Package 'wbcmd'

Title: Wrapper Functions for 'Connectome Workbench' Commands
Description: Provides R wrapper functions for the 'Connectome Workbench' command-line tool ('wb_command'). Includes a central dispatcher for executing workbench commands, environment detection, and convenience wrappers for common operations on Connectivity Informatics Technology Initiative (CIFTI), Geometry Informatics Technology Initiative (GIFTI), and surface files.
Authors: Athanasia Mo Mowinckel [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-5756-0223>)
Maintainer: Athanasia Mo Mowinckel <[email protected]>
License: MIT + file LICENSE
Version: 0.1.0
Built: 2026-05-31 06:56:47 UTC
Source: https://github.com/lcbc-uio/wbcmd

Help Index

Check the result of a workbench command

Description

Validates the outcome of a wb_command execution by inspecting the exit status and whether the expected output file was produced.

Usage

check_wb_result(
  res,
  fe_before = NA,
  fe_after = NA,
  outfile = NULL,
  cmd_name = NULL
)

Arguments

res

The return value from system().
fe_before

Logical; did the output file exist before execution?
fe_after

Logical; does the output file exist after execution?
outfile

Path to the expected output file.
cmd_name

The command name, for diagnostic messages.

Value

res, invisibly.

Examples

check_wb_result(0L, fe_before = FALSE, fe_after = TRUE,
                outfile = "out.nii", cmd_name = "test")

Average multiple CIFTI files

Description

Wraps wb_command -cifti-average to compute the element-wise average across multiple CIFTI files.

Usage

cifti_average(
  cifti_out,
  cifti_in,
  weights = NULL,
  verbose = get_wb_verbosity()
)

Arguments

cifti_out

Path for the output averaged CIFTI file.
cifti_in

Character vector of input CIFTI file paths.
weights

Optional numeric vector of weights (same length as cifti_in).
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-average")in a session with wb_command available.

Examples

## Not run: 
cifti_average(
  "group_mean.dscalar.nii",
  c("subj01.dscalar.nii", "subj02.dscalar.nii", "subj03.dscalar.nii")
)

## End(Not run)

Compute correlation of CIFTI rows

Description

Wraps wb_command -cifti-correlation to generate a row-wise correlation matrix from a CIFTI file.

Usage

cifti_correlation(
  cifti_in,
  cifti_out,
  roi_override = NULL,
  weights = NULL,
  fisher_z = FALSE,
  no_demean = FALSE,
  covariance = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

cifti_in

Path to the input CIFTI file.
cifti_out

Path for the output correlation CIFTI file.
roi_override

Path to a CIFTI ROI file to restrict computation.
weights

Path to a text file of column weights.
fisher_z

Logical; apply Fisher z-transform to correlations?
no_demean

Logical; skip demeaning before correlation?
covariance

Logical; compute covariance instead of correlation?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-correlation")in a session with wb_command available.

Examples

## Not run: 
cifti_correlation(
  "data.dtseries.nii",
  "corr.dconn.nii",
  fisher_z = TRUE
)

## End(Not run)

Dilate a CIFTI file

Description

Wraps wb_command -cifti-dilate to fill in zeros or missing data with values from nearby brainordinates.

Usage

cifti_dilate(
  cifti_in,
  direction = c("COLUMN", "ROW"),
  surface_distance,
  volume_distance,
  cifti_out,
  left_surface = NULL,
  right_surface = NULL,
  nearest = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

cifti_in

Path to the input CIFTI file.
direction

Direction to dilate. One of "COLUMN" or "ROW".
surface_distance

Surface dilation distance in mm.
volume_distance

Volume dilation distance in mm.
cifti_out

Path for the output CIFTI file.
left_surface

Path to the left hemisphere surface.
right_surface

Path to the right hemisphere surface.
nearest

Logical; use nearest good value instead of weighted average?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-dilate")in a session with wb_command available.

Examples

## Not run: 
cifti_dilate(
  "data.dscalar.nii",
  direction = "COLUMN",
  surface_distance = 10,
  volume_distance = 10,
  cifti_out = "dilated.dscalar.nii",
  left_surface = "left.midthickness.surf.gii",
  right_surface = "right.midthickness.surf.gii"
)

## End(Not run)

Find clusters in a CIFTI file

Description

Wraps wb_command -cifti-find-clusters to threshold a CIFTI file and filter clusters by surface area and volume size.

Usage

cifti_find_clusters(
  cifti_in,
  surface_value_threshold,
  surface_minimum_area,
  volume_value_threshold,
  volume_minimum_size,
  direction = c("COLUMN", "ROW"),
  cifti_out,
  left_surface = NULL,
  right_surface = NULL,
  less_than = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

cifti_in

Path to the input CIFTI file.
surface_value_threshold

Minimum value for surface vertices.
surface_minimum_area

Minimum cluster surface area (mm^2).
volume_value_threshold

Minimum value for volume voxels.
volume_minimum_size

Minimum cluster volume size (mm^3).
direction

Direction to use. One of "ROW" or "COLUMN".
cifti_out

Path for the output CIFTI file.
left_surface

Path to the left hemisphere surface.
right_surface

Path to the right hemisphere surface.
less_than

Logical; find clusters below threshold instead of above?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-find-clusters")in a session with wb_command available.

Examples

## Not run: 
cifti_find_clusters(
  "zstats.dscalar.nii",
  surface_value_threshold = 2.3,
  surface_minimum_area = 100,
  volume_value_threshold = 2.3,
  volume_minimum_size = 200,
  direction = "COLUMN",
  cifti_out = "clusters.dscalar.nii",
  left_surface = "left.midthickness.surf.gii",
  right_surface = "right.midthickness.surf.gii"
)

## End(Not run)

Compute gradient of a CIFTI file

Description

Wraps wb_command -cifti-gradient to compute the spatial gradient of each column in a CIFTI file.

Usage

cifti_gradient(
  cifti_in,
  direction = c("COLUMN", "ROW"),
  cifti_out,
  left_surface = NULL,
  right_surface = NULL,
  surface_presmooth = NULL,
  volume_presmooth = NULL,
  average_output = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

cifti_in

Path to the input CIFTI file.
direction

Direction to take gradient. One of "COLUMN" or "ROW".
cifti_out

Path for the output gradient CIFTI file.
left_surface

Path to the left hemisphere surface.
right_surface

Path to the right hemisphere surface.
surface_presmooth

Surface pre-smoothing sigma in mm.
volume_presmooth

Volume pre-smoothing sigma in mm.
average_output

Logical; average the gradient across all maps?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-gradient")in a session with wb_command available.

Examples

## Not run: 
cifti_gradient(
  "data.dscalar.nii",
  direction = "COLUMN",
  cifti_out = "gradient.dscalar.nii",
  left_surface = "left.midthickness.surf.gii",
  right_surface = "right.midthickness.surf.gii"
)

## End(Not run)

Evaluate expression on CIFTI files

Description

Wraps wb_command -cifti-math to perform element-wise mathematical operations on CIFTI files using an expression language.

Usage

cifti_math(
  expression,
  cifti_out,
  var,
  fixnan = FALSE,
  override_mapping_check = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

expression

Math expression string (e.g. "(x - mean) / stdev").
cifti_out

Path for the output CIFTI file.
var

Named list of input CIFTI file paths. Names correspond to variable names used in expression.
fixnan

Logical; replace NaN results with 0?
override_mapping_check

Logical; skip map count check?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-math")in a session with wb_command available.

Examples

## Not run: 
cifti_math(
  "(x - y) / y",
  cifti_out = "pct_change.dscalar.nii",
  var = list(x = "post.dscalar.nii", y = "pre.dscalar.nii")
)

## End(Not run)

Parcellate a CIFTI file

Description

Wraps wb_command -cifti-parcellate to create parcellated data from a dense CIFTI file using a label parcellation.

Usage

cifti_parcellate(
  cifti_in,
  cifti_label,
  direction = c("COLUMN", "ROW"),
  cifti_out,
  spatial_weights = NULL,
  method = NULL,
  only_numeric = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

cifti_in

Path to the input CIFTI file.
cifti_label

Path to the parcellation label file (.dlabel.nii).
direction

Direction to parcellate along. One of "COLUMN" or "ROW".
cifti_out

Path for the output parcellated CIFTI file.
spatial_weights

Optional spatial weights specification. A list with one element: either left_area_surf and right_area_surf paths, or cifti_weights path.
method

Parcellation method. One of "MEAN" (default), "MAX", "MIN", "INDEXMAX", "INDEXMIN", "MEDIAN", "MODE", "COUNT_NONZERO", "SUM", "STDEV", "SAMPSTDEV", "PERCENTILE".
only_numeric

Logical; exclude non-numeric values?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-parcellate")in a session with wb_command available.

Examples

## Not run: 
cifti_parcellate(
  "data.dtseries.nii",
  "atlas.dlabel.nii",
  direction = "COLUMN",
  cifti_out = "parcellated.ptseries.nii"
)

## End(Not run)

Reduce a CIFTI file along a dimension

Description

Wraps wb_command -cifti-reduce to perform a reduction operation (e.g. mean, stdev) along a specified direction.

Usage

cifti_reduce(
  cifti_in,
  direction = c("ROW", "COLUMN"),
  operation = "MEAN",
  cifti_out,
  only_numeric = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

cifti_in

Path to the input CIFTI file.
direction

Direction to reduce. One of "ROW" or "COLUMN".
operation

Reduction operation. One of "MAX", "MIN", "INDEXMAX", "INDEXMIN", "SUM", "PRODUCT", "MEAN", "STDEV", "SAMPSTDEV", "VARIANCE", "TSNR", "COV", "L2NORM", "MEDIAN", "MODE", "COUNT_NONZERO".
cifti_out

Path for the output CIFTI file.
only_numeric

Logical; exclude non-numeric values?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-reduce")in a session with wb_command available.

Examples

## Not run: 
cifti_reduce(
  "data.dtseries.nii",
  direction = "ROW",
  operation = "MEAN",
  cifti_out = "mean.dscalar.nii"
)

## End(Not run)

Compute statistics on a CIFTI file

Description

Wraps wb_command -cifti-stats to compute statistics along CIFTI columns.

Usage

cifti_stats(
  cifti_in,
  operation = NULL,
  percentile = NULL,
  column = NULL,
  roi = NULL,
  show_map_name = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

cifti_in

Path to the input CIFTI file.
operation

Reduction operation. One of "MAX", "MIN", "INDEXMAX", "INDEXMIN", "SUM", "PRODUCT", "MEAN", "STDEV", "SAMPSTDEV", "VARIANCE", "TSNR", "COV", "L2NORM", "MEDIAN", "MODE", "COUNT_NONZERO".
percentile

Numeric percentile to compute (alternative to operation).
column

Integer; compute for a single column only (1-indexed).
roi

Path to a CIFTI ROI file.
show_map_name

Logical; print map name before each result?
verbose

Logical; print command output?

Value

Character vector of output lines (stats values).

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-stats")in a session with wb_command available.

Examples

## Not run: 
cifti_stats("data.dscalar.nii", operation = "MEAN")
cifti_stats("data.dscalar.nii", percentile = 95)

## End(Not run)

Compute weighted statistics on a CIFTI file

Description

Wraps wb_command -cifti-weighted-stats to compute spatially-weighted statistics along CIFTI columns.

Usage

cifti_weighted_stats(
  cifti_in,
  operation = NULL,
  percentile = NULL,
  spatial_weights = FALSE,
  cifti_weights = NULL,
  column = NULL,
  roi = NULL,
  show_map_name = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

cifti_in

Path to the input CIFTI file.
operation

One of "MEAN", "STDEV", "SAMPSTDEV", "SUM".
percentile

Numeric percentile (alternative to operation).
spatial_weights

Logical; use vertex areas and voxel volumes as weights?
cifti_weights

Path to a CIFTI file to use as weights.
column

Integer; compute for a single column only (1-indexed).
roi

Path to a CIFTI ROI file.
show_map_name

Logical; print map name before each result?
verbose

Logical; print command output?

Value

Character vector of output lines (stats values).

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-cifti-weighted-stats")in a session with wb_command available.

Examples

## Not run: 
cifti_weighted_stats("data.dscalar.nii", operation = "MEAN",
                     spatial_weights = TRUE)

## End(Not run)

Display information about a file

Description

Wraps wb_command -file-information to list information about a data file's content.

Usage

file_information(
  data_file,
  only_map_names = FALSE,
  only_number_of_maps = FALSE,
  only_metadata = FALSE,
  only_cifti_xml = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

data_file

Path to the input file.
only_map_names

Logical; show only map names?
only_number_of_maps

Logical; show only number of maps?
only_metadata

Logical; show only metadata?
only_cifti_xml

Logical; show only CIFTI XML (CIFTI files only)?
verbose

Logical; print command output?

Value

Character vector of information lines, invisibly.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-file-information")in a session with wb_command available.

Examples

## Not run: 
file_information("data.dscalar.nii")
file_information("data.dscalar.nii", only_map_names = TRUE)

## End(Not run)

Find the wb_command executable

Description

Searches for the wb_command binary using R options, environment variables, default installation paths, and PATH.

Usage

get_wb_path(simplify = TRUE)

Arguments

simplify

If TRUE, return just the path string. If FALSE, return the full settings list.

Value

Character path to wb_command, or a settings list when simplify = FALSE.

Examples

## Not run: 
get_wb_path()

## End(Not run)

Look up a workbench setting

Description

Resolves a setting by checking R options, then environment variables, then a list of default paths.

Usage

get_wb_setting(opt_var, env_var, defaults = NULL, is_path = TRUE)

Arguments

opt_var

Name of the R option (e.g. "wbcmd.path").
env_var

Name of the environment variable (e.g. "WB_PATH").
defaults

Character vector of fallback values to try.
is_path

If TRUE, checks whether the resolved value exists on disk.

Value

A list with elements value, source, and exists.

Examples

get_wb_setting("wbcmd.path", "WB_PATH", defaults = "/usr/bin")

Get the workbench verbosity setting

Description

Get the workbench verbosity setting

Usage

get_wb_verbosity()

Value

Logical indicating whether verbose output is enabled.

Examples

get_wb_verbosity()

Check if Connectome Workbench is available

Description

Check if Connectome Workbench is available

Usage

have_wb()

Value

TRUE if wb_command is found and executable.

Examples

have_wb()

Evaluate expression on metric files

Description

Wraps wb_command -metric-math to perform element-wise mathematical operations on metric files at each surface vertex.

Usage

metric_math(
  expression,
  metric_out,
  var,
  fixnan = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

expression

Math expression string (e.g. "(x - mean) / stdev").
metric_out

Path for the output metric file.
var

Named list of input metric file paths. Names correspond to variable names used in expression.
fixnan

Logical; replace NaN results with 0?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-metric-math")in a session with wb_command available.

Examples

## Not run: 
metric_math(
  "abs(x - y)",
  metric_out = "diff.func.gii",
  var = list(x = "post.func.gii", y = "pre.func.gii")
)

## End(Not run)

Compute spatial statistics on a metric file

Description

Wraps wb_command -metric-stats to compute spatial statistics on a metric file.

Usage

metric_stats(
  metric_in,
  operation = NULL,
  percentile = NULL,
  column = NULL,
  roi = NULL,
  show_map_name = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

metric_in

Path to the input metric file.
operation

Reduction operation. One of "MAX", "MIN", "INDEXMAX", "INDEXMIN", "SUM", "PRODUCT", "MEAN", "STDEV", "SAMPSTDEV", "VARIANCE", "TSNR", "COV", "L2NORM", "MEDIAN", "MODE", "COUNT_NONZERO".
percentile

Numeric percentile to compute (alternative to operation).
column

Integer; compute for a single column only (1-indexed).
roi

Path to a metric ROI file.
show_map_name

Logical; print map name before each result?
verbose

Logical; print command output?

Value

Character vector of output lines (stats values).

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-metric-stats")in a session with wb_command available.

Examples

## Not run: 
metric_stats("thickness.func.gii", operation = "MEAN")

## End(Not run)

Set the path to wb_command

Description

Set the path to wb_command

Usage

set_wb_path(path, check = TRUE)

Arguments

path

Path to the wb_command executable.
check

If TRUE, verify the path exists before setting.

Value

The previous value of the option, invisibly.

Examples

## Not run: 
set_wb_path("/opt/workbench/bin/wb_command")

## End(Not run)

Compute surface curvature

Description

Wraps wb_command -surface-curvature to compute mean and/or Gaussian curvature of a surface.

Usage

surface_curvature(
  surface_in,
  mean_out = NULL,
  gauss_out = NULL,
  verbose = get_wb_verbosity()
)

Arguments

surface_in

Path to the input surface file.
mean_out

Path for the output mean curvature metric file.
gauss_out

Path for the output Gaussian curvature metric file.
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-surface-curvature")in a session with wb_command available.

Examples

## Not run: 
surface_curvature(
  "lh.midthickness.surf.gii",
  mean_out = "lh.mean_curv.func.gii"
)

## End(Not run)

Measure distortion between surfaces

Description

Wraps wb_command -surface-distortion to compute distortion between two surfaces on the same mesh.

Usage

surface_distortion(
  surface_reference,
  surface_distorted,
  metric_out,
  smooth = NULL,
  caret5_method = FALSE,
  edge_method = FALSE,
  local_affine_method = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

surface_reference

Path to the reference surface.
surface_distorted

Path to the distorted surface.
metric_out

Path for the output distortion metric file.
smooth

Smoothing sigma for area distortion (mm). Only used with the default area-based method.
caret5_method

Logical; use the Caret5 method?
edge_method

Logical; use edge-based distortion?
local_affine_method

Logical; use local affine method?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-surface-distortion")in a session with wb_command available.

Examples

## Not run: 
surface_distortion(
  "lh.sphere.surf.gii",
  "lh.sphere.reg.surf.gii",
  "lh.distortion.func.gii"
)

## End(Not run)

Generate inflated surface

Description

Wraps wb_command -surface-generate-inflated to create inflated and very-inflated surfaces from an anatomical surface.

Usage

surface_generate_inflated(
  anatomical_surface,
  inflated_out,
  very_inflated_out,
  iterations_scale = NULL,
  verbose = get_wb_verbosity()
)

Arguments

anatomical_surface

Path to the input anatomical surface file.
inflated_out

Path for the output inflated surface.
very_inflated_out

Path for the output very-inflated surface.
iterations_scale

Scale factor for inflation iterations. Default is 1.0; use 2.5 for 164k meshes.
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-surface-generate-inflated")in a session with wb_command available.

Examples

## Not run: 
surface_generate_inflated(
  "lh.midthickness.surf.gii",
  "lh.inflated.surf.gii",
  "lh.very_inflated.surf.gii"
)

## End(Not run)

Compute geodesic distance from a vertex

Description

Wraps wb_command -surface-geodesic-distance to compute the geodesic distance from a single vertex to all other vertices on a surface.

Usage

surface_geodesic_distance(
  surface_in,
  vertex,
  metric_out,
  limit = NULL,
  corrected_areas = NULL,
  verbose = get_wb_verbosity()
)

Arguments

surface_in

Path to the input surface file.
vertex

Index of the source vertex (0-indexed).
metric_out

Path for the output metric file.
limit

Maximum geodesic distance in mm. Vertices beyond this distance get value -1.
corrected_areas

Path to a metric file of corrected vertex areas (for group-average surfaces).
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-surface-geodesic-distance")in a session with wb_command available.

Examples

## Not run: 
surface_geodesic_distance(
  "lh.midthickness.surf.gii",
  vertex = 0,
  metric_out = "geodesic.func.gii",
  limit = 100
)

## End(Not run)

Display surface information

Description

Wraps wb_command -surface-information to print summary information about a surface file (vertices, triangles, bounding box, spacing).

Usage

surface_information(surface_in, verbose = get_wb_verbosity())

Arguments

surface_in

Path to the input surface file.
verbose

Logical; print command output?

Value

Character vector of information lines, invisibly.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-surface-information")in a session with wb_command available.

Examples

## Not run: 
surface_information("lh.midthickness.surf.gii")

## End(Not run)

Compute vertex areas of a surface

Description

Wraps wb_command -surface-vertex-areas to measure the surface area (in mm^2) that each vertex is responsible for.

Usage

surface_vertex_areas(surface_in, metric_out, verbose = get_wb_verbosity())

Arguments

surface_in

Path to the input surface file.
metric_out

Path for the output metric file.
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-surface-vertex-areas")in a session with wb_command available.

Examples

## Not run: 
surface_vertex_areas(
  "lh.midthickness.surf.gii",
  "lh.vertex_areas.func.gii"
)

## End(Not run)

Evaluate expression on volume files

Description

Wraps wb_command -volume-math to perform element-wise mathematical operations on volume files at each voxel.

Usage

volume_math(
  expression,
  volume_out,
  var,
  fixnan = FALSE,
  verbose = get_wb_verbosity()
)

Arguments

expression

Math expression string (e.g. "(x - y) / y * 100").
volume_out

Path for the output volume file.
var

Named list of input volume file paths. Names correspond to variable names used in expression.
fixnan

Logical; replace NaN results with 0?
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-volume-math")in a session with wb_command available.

Examples

## Not run: 
volume_math(
  "clamp(x, 0, 100)",
  volume_out = "clamped.nii.gz",
  var = list(x = "input.nii.gz")
)

## End(Not run)

Map volume data to a surface

Description

Wraps wb_command -volume-to-surface-mapping to project volume data onto a surface mesh.

Usage

volume_to_surface_mapping(
  volume_in,
  surface,
  metric_out,
  method = c("trilinear", "enclosing", "cubic", "ribbon-constrained", "myelin-style"),
  inner_surface = NULL,
  outer_surface = NULL,
  verbose = get_wb_verbosity()
)

Arguments

volume_in

Path to the input volume file.
surface

Path to the surface to map onto.
metric_out

Path for the output metric file.
method

Mapping method. One of "trilinear", "enclosing", "cubic", "ribbon-constrained", "myelin-style".
inner_surface

Path to the inner surface (required for "ribbon-constrained" and "myelin-style").
outer_surface

Path to the outer surface (required for "ribbon-constrained" and "myelin-style").
verbose

Logical; print command output?

Value

The result of the underlying wb_cmd() call.

Connectome Workbench Help

Connectome Workbench is not installed. Run wb_help("-volume-to-surface-mapping")in a session with wb_command available.

Examples

## Not run: 
volume_to_surface_mapping(
  "bold.nii.gz",
  "lh.midthickness.surf.gii",
  "lh.bold.func.gii",
  method = "ribbon-constrained",
  inner_surface = "lh.white.surf.gii",
  outer_surface = "lh.pial.surf.gii"
)

## End(Not run)

Execute a Connectome Workbench command

Description

Central dispatcher for all wb_command operations. Command wrappers call this function to construct, execute, and validate workbench commands.

Usage

wb_cmd(
  cmd,
  args = character(),
  ...,
  verbose = get_wb_verbosity(),
  intern = verbose
)

Arguments

cmd

The wb_command subcommand (e.g. "-cifti-separate").
args

Character vector of arguments to pass after cmd.
...

Additional arguments, currently unused.
verbose

Logical; print command output? Defaults to get_wb_verbosity().
intern

Logical; capture output as character vector? Defaults to the value of verbose.

Value

If intern = TRUE, a character vector of command output. Otherwise the exit status (integer).

Examples

## Not run: 
wb_cmd("-version")
wb_cmd("-cifti-separate", c("input.dscalar.nii", "COLUMN"))

## End(Not run)

Access wb_command help text

Description

Retrieves the help text for a given wb_command subcommand.

Usage

wb_help(cmd = NULL)

Arguments

cmd

The subcommand to get help for (e.g. "-cifti-separate"). If NULL, shows the top-level help listing all subcommands.

Value

Character vector of help text lines, invisibly.

Examples

## Not run: 
wb_help()
wb_help("-cifti-separate")

## End(Not run)

Render wb_command CLI help as Rd markup

Description

Called at render time by ⁠\Sexpr⁠ in generated .Rd files. Returns valid Rd markup showing CLI help or a fallback message.

Usage

wb_help_rd(cmd)

Arguments

cmd

The wb_command subcommand (e.g. "-cifti-average").

Value

Character string of Rd markup.

Examples

## Not run: 
wb_help_rd("-cifti-average")

## End(Not run)

Situation report for Connectome Workbench

Description

Prints a diagnostic summary of the workbench environment, including path detection, version, and system information.

Usage

wb_sitrep()

Value

A list of diagnostic information, invisibly.

Examples

## Not run: 
wb_sitrep()

## End(Not run)

Get Connectome Workbench version

Description

Get Connectome Workbench version

Usage

wb_version()

Value

Character string with the workbench version, or an empty string if unavailable.

Examples

## Not run: 
wb_version()

## End(Not run)