Workbench Command is a set of command-line tools that can be used to perform simple and complex operations within Connectome Workbench.
RESAMPLE A CIFTI FILE TO A NEW CIFTI SPACE
wb_command -cifti-resample
<cifti-in> - the cifti file to resample
<direction> - the direction of the input that should be resampled, ROW or
COLUMN
<cifti-template> - a cifti file containing the cifti space to resample to
<template-direction> - the direction of the template to use as the
resampling space, ROW or COLUMN
<surface-method> - specify a surface resampling method
<volume-method> - specify a volume interpolation method
<cifti-out> - output - the output cifti file
[-smooth-edges] - smooth the probability maps before the popularity step,
to reduce jaggedness at the cost of fidelity
<kernel-size> - the smoothing amount to use, gaussian sigma in mm
[-fwhm] - use specified kernel size as full width at half maximum,
rather than sigma
[-surface-largest] - use largest weight instead of weighted average or
popularity when doing surface resampling
[-volume-predilate] - dilate the volume components before resampling
<dilate-mm> - distance, in mm, to dilate
[-nearest] - use nearest value dilation
[-weighted] - use weighted dilation (default)
[-exponent] - specify exponent in weighting function
<exponent> - exponent 'n' to use in (1 / (distance ^ n)) as the
weighting function (default 7)
[-legacy-cutoff] - use v1.3.2 logic for the kernel cutoff
[-surface-postdilate] - dilate the surface components after resampling
<dilate-mm> - distance, in mm, to dilate
[-nearest] - use nearest value dilation
[-linear] - use linear dilation
[-weighted] - use weighted dilation (default for non-label data)
[-exponent] - specify exponent in weighting function
<exponent> - exponent 'n' to use in (area / (distance ^ n)) as
the weighting function (default 6)
[-legacy-cutoff] - use v1.3.2 logic for the kernel cutoff
[-left-spheres] - specify spheres for left surface resampling
<current-sphere> - a sphere with the same mesh as the current left
surface
<new-sphere> - a sphere with the new left mesh that is in register
with the current sphere
[-left-area-surfs] - specify left surfaces to do vertex area
correction based on
<current-area> - a relevant left anatomical surface with current
mesh
<new-area> - a relevant left anatomical surface with new mesh
[-left-area-metrics] - specify left vertex area metrics to do area
correction based on
<current-area> - a metric file with vertex areas for the current
mesh
<new-area> - a metric file with vertex areas for the new mesh
[-right-spheres] - specify spheres for right surface resampling
<current-sphere> - a sphere with the same mesh as the current right
surface
<new-sphere> - a sphere with the new right mesh that is in register
with the current sphere
[-right-area-surfs] - specify right surfaces to do vertex area
correction based on
<current-area> - a relevant right anatomical surface with current
mesh
<new-area> - a relevant right anatomical surface with new mesh
[-right-area-metrics] - specify right vertex area metrics to do area
correction based on
<current-area> - a metric file with vertex areas for the current
mesh
<new-area> - a metric file with vertex areas for the new mesh
[-cerebellum-spheres] - specify spheres for cerebellum surface resampling
<current-sphere> - a sphere with the same mesh as the current
cerebellum surface
<new-sphere> - a sphere with the new cerebellum mesh that is in
register with the current sphere
[-cerebellum-area-surfs] - specify cerebellum surfaces to do vertex
area correction based on
<current-area> - a relevant cerebellum anatomical surface with
current mesh
<new-area> - a relevant cerebellum anatomical surface with new mesh
[-cerebellum-area-metrics] - specify cerebellum vertex area metrics to
do area correction based on
<current-area> - a metric file with vertex areas for the current
mesh
<new-area> - a metric file with vertex areas for the new mesh
[-affine] - repeatable - add an affine transformation for the volume
components
<affine-file> - the affine file to use
[-flirt] - MUST be used if affine is a flirt affine
<source-volume> - the source volume used when generating the affine
<target-volume> - the target volume used when generating the affine
[-affine-series] - repeatable - add an independent affine per-map for the
volume components
<affine-series> - text file containing 12 or 16 numbers per line, each
being a row-major flattened affine
[-flirt] - MUST be used if the affines are flirt affines
<source-volume> - the source volume used when generating the affine
<target-volume> - the target volume used when generating the affine
[-warpfield] - repeatable - add a warpfield for the volume components
<warpfield> - the warpfield to use
[-fnirt] - MUST be used if using a fnirt warpfield
<source-volume> - the source volume used when generating the
warpfield
Resample cifti data to a different brainordinate space. Use COLUMN for
the direction to resample dscalar, dlabel, or dtseries. Resampling both
dimensions of a dconn requires running this command twice, once with
COLUMN and once with ROW. If you are resampling a dconn and your machine
has a large amount of memory, you might consider using
-cifti-resample-dconn-memory to avoid writing and rereading an
intermediate file. The <template-direction> argument should usually be
COLUMN, as dtseries, dscalar, and dlabel all have brainordinates on that
direction. If spheres are not specified for a surface structure which
exists in the cifti files, its data is copied without resampling or
dilation. Dilation is done with the 'weighted' method by default (except
for label data on the surface - volume label data uses weighted
popularity logic by default), and is done on <new-sphere> for surface
data. Volume components are padded before dilation so that dilation
doesn't run into the edge of the component bounding box. If neither
-affine nor -warpfield are specified, the identity transform is assumed
for the volume data.
The recommended resampling methods are ADAP_BARY_AREA and CUBIC (cubic
spline), except for label data which should use ADAP_BARY_AREA and LABEL.
Using ADAP_BARY_AREA requires specifying an area option to each used
-*-spheres option.
The <volume-method> argument must be one of the following:
CUBIC
ENCLOSING_VOXEL
TRILINEAR
LABEL
The <surface-method> argument must be one of the following:
ADAP_BARY_AREA
BARYCENTRIC