cteMaskImageUsingRegions.sh

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This script takes an image, for example containing grey matter probability values, and a 
registered atlas containing region labels, and extracts the specified regions and masks the image.

Usage: cteMaskImageUsingRegions.sh data.nii atlas.nii output.nii [options] 

Mandatory Arguments:

  data.nii                 : The data of interest, for example, grey matter probability values.
  
  atlas.nii                : A registered atlas containing region labels.
  
  output.nii               : Output image
  
Options:

  -regions 1,2,3,4,5       : Comma separated list of region numbers.
  
  -mask_value              : Value with which to mask. Default 1.
                             If you specify 0, then background=1, foreground=0 and the mask is multiplied by the image.
                             If you specify !0, then background=0, foreground is the value you specify, and the mask is injected into the image.
                             
  -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.