@measure_erosion_thick - compute thickness of mask using erosion method
@measure_erosion_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, erosion_thickdir is used

This script finds thickness by eroding voxels away, using facing voxels
a layer at a time.

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
  -surfsmooth mm smooth surface map of thickness by mm millimeters
                 default is 8 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)
  -surfsmooth_method heattype heat method used for smoothing surfaces
                 default is HEAT_07 but HEAT_05 is also useful for models

   erosion_depth.nii.gz - depth dataset
   erosion_thick.nii.gz - volumetric thickness dataset
   erosion_thick_smooth.nii.gz - smoothed volumetric thickness dataset
   erosion_thick.niml.dset - unsmoothed thickness mapped to surface nodes
   erosion_thick_smooth_nn_mm.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: