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This script is a convenient wrapper round our NifTK programs to run a symmetric affine registration.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/symmetricReg.sh target.img source.img rreg-out.dof targetOut.img sourceOut.img 

Mandatory Arguments:
 
  target.img             : target (or baseline) image
  source.img             : source (or repeat) image
  rreg-out.dof           : affine registration transformation file
  targetOut.img          : target (or baseline) image resampled to midpoint
  sourceOut.img          : source (or repeat) image resampled to midpoint
      
Options:

  -troi    target.roi    : Target (or baseline) region of interest (MIDAS Format)
  -troiOut targetOut.roi : Target (or baseline) region resampled to midpoint
  
  -sroi    source.roi    : Source (or repeat) region of interest (MIDAS Format)
  -sroiOut sourceOut.roi : Source (or repeat) region resampled to midpoint
  
  -dof n                 : Degrees of freedom for rigid/affine registration [ default 9, use 6, 9 or 12 ]
  -dil m                 : Number of dilations to apply to masks when optimising scaling [ default 8 ]
  
  -tmpdir dir            : Set temporary workspace directory (If not set, will
                           use environment variable $TMPDIR, and then allocate
                           one in /tmp (e.g., /tmp/symmetricReg.20996) if $TMPDIR not set

  -keeptmp               : Keep temporary workspace directory
  
  -justreslice           : If the dof file exists, don't do registration, just 
                           do the reslicing.