@thickness_master -maskset maskset -surfset surfacedset.gii -outdir basethickdir

where maskset is the dataset to find thickness
 using the largest non-zero value in the mask.
 If dataset has values -2,-1 and 1 for different regions, this script
 calculates the thickness only for voxels with a value of 1
surfset is a surface to use to find normals into the volume
outdirbase is in directory thickdirbase_.... If not specified, the default is thick

This script calls the three types of thickness scripts
  @measure_bb_thick - ball and box method
  @measure_erosion_thick - erosion method
  @measure_in2out_thick - in2out method

Main options:
  -maskset mydset      mask dataset for input
  -surfset mydset.gii  surface dataset onto which to map thickness
                       (probably a pial/gray matter surface)
  -outdir thick_base output directory basename. The output will be placed
                 in a directory with thick_base in its name:
                    mmmm_bb, mmmm_erode, mmmm_in2out

Other options:

  takes all options from the three @measure_... scripts

   see Output section of help for each of the method scripts
   This script produces a quick visualization script to see
   thickness maps in suma for all three methods
See related scripts and programs for computing thickness: