
                             01727-003-1_resc        Mat_01727_1196694584    03061-003-1_resc        Pro_03061_1197570313

  outputDir                : is where the output is writen to.
  parameterFile            : Compulsory parameter file. Look under midasffd package for examples.
    
Options:

  -m 6|9|12                : the registration model DOF           [default 9   ]
  -l 0.0<->1.0             : is the lower BSI threshold           [default 0.45]
  -u 0.0<->1.0             : is the upper BSI threshold           [default 0.65]
  -d integer               : number of dilations to apply to mask [default 0   ]  
  -dbc                     : include differential bias correction [default off ]  
  -justdbc                 : for running just the dbc in case you forgot it!                               
                             Assumes you already ran the registration via this script,
                             as it looks for certain files that this script creates.