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This script runs TBSS stats on a batch of images.

Usage: tbssBasicStats.sh directory [-g <int> <int> | -d <design.mat> <design.con> ] [ options ]

Mandatory Arguments:
    
  directory                : A directory containing a TBSS study
  
                             EITHER
                     
  -g <int> <int>           : -g followed by exactly two numbers indicating the numbers
                             in your control group and numbers in your patient group.
                             This script then generates the most basic 2 group comparison
                             by calling "design_ttest2 design <int> <int>" as mentioned
                             on FSL webpage.
                     
                             OR
                     
  -d <filename> <filename> : -d followed by two filenames, corresponding to your
                             design matrix and contast matrix.
                                                  
                             Note, the groups are processed alphabetically in tbssGroup.sh 
                             (the last script you ran).
                     
Optional Arguments:
                  
  -n <int>                 : Number of permutations [default 500, set to 0 for exhaustive ]
  -e email                 : Specify an email address, to be notified upon completion.                    
  -z emailServer           : Specify a mail server, [default smtp.drc.ion.ucl.ac.uk]                    
  -t ImageType             : Compute stats for a type other than FA, ImageType should match the column header use in the datafile for tbssGroup.sh