(Note: This page is automatically generated. Please do not attempt to edit it!)
MIDAS FFD Region propogation script. Performs an affine + FFD registration
of baseline.img to repeat.img, and uses the transformation to propogate
baseline.roi onto the repeat.img, with repeat.roi the output. 
The FFD proceeds in 32mm, 16mm and 8mm control point spacings.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/propogateRegion.sh baseline.img repeat.img baseline.roi repeat.roi [-options]

Mandatory Arguments:

  baseline.img      : Baseline image that has had a segmentation done
  baseline.roi      : Baseline brain region  
  repeat.img        : Repeat image, not segmented
  repeat.roi        : Repeat brain region, to be computed

Options:

  -areg             : Perform affine registration only
  -coarse           : Perform affine + coarse FFD registration only (32mm)
  -xsubject         : Scans are cross subject, go down to 4mm control point spacings
  -morph            : Perform morphological operations to tidy up region.
                    : (Ops = 1 unconditional erosion, 2 60%-160% mean brain dils)
  -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/propReg.20613) if $TMPDIR not set

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