@measure_bb_thick - compute thickness of mask using ball and box method
usage:
@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
Output:
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:
