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This script is a convenient wrapper round our standard AIR to standard space.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/regAIR-standard-space.sh imageDir regionDir fileContainingImageNames outputDir [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.
  
Option:  
  -rreg_init               : Use rreg for initialisation. 
  -dof9                    : Use 9dof all the way.