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This script is a wrapper which calls Brain-MAPS.sh to perform automated brain segmentation. The input image should be in sagittal slices, unless "-use_orientation yes" is specified for Midas images. 

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/Brain-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:  

  -staple_counts    : a range of number of segmentations to STAPLE [8 8]. 
  -mrf_weighting    : MRF weight after STAPLE [0.2]. 
  -template_library : location of the template library [/var/drc/software/32bit/niftk-data/hippo-template-library]. 
  -dilation_for_f3d : dilation of the mask before F3D nreg [4]. 
  -nreg             : nreg to use (f3d or ffd) [f3d]. 
  -f3d_brain_prereg : f3d to use whole image pre-registration (yes or no) [no]. 
  -areg             : areg to use (air or irtk_areg) [air]. 
  -cpp              : control point spacing [5]. 
  -f3d_energy       : bending energy for f3d [0.01].
  -f3d_iterations   : number of iterations in f3d [300]. 
  -confidence       : confidence used in the STAPLE [0.5]. 
  -vents_or_not     : include vents in the brain segmentation [no]. 
  -remove_dir       : remove results directories to save space [no]. 
  -use_orientation  : use the orientation flag in Midas [no]. 
  -leaveoneout      : apply the leave-one-out test [yes].
  -kmeans           : use kmeans-clustering to determine intensity for condition dilation [no]. 
  -init_9dof        : use 9dof for the global reg initialisatino. 
  -cd_mode          : conditional dilation mode [2]. 
  -blur_9dof        : use bluring in 9dof [no].
  -reset_vox_offset : reset vox_offset to 0 [no].