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Fill lesion volume with simulated WM pixel intensities

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/niftkFillLesions.sh [options] -in input_file -orient <value> -mask mask_file -out output_file

Mandatory arguments: 

  -in     : input file 
  -orient <value> : input images are in AXIAL (a), CORONAL (c) or SAGITALL (s) orientation
  -mask <mask file> : lesion mask file 
  -out <file name>  : file name for new image 

Optional Arguments: 
  -bet      : variations on default BET functionality: B, S, R or Z. (see BET for more information), by default -B
  -f      : fractional intensity threshold (0->1); by default 0.1.
  -b <mask file>  : use existing brain mask file
  -d <dilation>   : dilate lesion mask: none (N), soft 2D (S) or hard 3D (H) [by default none (N)]
  -l <distance>   : length scale of non-uniformity. Default=35 (mm)
  -t2     : T2 image as input [by default T1]
  -debug    : debug (don't delete temporary intermediate images)
  -same     : Always use the same temp directory for computing (this option is useful mixed with -debug)

Advanced Options: 
  -z      : delete orientation to the input mask files
  -r      : swap left/right and delete orientation to the file obtained by nu_correct