(Note: This page is automatically generated. Please do not attempt to edit it!)
Takes a segmented GM/WM/CSF labelled image, and refines it by using Chloe Hutton's
method of growing the GM outwards, calculating thickness, and detecting sulci voxels.
See: Hutton et. al. NeuroImage 2008 paper: doi:10.1016/j.neuroimage.2008.01.027

Usage: cteRefineLabelImage.sh label.nii output.nii [options] 

Mandatory Arguments:

    label.nii              : Label image, containing exactly 3 distinct values, corresponding
                             to GM, WM, CSF. Default is assumed to be WM=1, GM=2, CSF=3
                      
    output.nii             : The output.
    
Options:

    -white                 : The white value in label.nii. Default 1

    -grey                  : The grey value in label.nii. Default 2
        
    -csf                   : The csf value in label.nii. Default 3

    -tmproot <directory>   : Define a root directory for temporary files. Default /tmp
                             The difference between this option and the next, is that this
                             one takes the root directory (eg. /tmp) and creates a sub directory
                             with a process ID in it. (eg. /tmp/seg.1234) whereas the next option
                             just uses exactly what you give it.
                            
    -tmpdir <directory>    : Set temporary workspace directory.

    -keeptmp               : Keep temporary workspace directory