:orphan: .. _ahelp_@measure_bb_thick: ***************** @measure_bb_thick ***************** .. contents:: :local: | .. code-block:: none @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: