@measure_erosion_thick - compute thickness of mask using erosion method
usage:
@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
Output:
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:
