@surf_to_vol_spackle.csh
usage:
@surf_to_vol_spackle -maskset mymask.nii.gz -spec mysurfs.spec \
-surfA smoothwm -surfB pial -surfset thickness.niml.dset \
-prefix vol_thick
Project data from a surface dataset into a volume primarily using
3dSurf2Vol but then filling any holes with an iterative smoothing
procedure. If two surfaces are provided, then the dataset is filled
between corresponding nodes. The filling is done by smoothing the
holes with a local non-zero mean (or mode) in a spherical neighborhood.
Holes come about because the lines from surfaces can miss some voxels.
These are more likely with sparse surfaces, but can still happen
even with high-resolution surfaces.
Required (mostly) options:
-maskset mymask.nii mask dataset in which to project surface measures
-spec mysurfs.spec Surface specification file with list of surfaces
-surfA mysurf1 nameof first surface, e.g. smoothwm, pial,....
-surfB mysurf2 name of second surface.
If not included, computes using normal vector
-surfset data.niml.dset dataset of surface measures
-prefix mmmm basename of output. Final name used is prefix.nii.gz
Other options:
-f_pn_mm mm.m normal vector length if only using a single surface
(default 2 mm) (only applies if no surfB used)
-meanrad mm.m radius for search for mean to fill holes
(default 2 mm)
-nsteps nn number of steps on line segments (default 10)
-keep_temp_files do not remove any of the temporary files
(default is to remove them)
-maxiters nn maximum number of smoothing and filling iterations
(default is 4)
-mode use mode instead of non-zero median (appropriate for ROIs)
-datum cccc set datum type to byte, short or float
instead of maskset type. mode triggers -datum short
-ignore_unknown_options ignore additional options that are not needed
Example usage:
@surf_to_vol_spackle -maskset leftmask_1mm.nii.gz -spec quick.spec \
-surfA anat.gii -surfset v2s_inout_max_smooth2mm.niml.dset \
-prefix vol_thick_ave -maxiters 10
See related scripts and programs:
