(Note: This page is automatically generated. Please do not attempt to edit it!)
This script runs a scaling algorithm based loosely on Freeborough Fox JCAT 20(6) 1996, 1012-1022,
except this is all intensity based, and needs a special version of areg.

Also requires FSL to be installed.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/regADNIScaling.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 written to.

Options:

  -l 0.0<->1.0             : is the lower BSI threshold                   [default 0.45]
  -u 0.0<->1.0             : is the upper BSI threshold                   [default 0.65]
  -d                       : number of dilations to apply to skull mask   [default 5   ]
  -i                       : number of iterations between m DOF and 3 DOF [default 2   ]
  -pbrain                  : params file for brain reg                    
  -pskull                  : params file for skull reg