@measure_bb_thick - compute thickness of mask using ball and box method
@measure_bb_thick -maskset maskset -surfset surfacedset.gii -outdir thickdir

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
output is in directory thickdir. If not specified, bb_thickdir is used

This script finds thickness by finding the largest sphere or cube that fits
within the mask at each voxel. The cube search has little effect on
surface mapping of thickness, affecting only some edges in the volume.
If one is primarily interested in the surface mapping, then consider
the -balls_only to skip the cube search.

Because of limitations in the growth of the spheres used in this method,
it is recommended to use oversampled data, particularly when using 1mm data
See -resample option below

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 thickdir     output directory

Other options:

  -resample mm   resample input to mm in millimeters (put a number here)
                 set this to half a voxel or \"auto\".
                 No resampling is done by default
                 Resampling is highly recommended for most 1mm data
  -increment mm  test thickness at increments of sub-voxel distance
                 default is 1/4 voxel minimum distance (in-plane)
  -surfsmooth mm smooth surface map of thickness by mm millimeters
                 default is 6 mm
  -smoothmm mm  smooth volume by mm FWHM in mask
                 default is 2*voxelsize of mask or resampled mask
  -maxthick mm   search for maximum thickness value of mm millimeters
                 default is 6 mm
  -depthsearch mm map to surface by looking for max along mm millimeter
                 normal vectors. default is 3 mm
  -keep_temp_files do not delete the intermediate files (for testing)
  -balls_only    calculate only with spheres and skip boxes
  -surfsmooth_method heattype heat method used for smoothing surfaces
                 default is HEAT_07 but HEAT_05 is also useful for models

   maxfill.nii.gz - thickness/depth dataset
   bb_thick.nii.gz - volumetric thickness dataset
   bb_thick_smooth.nii.gz - smoothed volumetric thickness dataset
   bb_thick.niml.dset - unsmoothed thickness mapped to surface nodes
   bb_thick_smooth.niml.dset - smoothed thickness mapped to surface nodes

   Other datasets included in output:
   maskset.nii.gz, maskset_rs.nii.gz - mask and optional resampled mask
   anat.gii - surface representation of mask volume
   quick.spec - simple specification file for surface to use with suma commands

See related scripts and programs for computing thickness: