updateParcellation.sh

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This script will run a groupwise parcellation update.

Usage: updateParcellation.sh [ options ] AAAAA BBBBB CCCCC DDDDD etc.

  All arguments after the options are directories containing an input VTK file containing the 2 FreeSurfer sphere's + connections derived from tractography.
  
Options:

  -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.
  
  -loopIters               : Maximum number of loop iterations, where we register then update group wise mean.
  
  -regIters                : Maximum number of registration iterations.

  -numLabels               : Number of labels. Default 72, i.e. FreeSurfers 36 for each hemisphere.
  
  -nameInput               : Name of input file (without file extension, as we only process .vtk files).
  
  -nameOutput              : Name of output file (without file extension, as we only process .vtk files).
  
  -smoothingIters          : Number of smoothing iterations
  
  -gamma                   : Gamma for smoothing
  
  -stepSize                : Step size