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
[-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
[-affine] - use an affine transformation on 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
[-warpfield] - use a warpfield on 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
[-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
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 'nearest' method, 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
ENCLOSING_VOXEL. 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
The <surface-method> argument must be one of the following:
ADAP_BARY_AREA
BARYCENTRIC