regAIR.sh

(Note: This page is automatically generated. Please do not attempt to edit it!)

This script is a convenient wrapper round our standard AIR and BSI process.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/regAIR.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 writen to.
  
Options:

  -m 6|9|12                : the registration model DOF           [default 9   ]
  -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 integer               : number of dilations to apply to mask [default 0   ]
  -s 2|3                   : 2|3 the number of stages             [default 3   ]
                             If you put a minus before the number, the registration ONLY does that stage.
                             ie. -s -3 means, JUST do stage 3.
  -x 1|2|3                 : cost function in alignlinear         [default 1   ]
  -dbc                     : include differential bias correction [default off ]
  -mayo                    : mayo style                           [default off ]
                             This sets:
                               -t2 = max image value
                               -r 100, -h 30
                               -e2 off, i.e. no repeat mask
                               -q  off
                               
  -justdbc                 : for running just the dbc in case you forgot it!                               
                             Assumes you already ran the registration via this script,
                             as it looks for certain files that this script creates.
                             
  -air_init air_init       : Use the input air init file for initialisation.