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This script is a wrapper which calls Hippo-MAPS.sh to perform automated hippocampal segmentation.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/Hippo-MAPS-batch.sh input_file output_dir 

Mandatory Arguments:
 
  input_file : is the input file containing paths to your images and regions. 
  output_dir : is the output directory. 
  
Optional arguements:  

  -mean_brain_intensity : specifiy the mean brain intensity to use [default: from the brain region]. 
  -remove_dir           : remove directories containing intermediate results. 
  -leave_one_out        : do leave one out experiment by skipping the same image name. 
  -library              : option to specify the location of template library index. 
  -threshold (no/upper/lower/both) : specify to use no, upper, lower threshold or both threshold [default: both]. 
  -staple_count a b     : number of segmentations (from a to b) to combine [default: 8 8]. 
  -only_staple          : only combine the results and do not do any registration. 
  -skip_side (no/left/right) : skip process the no, left or right side.