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MIDAS niftkFFD registration driver. This script is used as a MIDAS
wrapper to the NifTK program niftkFFD for Free Form Deformation.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/regFFD.sh target.img source.img nreg-out.dof [-options]

Where

  target.img = target (or baseline) image
  source.img = source (or repeat) image (image to be warped)
  nreg-out.dof = Freeform registration transformation file
  
and [-options] are any of:

  -troi target.roi
              Target (or baseline) region of interest (MIDAS Format)

  -sroi source.roi
              Source (or repeat) region of interest (MIDAS Format)           
  
  -jac  jacobian.hdr
              Image of jacobian values
              
  -str  filename.str
              MIDAS stretch file 
              
  -vec  filename.vec
              MIDAS vec file

  -res  filename.hdr
              Resampled output image

  -dil n      Number of dilations outside target.roi (if specified by -troi)
              in order to give the freeform deformation room to move
              (Default = 4)

  -inc res n  Resolution steps where res = final (smallest) control point spacing in mm 
              (Default = 2.5) and n = number of resolutions levels 
              (Default = 3)
              
  -lev b e    Which resolution levels to do
              b = begin (start at 0, default 0)
              e = end   (goes up to number of resolutions levels minus 1, default 2)
              
  -adof affine.dof
              Affine dof filename

  -invertAffine
              Invert the affine transformation.
                             
  -F3D        Use F3D recalage for Free Form Deformation
  
  -tmpdir dir Set temporary workspace directory (If not set, will
              use environment variable $TMPDIR, and then allocate
              one in /tmp (e.g., /tmp/regFFD.20924) if $TMPDIR not set

  -keeptmp    Keep temporary workspace directory (default = remove)

  -interp [int] where int is 1 (Nearest), 2 (Linear), 3 (BSpline), 4 (Sinc),
              to specify interpolation mode for resampled image
              
  -iters [int] to specify the number of iterations