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This script runs TBSS on a batch of images, from initial FA images up to (and not including) the stats stage.

Usage: tbssGroup.sh dataFile [ options ]

Mandatory Arguments:
    
  dataFile         : A file containing your patient group identifier, and image filename.
  
                     Group FileName
                     C     /var/drc/scratch1/...<etc>...<etc>.../01001-001-1.img
                     C     /var/drc/scratch1/...<etc>...<etc>.../01002-001-1.img
                     P     /var/drc/scratch1/...<etc>...<etc>.../01003-001-1.img
                     P     /var/drc/scratch1/...<etc>...<etc>.../01004-001-1.img
                  
                  
                     Group can be any identifier for your group:
                       e.g. 'C' for control, 'P' for patient
                       e.g. 1,2,3
                    
                       DONT put spaces in these identifiers, as we use it to construct a file name.
                       Also, TBSS processes image file names alphabetically, so the group ID should 
                       preferably be selected so that the control group is first. So, C and P are
                       not bad suggestions.

Optional Arguments:

  -s directoryName : Sub-directory name.  The whole study gets put in a subdirectory
                     relative to where you are running this command from.
                     Default is todays date. e.g. 2009-05-11-17-31-38
  
  -e email         : Specify an email address, to be notified upon completion.                    
  -z emailServer   : Specify a mail server, [default smtp.drc.ion.ucl.ac.uk]                    
  -f <int>         : first line in file to start at
  -l <int>         : last line in file to finish at  
  
  -t <float>       : FA Threshold to threshold skeleton at [default 0.2]               

  -o               : FA source image orientation (e.g. as they are stored in Midas) [default LPS]
  -p               : FA target image orientation (e.g. as we want them in TBSS pipeline) [default LAS]

  -a               : Additional image types in datafile, identify from header information and import
  -b <f val>       : Use b0 BET masking on the FA volumes, needs the -a option and a b0 column