Provided by: connectome-workbench_1.4.2-1build1_amd64 
NAME
wb_command - command-line program for performing a variety of algorithmic tasks using
volume, surface, and grayordinate data
SYNOPSIS
<class-name>
DESCRIPTION
-add-to-spec-file ADD A FILE TO A SPECIFICATION FILE
wb_command -add-to-spec-file
<specfile> - the specification file to add to <structure> - the structure of the
data file <filename> - the path to the file
The resulting spec file overwrites the existing spec file.
If the spec
file doesn't exist, it is created with default metadata.
The structure
argument must be one of the following:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-annotation-resample RESAMPLE AN ANNOTATION FILE TO DIFFERENT MESHES
wb_command -annotation-resample
<annotation-in> - the annotation file to resample <annotation-out> - name of
resampled annotation file
[-surface-pair] - repeatable - pair of surfaces for resampling surface
annotations for one structure <source-surface> - the midthickness surface of the
current mesh the
annotations use
<target-surface> - the midthickness surface of the mesh the
annotations should be transferred to
Resample an annotation file from the source mesh to the target mesh.
Only annotations in surface space are modified, no changes are made to annotations
in other spaces. The -surface-pair option may be repeated for additional
structures used by surface space annotations.
-backend-average-dense-roi CONNECTOME DB BACKEND COMMAND FOR CIFTI AVERAGE DENSE ROI
wb_command -backend-average-dense-roi
<index-list> - comma separated list of cifti indexes to average <out-file> - file
to write the average row to
This command is probably not the one you are looking for, try
-cifti-average-dense-roi. It takes the list of cifti files to average from
standard input, and writes its output as little endian, 32-bit integer of row size
followed by the row as 32-bit floats.
-backend-average-roi-correlation CONNECTOME DB BACKEND COMMAND FOR CIFTI AVERAGE ROI
CORRELATION
wb_command -backend-average-roi-correlation
<index-list> - comma separated list of cifti indexes to average and then
correlate
<out-file> - file to write the average row to
This command is probably not the one you are looking for, try
-cifti-average-roi-correlation. It takes the list of cifti files to average from
standard input, and writes its output as little endian, 32-bit integer of row size
followed by the row as 32-bit floats.
-border-export-color-table WRITE BORDER NAMES AND COLORS AS TEXT
wb_command -border-export-color-table
<border-file> - the input border file <table-out> - output - the output text file
[-class-colors] - use class colors instead of the name colors
Takes the names and colors of each border, and writes it to the same format as
-metric-label-import expects. By default, the borders are colored by border name,
specify -class-colors to color them by class instead. The key values start at 1
and follow the order of the borders in the file.
-border-file-export-to-caret5 EXPORT BORDER FILE TO CARET5 FILE FORMAT
wb_command -border-file-export-to-caret5
<border-file> - workbench border file <output-file-prefix> - prefix for name of
output caret5
border/borderproj/bordercolor files
[-surface] - repeatable - specify an input surface
<surface-in> - a surface file for unprojection of borders
A Workbench border file may contain borders for multiple structures and borders
that are both projected and unprojected. It also contains a color table for the
borders.
Caret5 has both border (unprojected) and border projection (projected) files. In
addition, each Caret5 border or border projection file typically contains data for
a single structure. Caret5 also uses a border color file that associates colors
with the names of the borders.
This command will try to output both Caret5 border and border projection files.
Each output border/border projection file will contains data for one structure so
there may be many files created. The structure name is included in the name of
each border or border projection file that is created.
One Caret5 border color file will also be produced by this command.
Providing surface(s) as input parameters is optional, but recommended. Surfaces
may be needed to create both projected and/or unprojected coordinates of borders.
If there is a failure to produce an output border or border projection due to a
missing surface with the matching structure, an error message will be displayed and
some output files will not be created.
When writing new files, this command will overwrite a file with the same name.
-border-length REPORT LENGTH OF BORDERS
wb_command -border-length
<border> - the input border file <surface> - the surface to measure the borders on
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
[-separate-pieces] - report lengths for multi-part borders as separate
numbers
[-hide-border-name] - don't print border name before each output
For each border, print its length along the surface, in mm.
If a border
has multiple parts, their lengths are summed before printing, unless
-separate-pieces is specified.
The -corrected-areas option is intended for when the length is not meaningfully
measurable on individual surfaces, it is only an approximate correction for the
reduction in structure of a group average surface.
-border-merge MERGE BORDER FILES INTO A NEW FILE
wb_command -border-merge
<border-file-out> - output - the output border file
[-border] - repeatable - specify an input border file
<border-file-in> - a border file to use borders from
[-select] - repeatable - select a single border to use
<border> - the border number or name
[-up-to] - use an inclusive range of borders
<last-border> - the number or name of the last column to include
[-reverse] - use the range in reverse order
Takes one or more border files and makes a new border file from the borders in
them.
Example: wb_command -border-merge out.border -border first.border -select 1 -border
second.border
This example would take the first border from first.border, followed by all borders
from second.border, and write these to out.border.
-border-resample RESAMPLE A BORDER FILE TO A DIFFERENT MESH
wb_command -border-resample
<border-in> - the border file to resample <current-sphere> - a sphere surface with
the mesh that the metric is
currently on
<new-sphere> - a sphere surface that is in register with <current-sphere>
and has the desired output mesh
<border-out> - output - the output border file
Resamples a border file, given two spherical surfaces that are in register. Only
borders that have the same structure as current-sphere will be resampled.
-border-to-rois MAKE METRIC ROIS FROM BORDERS
wb_command -border-to-rois
<surface> - the surface the borders are drawn on <border-file> - the border file
<metric-out> - output - the output metric file
[-border] - create ROI for only one border
<name> - the name of the border
[-inverse] - use inverse selection (outside border)
[-include-border] - include vertices the border is closest to
By default, draws ROIs inside all borders in the border file, as separate metric
columns.
-border-to-vertices DRAW BORDERS AS VERTICES IN A METRIC FILE
wb_command -border-to-vertices
<surface> - the surface the borders are drawn on <border-file> - the border file
<metric-out> - output - the output metric file
[-border] - create ROI for only one border
<name> - the name of the border
Outputs a metric with 1s on vertices that follow a border, and 0s elsewhere. By
default, a separate metric column is created for each border.
-cifti-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A CIFTI LABEL MAP
wb_command -cifti-all-labels-to-rois
<label-in> - the input cifti label file <map> - the number or name of the label map
to use <cifti-out> - output - the output cifti file
The output cifti file is a dscalar file with a column (map) for each label in the
specified input map, other than the ??? label, each of which contains a binary ROI
of all brainordinates that are set to the corresponding label.
Most of the time, specifying '1' for the <map> argument will do what is desired.
-cifti-average AVERAGE CIFTI FILES
wb_command -cifti-average
<cifti-out> - output - output cifti file
[-exclude-outliers] - exclude outliers by standard deviation of each
element across files <sigma-below> - number of standard deviations below the mean
to
include
<sigma-above> - number of standard deviations above the mean to
include
[-cifti] - repeatable - specify an input file
<cifti-in> - the input cifti file
[-weight] - give a weight for this file
<weight> - the weight to use
Averages cifti files together.
Files without -weight specified are given
a weight of 1.
If -exclude-outliers is specified, at each element, the
data across all files is taken as a set, its unweighted mean and sample standard
deviation are found, and values outside the specified number of standard deviations
are excluded from the (potentially weighted) average at that element.
-cifti-average-dense-roi AVERAGE CIFTI ROWS ACROSS SUBJECTS BY ROI
wb_command -cifti-average-dense-roi
<cifti-out> - output - output cifti dscalar file
[-cifti-roi] - cifti file containing combined weights
<roi-cifti> - the roi cifti file
[-in-memory] - cache the roi in memory so that it isn't re-read for
each input cifti
[-left-roi] - weights to use for left hempsphere
<roi-metric> - the left roi as a metric file
[-right-roi] - weights to use for right hempsphere
<roi-metric> - the right roi as a metric file
[-cerebellum-roi] - weights to use for cerebellum surface
<roi-metric> - the cerebellum roi as a metric file
[-vol-roi] - voxel weights to use
<roi-vol> - the roi volume file
[-left-area-surf] - specify the left surface for vertex area correction
<left-surf> - the left surface file
[-right-area-surf] - specify the right surface for vertex area correction
<right-surf> - the right surface file
[-cerebellum-area-surf] - specify the cerebellum surface for vertex area
correction <cerebellum-surf> - the cerebellum surface file
[-cifti] - repeatable - specify an input cifti file
<cifti-in> - a cifti file to average across
Averages rows for each map of the ROI(s), across all files.
ROI maps are
treated as weighting functions, including negative values.
For
efficiency, ensure that everything that is not intended to be used is zero in the
ROI map. If -cifti-roi is specified, -left-roi, -right-roi, -cerebellum-roi, and
-vol-roi must not be specified. If multiple non-cifti ROI files are specified,
they must have the same number of columns.
-cifti-average-roi-correlation CORRELATE ROI AVERAGE WITH ALL ROWS THEN AVERAGE ACROSS
SUBJECTS
wb_command -cifti-average-roi-correlation
<cifti-out> - output - output cifti file
[-cifti-roi] - cifti file containing combined weights
<roi-cifti> - the roi cifti file
[-in-memory] - cache the roi in memory so that it isn't re-read for
each input cifti
[-left-roi] - weights to use for left hempsphere
<roi-metric> - the left roi as a metric file
[-right-roi] - weights to use for right hempsphere
<roi-metric> - the right roi as a metric file
[-cerebellum-roi] - weights to use for cerebellum surface
<roi-metric> - the cerebellum roi as a metric file
[-vol-roi] - voxel weights to use
<roi-vol> - the roi volume file
[-left-area-surf] - specify the left surface for vertex area correction
<left-surf> - the left surface file
[-right-area-surf] - specify the right surface for vertex area correction
<right-surf> - the right surface file
[-cerebellum-area-surf] - specify the cerebellum surface for vertex area
correction <cerebellum-surf> - the cerebellum surface file
[-cifti] - repeatable - specify an input cifti file
<cifti-in> - a cifti file to average across
Averages rows for each map of the ROI(s), takes the correlation of each ROI average
to the rest of the rows in the same file, applies the fisher small z transform,
then averages the results across all files. ROIs are always treated as weighting
functions, including negative values. For efficiency, ensure that everything that
is not intended to be used is zero in the ROI map. If -cifti-roi is specified,
-left-roi, -right-roi, -cerebellum-roi, and -vol-roi must not be specified. If
multiple non-cifti ROI files are specified, they must have the same number of
columns.
-cifti-change-mapping CONVERT TO SCALAR, COPY MAPPING, ETC
wb_command -cifti-change-mapping
<data-cifti> - the cifti file to use the data from <direction> - which direction on
<data-cifti> to replace the mapping <cifti-out> - output - the output cifti file
[-series] - set the mapping to series
<step> - increment between series points <start> - start value of the series
[-unit] - select unit for series (default SECOND)
<unit> - unit identifier
[-scalar] - set the mapping to scalar
[-name-file] - specify names for the maps
<file> - text file containing map names, one per line
[-from-cifti] - copy mapping from another cifti file
<template-cifti> - a cifti file containing the desired mapping <direction> - which
direction to copy the mapping from
Take an existing cifti file and change one of the mappings.
Exactly one
of -series, -scalar, or -from-cifti must be specified.
The direction can
be either an integer starting from 1, or the strings 'ROW' or 'COLUMN'.
The argument to -unit must be one of the following:
SECOND HERTZ METER RADIAN
-cifti-convert DUMP CIFTI MATRIX INTO OTHER FORMATS
wb_command -cifti-convert
[-to-gifti-ext] - convert to GIFTI external binary
<cifti-in> - the input cifti file <gifti-out> - output - the output gifti file
[-from-gifti-ext] - convert a GIFTI made with this command back into a
CIFTI <gifti-in> - the input gifti file <cifti-out> - output - the output cifti
file
[-reset-timepoints] - reset the mapping along rows to timepoints,
taking length from the gifti file <timestep> - the desired time between frames
<timestart> - the desired time offset of the initial frame
[-unit] - use a unit other than time
<unit> - unit identifier (default SECOND)
[-reset-scalars] - reset mapping along rows to scalars, taking length
from the gifti file
[-column-reset-scalars] - reset mapping along columns to scalar
(useful for changing number of series in a sdseries file)
[-replace-binary] - replace data with a binary file
<binary-in> - the binary file that contains replacement data
[-flip-endian] - byteswap the binary file
[-transpose] - transpose the binary file
[-to-nifti] - convert to NIFTI1
<cifti-in> - the input cifti file <nifti-out> - output - the output nifti file
[-smaller-file] - use better-fitting dimension lengths
[-smaller-dims] - minimize the largest dimension, for tools that don't
like large indices
[-from-nifti] - convert a NIFTI (1 or 2) file made with this command back
into CIFTI <nifti-in> - the input nifti file <cifti-template> - a cifti file with
the dimension(s) and mapping(s)
that should be used
<cifti-out> - output - the output cifti file
[-reset-timepoints] - reset the mapping along rows to timepoints,
taking length from the nifti file <timestep> - the desired time between frames
<timestart> - the desired time offset of the initial frame
[-unit] - use a unit other than time
<unit> - unit identifier (default SECOND)
[-reset-scalars] - reset mapping along rows to scalars, taking length
from the nifti file
[-to-text] - convert to a plain text file
<cifti-in> - the input cifti file <text-out> - output - the output text file
[-col-delim] - choose string to put between elements in a row
<delim-string> - the string to use (default is a tab character)
[-from-text] - convert from plain text to cifti
<text-in> - the input text file <cifti-template> - a cifti file with the
dimension(s) and mapping(s)
that should be used
<cifti-out> - output - the output cifti file
[-col-delim] - specify string that is between elements in a row
<delim-string> - the string to use (default is any whitespace)
[-reset-timepoints] - reset the mapping along rows to timepoints,
taking length from the text file <timestep> - the desired time between frames
<timestart> - the desired time offset of the initial frame
[-unit] - use a unit other than time
<unit> - unit identifier (default SECOND)
[-reset-scalars] - reset mapping along rows to scalars, taking length
from the text file
This command is used to convert a full CIFTI matrix to/from formats that can be
used by programs that don't understand CIFTI. You must specify exactly one of
-to-gifti-ext, -from-gifti-ext, -to-nifti, -from-nifti, -to-text, or -from-text.
If you want to write an existing CIFTI file with a different CIFTI version, see
-file-convert, and its -cifti-version-convert option.
If you want part of the CIFTI file as a metric, label, or volume file, see
-cifti-separate. If you want to create a CIFTI file from metric and/or volume
files, see the -cifti-create-* commands.
If you want to import a matrix that is restricted to an ROI, first create a
template CIFTI file matching that ROI using a -cifti-create-* command. After
importing to CIFTI, you can then expand the file into a standard brainordinates
space with -cifti-create-dense-from-template. If you want to export only part of a
CIFTI file, first create an roi-restricted CIFTI file with
-cifti-restrict-dense-mapping.
The -transpose option to -from-gifti-ext is needed if the replacement binary file
is in column-major order.
The -unit options accept these values:
SECOND HERTZ METER RADIAN
-cifti-correlation GENERATE CORRELATION OF ROWS IN A CIFTI FILE
wb_command -cifti-correlation
<cifti> - input cifti file <cifti-out> - output - output cifti file
[-roi-override] - perform correlation from a subset of rows to all rows
[-left-roi] - use an roi for left hempsphere
<roi-metric> - the left roi as a metric file
[-right-roi] - use an roi for right hempsphere
<roi-metric> - the right roi as a metric file
[-cerebellum-roi] - use an roi for cerebellum
<roi-metric> - the cerebellum roi as a metric file
[-vol-roi] - use an roi for volume
<roi-vol> - the volume roi file
[-cifti-roi] - use a cifti file for combined rois
<roi-cifti> - the cifti roi file
[-weights] - specify column weights
<weight-file> - text file containing one weight per column
[-fisher-z] - apply fisher small z transform (ie, artanh) to correlation
[-no-demean] - instead of correlation, do dot product of rows, then
normalize by diagonal
[-covariance] - compute covariance instead of correlation
[-mem-limit] - restrict memory usage
<limit-GB> - memory limit in gigabytes
For each row (or each row inside an roi if -roi-override is specified), correlate
to all other rows. The -cifti-roi suboption to -roi-override may not be specified
with any other -*-roi suboption, but you may specify the other -*-roi suboptions
together.
When using the -fisher-z option, the output is NOT a Z-score, it is artanh(r), to
do further math on this output, consider using -cifti-math.
Restricting the memory usage will make it calculate the output in chunks, and if
the input file size is more than 70% of the memory limit, it will also read through
the input file as rows are required, resulting in several passes through the input
file (once per chunk). Memory limit does not need to be an integer, you may also
specify 0 to calculate a single output row at a time (this may be very slow).
-cifti-correlation-gradient CORRELATE CIFTI ROWS AND TAKE GRADIENT
wb_command -cifti-correlation-gradient
<cifti> - the input cifti <cifti-out> - output - the output cifti
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-left-corrected-areas] - vertex areas to use instead of computing
them from the left surface <area-metric> - the corrected vertex areas, as a metric
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-right-corrected-areas] - vertex areas to use instead of computing
them from the right surface <area-metric> - the corrected vertex areas, as a metric
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-cerebellum-corrected-areas] - vertex areas to use instead of
computing them from the cerebellum surface <area-metric> - the corrected vertex
areas, as a metric
[-surface-presmooth] - smooth on the surface before computing the
gradient <surface-kernel> - the sigma for the gaussian surface smoothing
kernel, in mm
[-volume-presmooth] - smooth the volume before computing the gradient
<volume-kernel> - the sigma for the gaussian volume smoothing kernel,
in mm
[-undo-fisher-z] - apply the inverse fisher small z transform to the
input
[-fisher-z] - apply the fisher small z transform to the correlations
before taking the gradient
[-surface-exclude] - exclude vertices near each seed vertex from
computation <distance> - geodesic distance from seed vertex for the exclusion
zone, in mm
[-volume-exclude] - exclude voxels near each seed voxel from computation
<distance> - distance from seed voxel for the exclusion zone, in mm
[-covariance] - compute covariance instead of correlation
[-mem-limit] - restrict memory usage
<limit-GB> - memory limit in gigabytes
[-double-correlation] - do two correlations before taking the gradient
[-fisher-z-first] - after the FIRST correlation, apply fisher small z
transform (ie, artanh)
[-no-demean-first] - instead of correlation for the FIRST operation,
do dot product of rows, then normalize by diagonal
[-covariance-first] - instead of correlation for the FIRST operation,
compute covariance
For each structure, compute the correlation of the rows in the structure, and take
the gradients of the resulting rows, then average them. Memory limit does not need
to be an integer, you may also specify 0 to use as little memory as possible (this
may be very slow).
-cifti-create-dense-from-template CREATE CIFTI WITH MATCHING DENSE MAP
wb_command -cifti-create-dense-from-template
<template-cifti> - file to match brainordinates of <cifti-out> - output - the
output cifti file
[-series] - make a dtseries file instead of a dscalar
<step> - increment between series points <start> - start value of the series
[-unit] - select unit for series (default SECOND)
<unit> - unit identifier
[-volume-all] - specify an input volume file for all voxel data
<volume-in> - the input volume file
[-from-cropped] - the input is cropped to the size of the voxel data
in the template file
[-cifti] - repeatable - use input data from a cifti file
<cifti-in> - cifti file containing input data
[-metric] - repeatable - use input data from a metric file
<structure> - which structure to put the metric file into <metric-in> - input
metric file
[-label] - repeatable - use input data from surface label files
<structure> - which structure to put the label file into <label-in> - input label
file
[-volume] - repeatable - use a volume file for a single volume
structure's data <structure> - which structure to put the volume file into
<volume-in> - the input volume file
[-from-cropped] - the input is cropped to the size of the volume
structure
This command helps you make a new dscalar, dtseries, or dlabel cifti file that
matches the brainordinate space used in another cifti file. The template file must
have the desired brainordinate space in the mapping along the column direction (for
dtseries, dscalar, dlabel, and symmetric dconn this is always the case). All input
cifti files must have a brain models mapping along column and use the same volume
space and/or surface vertex count as the template for structures that they contain.
If any input files contain label data, then input files with non-label data are not
allowed, and the -series option may not be used.
Any structure that isn't covered by an input is filled with zeros or the unlabeled
key.
The <structure> argument of -metric, -label or -volume must be one of the
following:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
The argument to -unit must be one of the following:
SECOND HERTZ METER RADIAN
-cifti-create-dense-scalar CREATE A CIFTI DENSE SCALAR FILE
wb_command -cifti-create-dense-scalar
<cifti-out> - output - the output cifti file
[-volume] - volume component
<volume-data> - volume file containing all voxel data for all volume
structures
<structure-label-volume> - label volume file containing labels for
cifti structures
[-left-metric] - metric for left surface
<metric> - the metric file
[-roi-left] - roi of vertices to use from left surface
<roi-metric> - the ROI as a metric file
[-right-metric] - metric for right surface
<metric> - the metric file
[-roi-right] - roi of vertices to use from right surface
<roi-metric> - the ROI as a metric file
[-cerebellum-metric] - metric for the cerebellum
<metric> - the metric file
[-roi-cerebellum] - roi of vertices to use from right surface
<roi-metric> - the ROI as a metric file
[-name-file] - use a text file to set all map names
<file> - text file containing map names, one per line
All input files must have the same number of columns/subvolumes.
Only
the specified components will be in the output cifti file.
Map names
will be taken from one of the input files.
At least one component must
be specified.
See -volume-label-import and -volume-help for format details of label volume files.
The structure-label-volume should have some of the label names from this list, all
other label names will be ignored:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-cifti-create-dense-timeseries CREATE A CIFTI DENSE TIMESERIES
wb_command -cifti-create-dense-timeseries
<cifti-out> - output - the output cifti file
[-volume] - volume component
<volume-data> - volume file containing all voxel data for all volume
structures
<structure-label-volume> - label volume file containing labels for
cifti structures
[-left-metric] - metric for left surface
<metric> - the metric file
[-roi-left] - roi of vertices to use from left surface
<roi-metric> - the ROI as a metric file
[-right-metric] - metric for left surface
<metric> - the metric file
[-roi-right] - roi of vertices to use from right surface
<roi-metric> - the ROI as a metric file
[-cerebellum-metric] - metric for the cerebellum
<metric> - the metric file
[-roi-cerebellum] - roi of vertices to use from right surface
<roi-metric> - the ROI as a metric file
[-timestep] - set the timestep
<interval> - the timestep, in seconds (default 1.0)
[-timestart] - set the start time
<start> - the time at the first frame, in seconds (default 0.0)
[-unit] - use a unit other than time
<unit> - unit identifier (default SECOND)
All input files must have the same number of columns/subvolumes.
Only
the specified components will be in the output cifti.
At least one
component must be specified.
See -volume-label-import and -volume-help for format details of label volume files.
The structure-label-volume should have some of the label names from this list, all
other label names will be ignored:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
The -unit option accepts these values:
SECOND HERTZ METER RADIAN
-cifti-create-label CREATE A CIFTI LABEL FILE
wb_command -cifti-create-label
<cifti-out> - output - the output cifti file
[-volume] - volume component
<label-volume> - label volume file containing the data to be copied
<structure-label-volume> - label volume file that defines which voxels
to use
[-left-label] - label file for left surface
<label> - the label file
[-roi-left] - roi of vertices to use from left surface
<roi-metric> - the ROI as a metric file
[-right-label] - label for left surface
<label> - the label file
[-roi-right] - roi of vertices to use from right surface
<roi-metric> - the ROI as a metric file
[-cerebellum-label] - label for the cerebellum
<label> - the label file
[-roi-cerebellum] - roi of vertices to use from right surface
<roi-metric> - the ROI as a metric file
All input files must have the same number of columns/subvolumes.
Only
the specified components will be in the output cifti.
At least one
component must be specified.
The -volume option requires two volume arguments, the label-volume argument
contains all labels you want to display (e.g. nuclei of the thalamus), whereas the
structure-label-volume argument contains all CIFTI voxel-based structures you want
to include data within (e.g. THALAMUS_LEFT, THALAMUS_RIGHT, etc). See
-volume-label-import and -volume-help for format details of label volume files. If
you just want the labels in voxels to be the structure names, you may use the same
file for both arguments. The structure-label-volume must use some of the label
names from this list, all other label names in the structure-label-volume will be
ignored:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-cifti-create-parcellated-from-template MATCH PARCELS TO TEMPLATE BY NAME
wb_command -cifti-create-parcellated-from-template
<cifti-template> - a cifti file with the template parcel mapping along
column
<modify-direction> - which dimension of the output file should match the
template (integer, 'ROW', or 'COLUMN')
<cifti-out> - output - the output cifti file
[-fill-value] - specify value to be used in parcels that don't match
<value> - value to use (default 0)
[-cifti] - repeatable - specify an input cifti file
<cifti-in> - the input parcellated cifti file
For each parcel name in the template mapping, find that name in an input cifti file
and use its data in the output file. All input cifti files must have a parcels
mapping along <modify-direction> and matching mappings along other dimensions. The
direction can be either an integer starting from 1, or the strings 'ROW' or
'COLUMN'.
-cifti-create-scalar-series IMPORT SERIES DATA INTO CIFTI
wb_command -cifti-create-scalar-series
<input> - input file <cifti-out> - output - output cifti file
[-transpose] - use if the rows of the text file are along the scalar
dimension
[-name-file] - use a text file to set names on scalar dimension
<file> - text file containing names, one per line
[-series] - set the units and values of the series
<unit> - the unit to use <start> - the value at the first series point <step> - the
interval between series points
Convert a text file containing series of equal length into a cifti file. The text
file should have lines made up of numbers separated by whitespace, with no extra
newlines between lines.
The <unit> argument must be one of the following:
SECOND HERTZ METER RADIAN
-cifti-cross-correlation CORRELATE A CIFTI FILE WITH ANOTHER CIFTI FILE
wb_command -cifti-cross-correlation
<cifti-a> - first input cifti file <cifti-b> - second input cifti file <cifti-out>
- output - output cifti file
[-weights] - specify column weights
<weight-file> - text file containing one weight per column
[-fisher-z] - apply fisher small z transform (ie, artanh) to correlation
[-mem-limit] - restrict memory usage
<limit-GB> - memory limit in gigabytes
Correlates every row in <cifti-a> with every row in <cifti-b>.
The
mapping along columns in <cifti-b> becomes the mapping along rows in the output.
When using the -fisher-z option, the output is NOT a Z-score, it is artanh(r), to
do further math on this output, consider using -cifti-math.
Restricting the memory usage will make it calculate the output in chunks, by
reading through <cifti-b> multiple times.
-cifti-dilate DILATE A CIFTI FILE
wb_command -cifti-dilate
<cifti-in> - the input cifti file <direction> - which dimension to dilate along,
ROW or COLUMN <surface-distance> - the distance to dilate on surfaces, in mm
<volume-distance> - the distance to dilate in the volume, in mm <cifti-out> -
output - the output cifti file
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-left-corrected-areas] - vertex areas to use instead of computing
them from the left surface <area-metric> - the corrected vertex areas, as a metric
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-right-corrected-areas] - vertex areas to use instead of computing
them from the right surface <area-metric> - the corrected vertex areas, as a metric
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-cerebellum-corrected-areas] - vertex areas to use instead of
computing them from the cerebellum surface <area-metric> - the corrected vertex
areas, as a metric
[-bad-brainordinate-roi] - specify an roi of brainordinates to overwrite,
rather than zeros <roi-cifti> - cifti dscalar or dtseries file, positive values
denote
brainordinates to have their values replaced
[-nearest] - use nearest value
[-merged-volume] - treat volume components as if they were a single
component
[-legacy-mode] - use the math from v1.3.2 and earlier for weighted
dilation
For all data values designated as bad, if they neighbor a good value or are within
the specified distance of a good value in the same kind of model, replace the value
with a distance weighted average of nearby good values, otherwise set the value to
zero. If -nearest is specified, it will use the value from the closest good value
within range instead of a weighted average. When the input file contains label
data, nearest dilation is used on the surface, and weighted popularity is used in
the volume.
The -*-corrected-areas options are intended for dilating on group average surfaces,
but it is only an approximate correction for the reduction of structure in a group
average surface.
If -bad-brainordinate-roi is specified, all values, including those with value
zero, are good, except for locations with a positive value in the ROI. If it is
not specified, only values equal to zero are bad.
-cifti-erode ERODE A CIFTI FILE
wb_command -cifti-erode
<cifti-in> - the input cifti file <direction> - which dimension to dilate along,
ROW or COLUMN <surface-distance> - the distance to dilate on surfaces, in mm
<volume-distance> - the distance to dilate in the volume, in mm <cifti-out> -
output - the output cifti file
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-left-corrected-areas] - vertex areas to use instead of computing
them from the left surface <area-metric> - the corrected vertex areas, as a metric
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-right-corrected-areas] - vertex areas to use instead of computing
them from the right surface <area-metric> - the corrected vertex areas, as a metric
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-cerebellum-corrected-areas] - vertex areas to use instead of
computing them from the cerebellum surface <area-metric> - the corrected vertex
areas, as a metric
[-merged-volume] - treat volume components as if they were a single
component
For all data values that are empty (for label data, unlabeled, for other data,
zero), set the surrounding values to empty. The surrounding values are defined as
the immediate neighbors and all values in the same structure within the specified
distance (-merged-volume treats all voxels as one structure).
The -*-corrected-areas options are intended for eroding on group average surfaces,
but it is only an approximate correction.
-cifti-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A CIFTI FILE
wb_command -cifti-estimate-fwhm
<cifti> - the input cifti file
[-merged-volume] - treat volume components as if they were a single
component
[-column] - only output estimates for one column
<column> - the column number
[-whole-file] - estimate for the whole file at once, not each column
separately
[-demean] - subtract the mean image before estimating smoothness
[-surface] - repeatable - specify an input surface
<structure> - what structure to use this surface for <surface> - the surface file
Estimate the smoothness of the components of the cifti file, printing the estimates
to standard output. If -merged-volume is used, all voxels are used as a single
component, rather than separated by structure.
<structure> must be one of the following:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-cifti-export-dense-mapping WRITE INDEX TO ELEMENT MAPPING AS TEXT
wb_command -cifti-export-dense-mapping
<cifti> - the cifti file <direction> - which direction to export the mapping from,
ROW or COLUMN
[-volume-all] - export the the mapping of all voxels
<text-out> - output - the output text file
[-no-cifti-index] - don't write the cifti index in the output file
[-structure] - write the structure each voxel belongs to in the output
file
[-surface] - repeatable - export the the mapping of one surface structure
<structure> - the structure to output <text-out> - output - the output text file
[-no-cifti-index] - don't write the cifti index in the output file
[-volume] - repeatable - export the the mapping of one volume structure
<structure> - the structure to output <text-out> - output - the output text file
[-no-cifti-index] - don't write the cifti index in the output file
This command produces text files that describe the mapping from cifti indices to
surface vertices or voxels. All indices are zero-based. The default format for
-surface is lines of the form:
<cifti-index> <vertex>
The default format for -volume and -volume-all is lines of the form:
<cifti-index> <i> <j> <k>
For each <structure> argument, use one of the following strings:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-cifti-extrema FIND EXTREMA IN A CIFTI FILE
wb_command -cifti-extrema
<cifti> - the input cifti <surface-distance> - the minimum distance between extrema
of the same
type, for surface components
<volume-distance> - the minimum distance between extrema of the same
type, for volume components
<direction> - which dimension to find extrema along, ROW or COLUMN <cifti-out> -
output - the output cifti
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-surface-presmooth] - smooth on the surface before finding extrema
<surface-kernel> - the sigma for the gaussian surface smoothing
kernel, in mm
[-volume-presmooth] - smooth volume components before finding extrema
<volume-kernel> - the sigma for the gaussian volume smoothing kernel,
in mm
[-threshold] - ignore small extrema
<low> - the largest value to consider for being a minimum <high> - the smallest
value to consider for being a maximum
[-merged-volume] - treat volume components as if they were a single
component
[-sum-maps] - output the sum of the extrema maps instead of each map
separately
[-consolidate-mode] - use consolidation of local minima instead of a
large neighborhood
[-only-maxima] - only find the maxima
[-only-minima] - only find the minima
Finds spatial locations in a cifti file that have more extreme values than all
nearby locations in the same component (surface or volume structure). The input
cifti file must have a brain models mapping along the specified direction. COLUMN
is the direction that works on dtseries and dscalar. For dconn, if it is symmetric
use COLUMN, otherwise use ROW.
-cifti-false-correlation COMPARE CORRELATION LOCALLY AND ACROSS/THROUGH SULCI/GYRI
wb_command -cifti-false-correlation
<cifti-in> - the cifti file to use for correlation <3D-dist> - maximum 3D distance
to check around each vertex <geo-outer> - maximum geodesic distance to use for
neighboring
correlation
<geo-inner> - minimum geodesic distance to use for neighboring
correlation
<cifti-out> - output - the output cifti dscalar file
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-dump-text] - dump the raw measures used to a text file
<text-out> - the output text file
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-dump-text] - dump the raw measures used to a text file
<text-out> - the output text file
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-dump-text] - dump the raw measures used to a text file
<text-out> - the output text file
For each vertex, compute the average correlation within a range of geodesic
distances that don't cross a sulcus/gyrus, and the correlation to the closest
vertex crossing a sulcus/gyrus. A vertex is considered to cross a sulcus/gyrus if
the 3D distance is less than a third of the geodesic distance. The output file
contains the ratio between these correlations, and some additional maps to help
explain the ratio.
-cifti-find-clusters FILTER CLUSTERS BY AREA/VOLUME
wb_command -cifti-find-clusters
<cifti> - the input cifti <surface-value-threshold> - threshold for surface data
values <surface-minimum-area> - threshold for surface cluster area, in mm^2
<volume-value-threshold> - threshold for volume data values <volume-minimum-size> -
threshold for volume cluster size, in mm^3 <direction> - which dimension to use for
spatial information, ROW or
COLUMN
<cifti-out> - output - the output cifti
[-less-than] - find values less than <value-threshold>, rather than
greater
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-corrected-areas] - vertex areas to use instead of computing them
from the surface <area-metric> - the corrected vertex areas, as a metric
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-corrected-areas] - vertex areas to use instead of computing them
from the surface <area-metric> - the corrected vertex areas, as a metric
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-corrected-areas] - vertex areas to use instead of computing them
from the surface <area-metric> - the corrected vertex areas, as a metric
[-cifti-roi] - search only within regions of interest
<roi-cifti> - the regions to search within, as a cifti file
[-merged-volume] - treat volume components as if they were a single
component
[-size-ratio] - ignore clusters smaller than a given fraction of the
largest cluster in the structure <surface-ratio> - fraction of the structure's
largest cluster area <volume-ratio> - fraction of the structure's largest cluster
volume
[-distance] - ignore clusters further than a given distance from the
largest cluster in the structure <surface-distance> - how far from the largest
cluster a cluster can
be, edge to edge, in mm
<volume-distance> - how far from the largest cluster a cluster can be,
edge to edge, in mm
[-start] - start labeling clusters from a value other than 1
<startval> - the value to give the first cluster found
Outputs a cifti file with nonzero integers for all brainordinates within a large
enough cluster, and zeros elsewhere. The integers denote cluster membership (by
default, first cluster found will use value 1, second cluster 2, etc). Cluster
values are not reused across maps of the output, but instead keep counting up. The
input cifti file must have a brain models mapping on the chosen dimension, columns
for .dtseries, and either for .dconn. The ROI should have a brain models mapping
along columns, exactly matching the mapping of the chosen direction in the input
file. Data outside the ROI is ignored.
-cifti-gradient TAKE GRADIENT OF A CIFTI FILE
wb_command -cifti-gradient
<cifti> - the input cifti <direction> - which dimension to take the gradient along,
ROW or COLUMN <cifti-out> - output - the output cifti
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-left-corrected-areas] - vertex areas to use instead of computing
them from the left surface <area-metric> - the corrected vertex areas, as a metric
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-right-corrected-areas] - vertex areas to use instead of computing
them from the right surface <area-metric> - the corrected vertex areas, as a metric
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-cerebellum-corrected-areas] - vertex areas to use instead of
computing them from the cerebellum surface <area-metric> - the corrected vertex
areas, as a metric
[-surface-presmooth] - smooth on the surface before computing the
gradient <surface-kernel> - the sigma for the gaussian surface smoothing
kernel, in mm
[-volume-presmooth] - smooth on the surface before computing the gradient
<volume-kernel> - the sigma for the gaussian volume smoothing kernel,
in mm
[-average-output] - output the average of the gradient magnitude maps
instead of each gradient map separately
[-vectors] - output gradient vectors
<vectors-out> - output - the vectors, as a dscalar file
Performs gradient calculation on each component of the cifti file, and optionally
averages the resulting gradients. The -vectors and -average-output options may not
be used together. You must specify a surface for each surface structure in the
cifti file. The COLUMN direction should be faster, and is the direction that works
on dtseries. For dconn, you probably want ROW, unless you are using
-average-output.
-cifti-label-adjacency MAKE ADJACENCY MATRIX OF A CIFTI LABEL FILE
wb_command -cifti-label-adjacency
<label-in> - the input cifti label file <adjacency-out> - output - the output cifti
pconn adjacency matrix
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
Find face-adjacent voxels and connected vertices that have different label values,
and count them for each pair. Put the resulting counts into a parcellated
connectivity file, with the diagonal being zero. This gives a rough estimate of
how long or expansive the border between two labels is.
-cifti-label-export-table EXPORT LABEL TABLE FROM CIFTI AS TEXT
wb_command -cifti-label-export-table
<label-in> - the input cifti label file <map> - the number or name of the label map
to use <table-out> - output - the output text file
Takes the label table from the cifti label map, and writes it to a text format
matching what is expected by -cifti-label-import.
-cifti-label-import MAKE A CIFTI LABEL FILE FROM A CIFTI FILE
wb_command -cifti-label-import
<input> - the input cifti file <label-list-file> - text file containing the values
and names for labels <output> - output - the output cifti label file
[-discard-others] - set any values not mentioned in the label list to the
??? label
[-unlabeled-value] - set the value that will be interpreted as unlabeled
<value> - the numeric value for unlabeled (default 0)
[-drop-unused-labels] - remove any unused label values from the label
table
Creates a cifti label file from a cifti file with label-like values.
You
may specify the empty string (use "") for <label-list-file>, which will be treated
as if it is an empty file. The label list file must have the following format (2
lines per label):
<labelname> <key> <red> <green> <blue> <alpha> ...
Label names are specified on a separate line from their value and color, in order
to let label names contain spaces. Whitespace is trimmed from both ends of the
label name, but is kept if it is in the middle of a label. Do not specify the
"unlabeled" key in the file, it is assumed that 0 means not labeled unless
-unlabeled-value is specified. The value of <key> specifies what value in the
imported file should be used as this label. The values of <red>, <green>, <blue>
and <alpha> must be integers from 0 to 255, and will specify the color the label is
drawn as (alpha of 255 means fully opaque, which is probably what you want).
By default, it will create new label names with names like LABEL_5 for any values
encountered that are not mentioned in the list file, specify -discard-others to
instead set these values to the "unlabeled" key.
-cifti-label-modify-keys CHANGE KEY VALUES IN A DLABEL FILE
wb_command -cifti-label-modify-keys
<cifti-in> - the input dlabel file <remap-file> - text file with old and new key
values <cifti-out> - output - the output dlabel file
[-column] - select a single column to use
<column> - the column number or name
<remap-file> should have lines of the form 'oldkey newkey', like so:
3 5 5 8 8 2
This would change the current label with key '3' to use the key '5' instead, 5
would use 8, and 8 would use 2. Any collision in key values results in the label
that was not specified in the remap file getting remapped to an otherwise unused
key. Remapping more than one key to the same new key, or the same key to more than
one new key, results in an error. This will not change the appearance of the file
when displayed, as it will change the key values in the data at the same time.
-cifti-label-probability FIND FREQUENCY OF CIFTI LABELS
wb_command -cifti-label-probability
<label-maps> - cifti dlabel file containing individual label maps from
many subjects
<probability-dscalar-out> - output - the relative frequencies of each
label at each vertex/voxel
[-exclude-unlabeled] - don't make a probability map of the unlabeled key
This command outputs a set of soft ROIs, one for each label in the input, where the
value is how many of the input maps had that label at that vertex/voxel, divided by
the number of input maps.
-cifti-label-to-border DRAW BORDERS AROUND CIFTI LABELS
wb_command -cifti-label-to-border
<cifti-in> - the input cifti dlabel file
[-placement] - set how far along the edge border points are drawn
<fraction> - fraction along edge from inside vertex (default 0.33)
[-column] - select a single column
<column> - the column number or name
[-border] - repeatable - specify output file for a surface structure
<surface> - the surface to use for neighbor and structure information <border-out>
- output - the output border file
For each surface, takes the labels on the matching structure and draws borders
around the labels. Use -column to only draw borders around one label map.
-cifti-label-to-roi MAKE A CIFTI LABEL INTO AN ROI
wb_command -cifti-label-to-roi
<label-in> - the input cifti label file <scalar-out> - output - the output cifti
scalar file
[-name] - select label by name
<label-name> - the label name that you want an roi of
[-key] - select label by key
<label-key> - the label key that you want an roi of
[-map] - select a single label map to use
<map> - the map number or name
For each map in <label-in>, a map is created in <scalar-out> where all locations
labeled with <label-name> or with a key of <label-key> are given a value of 1, and
all other locations are given 0. Exactly one of -name and -key must be specified.
Specify -map to use only one map from <label-in>.
-cifti-math EVALUATE EXPRESSION ON CIFTI FILES
wb_command -cifti-math
<expression> - the expression to evaluate, in quotes <cifti-out> - output - the
output cifti file
[-fixnan] - replace NaN results with a value
<replace> - value to replace NaN with
[-override-mapping-check] - don't check the mappings for compatibility,
only check length
[-var] - repeatable - a cifti file to use as a variable
<name> - the name of the variable, as used in the expression <cifti> - the cifti
file to use as this variable
[-select] - repeatable - select a single index from a dimension
<dim> - the dimension to select from (1-based) <index> - the index to use (1-based)
[-repeat] - repeat the selected values for each index of output in
this dimension
This command evaluates <expression> at each matrix element independently. There
must be at least one -var option (to get the output layout from), even if the
<name> specified in it isn't used in <expression>.
To select a single column from a 2D file (most cifti files are 2D), use -select 1
<index>, where <index> is 1-based. To select a single row from a 2D file, use
-select 2 <index>. Where -select is not used, the cifti files must have compatible
mappings (e.g., brain models and parcels mappings must match exactly except for
parcel names). Use -override-mapping-check to skip this checking.
Filenames are not valid in <expression>, use a variable name and a -var option with
matching <name> to specify an input file. The format of <expression> is as
follows:
Expressions consist of constants, variables, operators, parentheses, and functions,
in infix notation, such as 'exp(-x + 3) * scale'. Variables are strings of any
length, using the characters a-z, A-Z, 0-9, and _, but may not take the name of a
named constant. Currently, there is only one named constant, PI. The operators
are +, -, *, /, ^, >, <, >=, <=, ==, !=, !, &&, ||. These behave as in C, except
that ^ is exponentiation, i.e. pow(x, y), and takes higher precedence than other
binary operators (also, '-3^-4^-5' means '-(3^(-(4^-5)))'). The <=, >=, ==, and !=
operators are given a small amount of wiggle room, equal to one millionth of the
smaller of the absolute values of the values being compared.
Comparison and logical operators return 0 or 1, you can do masking with expressions
like 'x * (mask > 0)'. For all logical operators, an input is considered true iff
it is greater than 0. The expression '0 < x < 5' is not syntactically wrong, but
it will NOT do what is desired, because it is evaluated left to right, i.e. '((0 <
x) < 5)', which will always return 1, as both possible results of a comparison are
less than 5. A warning is generated if an expression of this type is detected.
Use something like 'x > 0 && x < 5' to get the desired behavior.
Whitespace between elements is ignored, ' sin ( 2 * x ) ' is equivalent to
'sin(2*x)', but 's in(2*x)' is an error. Implied multiplication is not allowed,
the expression '2x' will be parsed as a variable. Parentheses are (), do not use
[] or {}. Functions require parentheses, the expression 'sin x' is an error.
The following functions are supported:
sin: 1 argument, the sine of the argument (units are radians) cos: 1 argument, the
cosine of the argument (units are radians) tan: 1 argument, the tangent of the
argument (units are radians) asin: 1 argument, the inverse of sine of the argument,
in radians acos: 1 argument, the inverse of cosine of the argument, in radians
atan: 1 argument, the inverse of tangent of the argument, in radians atan2: 2
arguments, atan2(y, x) returns the inverse of tangent of
(y/x), in radians, determining quadrant by the sign of both arguments
sinh: 1 argument, the hyperbolic sine of the argument cosh: 1 argument, the
hyperbolic cosine of the argument tanh: 1 argument, the hyperboloc tangent of the
argument asinh: 1 argument, the inverse hyperbolic sine of the argument acosh: 1
argument, the inverse hyperbolic cosine of the argument atanh: 1 argument, the
inverse hyperboloc tangent of the argument ln: 1 argument, the natural logarithm of
the argument exp: 1 argument, the constant e raised to the power of the argument
log: 1 argument, the base 10 logarithm of the argument log2: 1 argument, the base 2
logarithm of the argument sqrt: 1 argument, the square root of the argument abs: 1
argument, the absolute value of the argument floor: 1 argument, the largest integer
not greater than the argument round: 1 argument, the nearest integer, with ties
rounded away from
zero
ceil: 1 argument, the smallest integer not less than the argument min: 2 arguments,
min(x, y) returns y if (x > y), x otherwise max: 2 arguments, max(x, y) returns y
if (x < y), x otherwise mod: 2 arguments, mod(x, y) = x - y * floor(x / y), or 0 if
y == 0 clamp: 3 arguments, clamp(x, low, high) = min(max(x, low), high)
-cifti-merge MERGE CIFTI TIMESERIES, SCALAR, OR LABEL FILES
wb_command -cifti-merge
<cifti-out> - output - output cifti file
[-cifti] - repeatable - specify an input cifti file
<cifti-in> - a cifti file to use columns from
[-column] - repeatable - select a single column to use
<column> - the column number (starting from 1) or name
[-up-to] - use an inclusive range of columns
<last-column> - the number or name of the last column to include
[-reverse] - use the range in reverse order
Given input CIFTI files which have matching mappings along columns, and for which
mappings along rows are the same type, all either series, scalars, or labels, this
command concatenates the specified columns horizontally (rows become longer).
Example: wb_command -cifti-merge out.dtseries.nii -cifti first.dtseries.nii -column
1 -cifti second.dtseries.nii
This example would take the first column from first.dtseries.nii, followed by all
columns from second.dtseries.nii, and write these columns to out.dtseries.nii.
-cifti-merge-dense MERGE CIFTI FILES ALONG DENSE DIMENSION
wb_command -cifti-merge-dense
<direction> - which dimension to merge along, ROW or COLUMN <cifti-out> - output -
the output cifti file
[-cifti] - repeatable - specify an input cifti file
<cifti-in> - a cifti file to merge
The input cifti files must have matching mappings along the direction not
specified, and the mapping along the specified direction must be brain models.
-cifti-merge-parcels MERGE CIFTI FILES ALONG PARCELS DIMENSION
wb_command -cifti-merge-parcels
<direction> - which dimension to merge along (integer, 'ROW', or
'COLUMN')
<cifti-out> - output - the output cifti file
[-cifti] - repeatable - specify an input cifti file
<cifti-in> - a cifti file to merge
The input cifti files must have matching mappings along the direction not
specified, and the mapping along the specified direction must be parcels. The
direction can be either an integer starting from 1, or the strings 'ROW' or
'COLUMN'.
-cifti-pairwise-correlation CORRELATE PAIRED ROWS BETWEEN TWO CIFTI FILES
wb_command -cifti-pairwise-correlation
<cifti-a> - first input cifti file <cifti-b> - second input cifti file <cifti-out>
- output - output cifti file
[-fisher-z] - apply fisher small z transform (ie, artanh) to correlation
[-override-mapping-check] - don't check the mappings for compatibility,
only check length
For each row in <cifti-a>, correlate it with the same row in <cifti-b>, and put the
result in the same row of <cifti-out>, which has only one column.
-cifti-palette SET PALETTE ON A CIFTI FILE
wb_command -cifti-palette
<cifti-in> - the cifti input <mode> - the mapping mode <cifti-out> - output - the
output cifti file
[-column] - select a single column for scalar maps
<column> - the column number or name
[-pos-percent] - percentage min/max for positive data coloring
<pos-min-%> - the percentile for the least positive data <pos-max-%> - the
percentile for the most positive data
[-neg-percent] - percentage min/max for negative data coloring
<neg-min-%> - the percentile for the least negative data <neg-max-%> - the
percentile for the most negative data
[-pos-user] - user min/max values for positive data coloring
<pos-min-user> - the value for the least positive data <pos-max-user> - the value
for the most positive data
[-neg-user] - user min/max values for negative data coloring
<neg-min-user> - the value for the least negative data <neg-max-user> - the value
for the most negative data
[-interpolate] - interpolate colors
<interpolate> - boolean, whether to interpolate
[-disp-pos] - display positive data
<display> - boolean, whether to display
[-disp-neg] - display positive data
<display> - boolean, whether to display
[-disp-zero] - display data closer to zero than the min cutoff
<display> - boolean, whether to display
[-palette-name] - set the palette used
<name> - the name of the palette
[-thresholding] - set the thresholding
<type> - thresholding setting <test> - show values inside or outside thresholds
<min> - lower threshold <max> - upper threshold
[-inversion] - specify palette inversion
<type> - the type of inversion
NOTE: The output file must be a different file than the input file.
For scalar maps, by default the palette is changed for every map, specify -column
to change only one map. Palette settings not specified will be taken from the
first column for scalar maps, and from the existing file palette for other mapping
types. The <mode> argument must be one of the following:
MODE_AUTO_SCALE MODE_AUTO_SCALE_ABSOLUTE_PERCENTAGE MODE_AUTO_SCALE_PERCENTAGE
MODE_USER_SCALE
The <name> argument to -palette-name must be one of the following:
ROY-BIG-BL videen_style Gray_Interp_Positive Gray_Interp PSYCH-FIXED RBGYR20
RBGYR20P RYGBR4_positive RGRBR_mirror90_pos Orange-Yellow POS_NEG_ZERO red-yellow
blue-lightblue FSL power_surf fsl_red fsl_green fsl_blue fsl_yellow RedWhiteBlue
cool-warm spectral RY-BC-BL magma JET256 PSYCH PSYCH-NO-NONE ROY-BIG clear_brain
fidl raich4_clrmid raich6_clrmid HSB8_clrmid POS_NEG
The <type> argument to -thresholding must be one of the following:
THRESHOLD_TYPE_OFF THRESHOLD_TYPE_NORMAL THRESHOLD_TYPE_FILE
The <test> argument to -thresholding must be one of the following:
THRESHOLD_TEST_SHOW_OUTSIDE THRESHOLD_TEST_SHOW_INSIDE
The <type> argument to -inversion must be one of the following:
OFF POSITIVE_WITH_NEGATIVE POSITIVE_NEGATIVE_SEPARATE
-cifti-parcel-mapping-to-label CREATE DLABEL FROM PARCELLATED FILE
wb_command -cifti-parcel-mapping-to-label
<cifti-in> - the input parcellated file <direction> - which dimension to take the
parcel map from, ROW or COLUMN <template-cifti> - a cifti file with the desired
dense mapping along
column
<dlabel-out> - output - the output dense label file
This command will output a dlabel file, useful for doing the same parcellation to
another dense file.
For ptseries, pscalar, plabel, pconn, and pdconn, using COLUMN for <direction> will
work.
-cifti-parcellate PARCELLATE A CIFTI FILE
wb_command -cifti-parcellate
<cifti-in> - the cifti file to parcellate <cifti-label> - a cifti label file to use
for the parcellation <direction> - which mapping to parcellate (integer, ROW, or
COLUMN) <cifti-out> - output - output cifti file
[-spatial-weights] - use voxel volume and either vertex areas or metric
files as weights
[-left-area-surf] - use a surface for left vertex areas
<left-surf> - the left surface to use, areas are in mm^2
[-right-area-surf] - use a surface for right vertex areas
<right-surf> - the right surface to use, areas are in mm^2
[-cerebellum-area-surf] - use a surface for cerebellum vertex areas
<cerebellum-surf> - the cerebellum surface to use, areas are in
mm^2
[-left-area-metric] - use a metric file for left vertex weights
<left-metric> - metric file containing left vertex weights
[-right-area-metric] - use a metric file for right vertex weights
<right-metric> - metric file containing right vertex weights
[-cerebellum-area-metric] - use a metric file for cerebellum vertex
weights <cerebellum-metric> - metric file containing cerebellum vertex
weights
[-cifti-weights] - use a cifti file containing weights
<weight-cifti> - the weights to use, as a cifti file
[-method] - specify method of parcellation (default MEAN, or MODE if
label data) <method> - the method to use to assign parcel values from the values
of member brainordinates
[-exclude-outliers] - exclude non-numeric values and outliers from each
parcel by standard deviation <sigma-below> - number of standard deviations below
the mean to
include
<sigma-above> - number of standard deviations above the mean to
include
[-only-numeric] - exclude non-numeric values
[-fill-value] - specify value to use in empty parcels (default 0)
<value> - the value to fill empty parcels with
[-nonempty-mask-out] - output a matching pscalar file that has 0s in
empty parcels, and 1s elsewhere <mask-out> - output - the output mask file
[-legacy-mode] - use the old behavior, parcels are defined by the
intersection between labels and valid data, and empty parcels are discarded
[-include-empty] - deprecated: now the default behavior
Each label (other than the unlabeled key) in the cifti label file will be treated
as a parcel, and all rows or columns of data within the parcel are averaged
together to form the parcel's output row or column. If -legacy-mode is specified,
parcels will be defined as the overlap between a label and the data, with no errors
for missing data vertices or voxels, and empty parcels discarded. The direction
can be either an integer starting from 1, or the strings 'ROW' or 'COLUMN'. For
dtseries or dscalar, use COLUMN. If you are parcellating a dconn in both
directions, parcellating by ROW first will use much less memory.
The parameter to the -method option must be one of the following:
MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based index of the
maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all values
PRODUCT: multiply all values MEAN: the mean of the data STDEV: the standard
deviation (N denominator) SAMPSTDEV: the sample standard deviation (N-1
denominator) VARIANCE: the variance of the data TSNR: mean divided by sample
standard deviation (N-1 denominator) COV: sample standard deviation (N-1
denominator) divided by mean L2NORM: square root of sum of squares MEDIAN: the
median of the data MODE: the mode of the data COUNT_NONZERO: the number of nonzero
elements in the data
The -*-weights options are mutually exclusive and may only be used with MEAN
(default), SUM, STDEV, SAMPSTDEV, VARIANCE, MEDIAN, or MODE (default for label
data).
-cifti-reduce PERFORM REDUCTION OPERATION ON A CIFTI FILE
wb_command -cifti-reduce
<cifti-in> - the cifti file to reduce <operation> - the reduction operator to use
<cifti-out> - output - the output cifti file
[-direction] - specify what direction to reduce along
<direction> - the direction (default ROW)
[-exclude-outliers] - exclude non-numeric values and outliers by standard
deviation <sigma-below> - number of standard deviations below the mean to
include
<sigma-above> - number of standard deviations above the mean to
include
[-only-numeric] - exclude non-numeric values
For the specified direction (default ROW), perform a reduction operation along that
direction. The direction can be either an integer starting from 1, or the strings
'ROW' or 'COLUMN'. The reduction operators are as follows:
MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based index of the
maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all values
PRODUCT: multiply all values MEAN: the mean of the data STDEV: the standard
deviation (N denominator) SAMPSTDEV: the sample standard deviation (N-1
denominator) VARIANCE: the variance of the data TSNR: mean divided by sample
standard deviation (N-1 denominator) COV: sample standard deviation (N-1
denominator) divided by mean L2NORM: square root of sum of squares MEDIAN: the
median of the data MODE: the mode of the data COUNT_NONZERO: the number of nonzero
elements in the data
-cifti-reorder REORDER THE PARCELS OR SCALAR/LABEL MAPS IN A CIFTI FILE
wb_command -cifti-reorder
<cifti-in> - input cifti file <direction> - which dimension to reorder along, ROW
or COLUMN <reorder-list> - a text file containing the desired order transformation
<cifti-out> - output - the reordered cifti file
The mapping along the specified direction must be parcels, scalars, or labels. For
pscalar or ptseries, use COLUMN to reorder the parcels. For dlabel, use ROW. The
<reorder-list> file must contain 1-based indices separated by whitespace (spaces,
newlines, tabs, etc), with as many indices as <cifti-in> has along the specified
dimension. These indices specify which current index should end up in that
position, for instance, if the current order is 'A B C D', and the desired order is
'D A B C', the text file should contain '4 1 2 3'.
-cifti-replace-structure REPLACE DATA IN A STRUCTURE IN A CIFTI FILE
wb_command -cifti-replace-structure
<cifti> - the cifti to modify <direction> - which dimension to interpret as a
single map, ROW or COLUMN
[-volume-all] - replace the data in all volume components
<volume> - the input volume
[-from-cropped] - the input is cropped to the size of the data
[-discard-unused-labels] - when operating on a dlabel file, drop any
unused label keys from the label table
[-label] - repeatable - replace the data in a surface label component
<structure> - the structure to replace the data of <label> - the input label file
[-metric] - repeatable - replace the data in a surface component
<structure> - the structure to replace the data of <metric> - the input metric
[-volume] - repeatable - replace the data in a volume component
<structure> - the structure to replace the data of <volume> - the input volume
[-from-cropped] - the input is cropped to the size of the component
You must specify at least one of -metric, -label, -volume, or -volume-all for this
command to do anything. Input volumes must line up with the output of
-cifti-separate. For dtseries/dscalar, use COLUMN, and if your matrix will be
fully symmetric, COLUMN is more efficient. The structure argument must be one of
the following:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-cifti-resample 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
-cifti-resample-dconn-memory USE LOTS OF MEMORY TO RESAMPLE DCONN
wb_command -cifti-resample-dconn-memory
<cifti-in> - the cifti file to resample <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 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)
[-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
This command does the same thing as running -cifti-resample twice, but uses memory
up to approximately 2x the size that the intermediate file would be. This is
because the intermediate dconn is kept in memory, rather than written to disk, and
the components before and after resampling/dilation have to be in memory at the
same time during the relevant computation. 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.
To get the v1.3.2 and earlier behavior of weighted dilation, specify exponent of 2
for surface and volume, and -legacy-cutoff for both surface and volume.
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
-cifti-restrict-dense-map EXCLUDE BRAINORDINATES FROM A CIFTI FILE
wb_command -cifti-restrict-dense-map
<cifti-in> - the input cifti <direction> - which dimension to change the mapping on
(integer, 'ROW',
or 'COLUMN')
<cifti-out> - output - the output cifti
[-cifti-roi] - cifti file containing combined rois
<roi-cifti> - the rois as a cifti file
[-left-roi] - vertices to use from left hemisphere
<roi-metric> - the left roi as a metric file
[-right-roi] - vertices to use from right hemisphere
<roi-metric> - the right roi as a metric file
[-cerebellum-roi] - vertices to use from cerebellum
<roi-metric> - the cerebellum roi as a metric file
[-vol-roi] - voxels to use
<roi-vol> - the roi volume file
Writes a modified version of <cifti-in>, where all brainordinates outside the
specified roi(s) are removed from the file. The direction can be either an integer
starting from 1, or the strings 'ROW' or 'COLUMN'. If -cifti-roi is specified, no
other -*-roi option may be specified. If not using -cifti-roi, any -*-roi options
not present will discard the relevant structure, if present in the input file.
-cifti-roi-average AVERAGE ROWS IN A SINGLE CIFTI FILE
wb_command -cifti-roi-average
<cifti-in> - the cifti file to average rows from <text-out> - output text file of
the average values
[-cifti-roi] - cifti file containing combined rois
<roi-cifti> - the rois as a cifti file
[-left-roi] - vertices to use from left hemisphere
<roi-metric> - the left roi as a metric file
[-right-roi] - vertices to use from right hemisphere
<roi-metric> - the right roi as a metric file
[-cerebellum-roi] - vertices to use from cerebellum
<roi-metric> - the cerebellum roi as a metric file
[-vol-roi] - voxels to use
<roi-vol> - the roi volume file
Average the rows that are within the specified ROIs, and write the resulting
average row to a text file, separated by newlines. If -cifti-roi is specified,
-left-roi, -right-roi, -cerebellum-roi, and -vol-roi must not be specified.
-cifti-rois-from-extrema CREATE CIFTI ROI MAPS FROM EXTREMA MAPS
wb_command -cifti-rois-from-extrema
<cifti> - the input cifti <surf-limit> - geodesic distance limit from vertex, in mm
<vol-limit> - euclidean distance limit from voxel center, in mm <direction> - which
dimension an extrema map is along, ROW or COLUMN <cifti-out> - output - the output
cifti
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-gaussian] - generate gaussian kernels instead of flat ROIs
<surf-sigma> - the sigma for the surface gaussian kernel, in mm <vol-sigma> - the
sigma for the volume gaussian kernel, in mm
[-overlap-logic] - how to handle overlapping ROIs, default ALLOW
<method> - the method of resolving overlaps
[-merged-volume] - treat volume components as if they were a single
component
For each nonzero value in each map, make a map with an ROI around that location.
If the -gaussian option is specified, then normalized gaussian kernels are output
instead of ROIs. The <method> argument to -overlap-logic must be one of ALLOW,
CLOSEST, or EXCLUDE. ALLOW is the default, and means that ROIs are treated
independently and may overlap. CLOSEST means that ROIs may not overlap, and that
no ROI contains vertices that are closer to a different seed vertex. EXCLUDE means
that ROIs may not overlap, and that any vertex within range of more than one ROI
does not belong to any ROI.
-cifti-separate WRITE A CIFTI STRUCTURE AS METRIC, LABEL OR VOLUME
wb_command -cifti-separate
<cifti-in> - the cifti to separate a component of <direction> - which direction to
separate into components, ROW or COLUMN
[-volume-all] - separate all volume structures into a volume file
<volume-out> - output - the output volume
[-roi] - also output the roi of which voxels have data
<roi-out> - output - the roi output volume
[-label] - output a volume label file indicating the location of
structures <label-out> - output - the label output volume
[-crop] - crop volume to the size of the data rather than using the
original volume size
[-label] - repeatable - separate a surface model into a surface label
file <structure> - the structure to output <label-out> - output - the output label
file
[-roi] - also output the roi of which vertices have data
<roi-out> - output - the roi output metric
[-metric] - repeatable - separate a surface model into a metric file
<structure> - the structure to output <metric-out> - output - the output metric
[-roi] - also output the roi of which vertices have data
<roi-out> - output - the roi output metric
[-volume] - repeatable - separate a volume structure into a volume file
<structure> - the structure to output <volume-out> - output - the output volume
[-roi] - also output the roi of which voxels have data
<roi-out> - output - the roi output volume
[-crop] - crop volume to the size of the component rather than using
the original volume size
For dtseries, dscalar, and dlabel, use COLUMN for <direction>, and if you have a
symmetric dconn, COLUMN is more efficient.
You must specify at least one of -metric, -volume-all, -volume, or -label for this
command to do anything. Output volumes will spatially line up with their original
positions, whether or not they are cropped. Volume files produced by separating a
dlabel file, or from the -label suboption of -volume-all, will be label volumes,
see -volume-help.
For each <structure> argument, use one of the following strings:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-cifti-smoothing SMOOTH A CIFTI FILE
wb_command -cifti-smoothing
<cifti> - the input cifti <surface-kernel> - the sigma for the gaussian surface
smoothing kernel,
in mm
<volume-kernel> - the sigma for the gaussian volume smoothing kernel, in
mm
<direction> - which dimension to smooth along, ROW or COLUMN <cifti-out> - output -
the output cifti
[-left-surface] - specify the left surface to use
<surface> - the left surface file
[-left-corrected-areas] - vertex areas to use instead of computing
them from the left surface <area-metric> - the corrected vertex areas, as a metric
[-right-surface] - specify the right surface to use
<surface> - the right surface file
[-right-corrected-areas] - vertex areas to use instead of computing
them from the right surface <area-metric> - the corrected vertex areas, as a metric
[-cerebellum-surface] - specify the cerebellum surface to use
<surface> - the cerebellum surface file
[-cerebellum-corrected-areas] - vertex areas to use instead of
computing them from the cerebellum surface <area-metric> - the corrected vertex
areas, as a metric
[-cifti-roi] - smooth only within regions of interest
<roi-cifti> - the regions to smooth within, as a cifti file
[-fix-zeros-volume] - treat values of zero in the volume as missing data
[-fix-zeros-surface] - treat values of zero on the surface as missing
data
[-merged-volume] - smooth across subcortical structure boundaries
The input cifti file must have a brain models mapping on the chosen dimension,
columns for .dtseries, and either for .dconn. By default, data in different
structures is smoothed independently (i.e., "parcel constrained" smoothing), so
volume structures that touch do not smooth across this boundary. Specify
-merged-volume to ignore these boundaries. Surface smoothing uses the
GEO_GAUSS_AREA smoothing method.
The -*-corrected-areas options are intended for when it is unavoidable to smooth on
group average surfaces, it is only an approximate correction for the reduction of
structure in a group average surface. It is better to smooth the data on
individuals before averaging, when feasible.
The -fix-zeros-* options will treat values of zero as lack of data, and not use
that value when generating the smoothed values, but will fill zeros with
extrapolated values. The ROI should have a brain models mapping along columns,
exactly matching the mapping of the chosen direction in the input file. Data
outside the ROI is ignored.
-cifti-stats STATISTICS ALONG CIFTI COLUMNS
wb_command -cifti-stats
<cifti-in> - the input cifti
[-reduce] - use a reduction operation
<operation> - the reduction operation
[-percentile] - give the value at a percentile
<percent> - the percentile to find
[-column] - only display output for one column
<column> - the column index (starting from 1)
[-roi] - only consider data inside an roi
<roi-cifti> - the roi, as a cifti file
[-match-maps] - each column of input uses the corresponding column
from the roi file
[-show-map-name] - print column index and name before each output
For each column of the input, a row of text is printed, resulting from the
specified reduction or percentile operation. If -roi is specified without
-match-maps, then each row contains as many numbers as there are maps in the ROI
file, separated by tab characters. Use -column to only give output for a single
data column. Exactly one of -reduce or -percentile must be specified.
The argument to the -reduce option must be one of the following:
MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based index of the
maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all values
PRODUCT: multiply all values MEAN: the mean of the data STDEV: the standard
deviation (N denominator) SAMPSTDEV: the sample standard deviation (N-1
denominator) VARIANCE: the variance of the data TSNR: mean divided by sample
standard deviation (N-1 denominator) COV: sample standard deviation (N-1
denominator) divided by mean L2NORM: square root of sum of squares MEDIAN: the
median of the data MODE: the mode of the data COUNT_NONZERO: the number of nonzero
elements in the data
-cifti-transpose TRANSPOSE A CIFTI FILE
wb_command -cifti-transpose
<cifti-in> - the input cifti file <cifti-out> - output - the output cifti file
[-mem-limit] - restrict memory usage
<limit-GB> - memory limit in gigabytes
The input must be a 2-dimensional cifti file.
The output is a cifti file
where every row in the input is a column in the output.
-cifti-vector-operation DO A VECTOR OPERATION ON CIFTI FILES
wb_command -cifti-vector-operation
<vectors-a> - first vector input file <vectors-b> - second vector input file
<operation> - what vector operation to do <cifti-out> - output - the output file
[-normalize-a] - normalize vectors of first input
[-normalize-b] - normalize vectors of second input
[-normalize-output] - normalize output vectors (not valid for dot
product)
[-magnitude] - output the magnitude of the result (not valid for dot
product)
Does a vector operation on two cifti files (that must have a multiple of 3
columns). Either of the inputs may have multiple vectors (more than 3 columns),
but not both (at least one must have exactly 3 columns). The -magnitude and
-normalize-output options may not be specified together, or with an operation that
returns a scalar (dot product). The <operation> parameter must be one of the
following:
DOT CROSS ADD SUBTRACT
-cifti-weighted-stats WEIGHTED STATISTICS ALONG CIFTI COLUMNS
wb_command -cifti-weighted-stats
<cifti-in> - the input cifti
[-spatial-weights] - use vertex area and voxel volume as weights
[-left-area-surf] - use a surface for left vertex areas
<left-surf> - the left surface to use, areas are in mm^2
[-right-area-surf] - use a surface for right vertex areas
<right-surf> - the right surface to use, areas are in mm^2
[-cerebellum-area-surf] - use a surface for cerebellum vertex areas
<cerebellum-surf> - the cerebellum surface to use, areas are in
mm^2
[-left-area-metric] - use a metric file for left vertex areas
<left-metric> - metric file containing left vertex areas
[-right-area-metric] - use a metric file for right vertex areas
<right-metric> - metric file containing right vertex areas
[-cerebellum-area-metric] - use a metric file for cerebellum vertex
areas <cerebellum-metric> - metric file containing cerebellum vertex
areas
[-cifti-weights] - use a cifti file containing weights
<weight-cifti> - the weights to use, as a cifti file
[-column] - only display output for one column
<column> - the column to use (1-based)
[-roi] - only consider data inside an roi
<roi-cifti> - the roi, as a cifti file
[-match-maps] - each column of input uses the corresponding column
from the roi file
[-mean] - compute weighted mean
[-stdev] - compute weighted standard deviation
[-sample] - estimate population stdev from the sample
[-percentile] - compute weighted percentile
<percent> - the percentile to find
[-sum] - compute weighted sum
[-show-map-name] - print map index and name before each output
If the mapping along column is brain models, for each column of the input, the
specified operation is done on each surface and across all voxels, and the results
are printed separately. For other mapping types, the operation is done on each
column, and one number per map is printed. Exactly one of -spatial-weights or
-cifti-weights must be specified. Use -column to only give output for a single
column. Use -roi to consider only the data within a region. Exactly one of -mean,
-stdev, -percentile or -sum must be specified.
Using -sum with -spatial-weights (or with -cifti-weights and a cifti containing
weights of similar meaning) is equivalent to integrating with respect to area and
volume. When the input is binary ROIs, this will therefore output the area or
volume of each ROI.
-class-add-member
Add members to class header (.h) and implementation (.cxx) files.
[-add-to-files] [-m <member-name> <data-type> <description>]...
If the -add-to-files is not specified, the code for the header and implementation
files is printed to the terminal.
If the -add-to-files is specified, the class files are expected to be in the
current directory and named <class-name>.h and <class-name>.cxx. The header file
must contain this text in its private section:
// ADD_NEW_MEMBERS_HERE
The implementation file must contain this text in its public section:
// ADD_NEW_METHODS_HERE
If either of these text string are missing, the code that would have been added to
the file(s) is printed to the terminal.
For each member, three text strings separated by a space must be provided and they
are the name of the member its data type, and a description of the member. If the
description contains spaces the description must be enclosed in double quotes ("").
If the data type begins with a capital letter, it is assumed to be the name of a
class. In this case, both const and non-const getters are created but not setter
is created. Otherwise, the data type is expected to be a primitive type and both a
getter and a setter are created. Note that AString and QString are treated as
primitive types.
-class-create
Create class header (.h) and implementation (.cxx) files.
Usage: <class-name>
[-copy] [-equal] [-event-class <event-type-enum>] [-event-listener] [-no-parent]
[-parent <parent-class-name>] [-scene] [-scene-sub-class]
OPTIONS
-copy
Adds copy constructor and assignment operator
-equal
Adds equality operator.
-event-class <event-type-enum>
When creating an Event subclass, using this option will automatically set the
parent class to Event and place the given event enumerated type value into the
parameter for the Event class constructor.
For the <event-type-enum> there is no need to prepend it with "EventTypeEnum::".
-event-listener
Implement the EventListenerInterface so that the class may listen for events.
-no-parent
Created class is not derived from any other class. By default, the parent class is
CaretObject.
-parent <parent-class-name>
Specify the parent (derived from) class. By default, the parent class is
CaretObject.
-scene
Implement the SceneableInterface so that instances of the class can be restored
from and saved to scenes.
-scene-sub-class
Adds methods that can be called by the superclass so that this sub-class can save
and restore data to and from scenes.
This option should only be used when creating a class whose super class implements
the SceneableInterface
-class-create-algorithm
Create Algorithm Class header (.h) and implementation (.cxx) files.
Usage: <algorithm-class-name>
<command-line-switch> <short-description>
algorithm-class-name
Required name of the algorithm class that MUST start with "Algorithm"
command-line-switch
Required command line switch for algorithm.
short-description
Required short description within double quotes.
-class-create-enum
Create enumerated type header (.h) and implementation (.cxx) files.
Usage: <enum-class-name>
<number-of-values> <auto-number>
enum-class-name
Name of the enumerated type.
Must end in "Enum"
number-of-values
Number of values in the enumerated type.
auto-number
Automatically generated integer codes corresponding to the enumerated values.
Value for this parameter are "true" and "false".
[enum-name-1] [enum-name-2]...[enum-name-N]
Optional names for the enumerated values.
If the number of names listed is greater than the "number-of-values" parameter, the
"number-of-values" will become the number of names. If the number of names is is
less than the "number-of-values", empty entries will be created.
-class-create-operation
Create Operation Class header (.h) and implementation (.cxx) files.
Usage: <operation-class-name>
<command-line-switch> <short-description> [-no-parameters]
operation-class-name
Required name of the operation class that MUST start with "Operation"
command-line-switch
Required command line switch for operation.
short-description
Required short description within double quotes.
-no-parameters
Optional parameter if the operation does not use parameters.
-convert-affine CONVERT AN AFFINE FILE BETWEEN CONVENTIONS
wb_command -convert-affine
[-from-world] - input is a NIFTI 'world' affine
<input> - the input affine
[-inverse] - for files that use 'target to source' convention
[-from-itk] - input is an ITK matrix
<input> - the input affine
[-from-flirt] - input is a flirt matrix
<input> - the input affine <source-volume> - the source volume used when generating
the input
affine
<target-volume> - the target volume used when generating the input
affine
[-to-world] - write output as a NIFTI 'world' affine
<output> - output - the output affine
[-inverse] - write file using 'target to source' convention
[-to-itk] - write output as an ITK affine
<output> - output - the output affine
[-to-flirt] - repeatable - write output as a flirt matrix
<output> - output - the output affine <source-volume> - the volume you want to
apply the transform to <target-volume> - the target space you want the transformed
volume to
match
NIFTI world matrices can be used directly on mm coordinates via matrix
multiplication, they use the NIFTI coordinate system, that is, positive X is right,
positive Y is anterior, and positive Z is superior. Note that wb_command assumes
that world matrices transform source coordinates to target coordinates, while other
tools may use affines that transform target coordinates to source coordinates.
The ITK format is used by ANTS.
You must specify exactly one -from option, but you may specify multiple -to
options, and -to-flirt may be specified more than once.
-convert-fiber-orientations CONVERT BINGHAM PARAMETER VOLUMES TO FIBER ORIENTATION FILE
wb_command -convert-fiber-orientations
<label-volume> - volume of cifti structure labels <fiber-out> - output - the output
fiber orientation file
[-fiber] - repeatable - specify the parameter volumes for a fiber
<mean-f> - mean fiber strength <stdev-f> - standard deviation of fiber strength
<theta> - theta angle <phi> - phi angle <psi> - psi angle <ka> - ka bingham
parameter <kb> - kb bingham parameter
Takes precomputed bingham parameters from volume files and converts them to the
format workbench uses for display. The <label-volume> argument must be a label
volume, where the labels use these strings:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-convert-matrix4-to-matrix2 GENERATES A MATRIX2 CIFTI FROM MATRIX4 WBSPARSE
wb_command -convert-matrix4-to-matrix2
<matrix4-wbsparse> - a wbsparse matrix4 file <counts-out> - output - the total
fiber counts, as a cifti file
[-distances] - output average trajectory distance
<distance-out> - output - the distances, as a cifti file
[-individual-fibers] - output files for each fiber direction
<fiber-1> - output - output file for first fiber <fiber-2> - output - output file
for second fiber <fiber-3> - output - output file for third fiber
This command makes a cifti file from the fiber counts in a matrix4 wbsparse file,
and optionally a second cifti file from the distances. Note that while the total
count is stored exactly, the per-fiber counts are stored as approximate fractions,
so the output of -individual-fibers will contain nonintegers.
-convert-matrix4-to-workbench-sparse CONVERT A 3-FILE MATRIX4 TO A WORKBENCH SPARSE FILE
wb_command -convert-matrix4-to-workbench-sparse
<matrix4_1> - the first matrix4 file <matrix4_2> - the second matrix4 file
<matrix4_3> - the third matrix4 file <orientation-file> - the .fiberTEMP.nii file
this trajectory file applies
to
<voxel-list> - list of white matter voxel index triplets as used in the
trajectory matrix
<wb-sparse-out> - output - the output workbench sparse file
[-surface-seeds] - specify the surface seed space
<seed-roi> - metric roi file of all vertices used in the seed space
[-volume-seeds] - specify the volume seed space
<cifti-template> - cifti file to use the volume mappings from <direction> -
dimension along the cifti file to take the mapping from,
ROW or COLUMN
Converts the matrix 4 output of probtrackx to workbench sparse file format.
Exactly one of -surface-seeds and -volume-seeds must be specified.
-convert-warpfield CONVERT A WARPFIELD BETWEEN CONVENTIONS
wb_command -convert-warpfield
[-from-world] - input is a NIFTI 'world' warpfield
<input> - the input warpfield
[-from-itk] - input is an ITK warpfield
<input> - the input warpfield
[-from-fnirt] - input is a fnirt warpfield
<input> - the input warpfield <source-volume> - the source volume used when
generating the input
warpfield
[-absolute] - warpfield was written in absolute convention, rather
than relative
[-to-world] - write output as a NIFTI 'world' warpfield
<output> - output - the output warpfield
[-to-itk] - write output as an ITK warpfield
<output> - output - the output warpfield
[-to-fnirt] - repeatable - write output as a fnirt warpfield
<output> - output - the output warpfield <source-volume> - the volume you want to
apply the warpfield to
NIFTI world warpfields can be used directly on mm coordinates via sampling the
three subvolumes at the coordinate and adding the sampled values to the coordinate
vector. They use the NIFTI coordinate system, that is, X is left to right, Y is
posterior to anterior, and Z is inferior to superior.
NOTE: this command does not invert the warpfield, and to warp a surface, you must
use the inverse of the warpfield that warps the corresponding volume.
The ITK format is used by ANTS.
You must specify exactly one -from option, but you may specify multiple -to
options, and -to-fnirt may be specified more than once.
-create-signed-distance-volume CREATE SIGNED DISTANCE VOLUME FROM SURFACE
wb_command -create-signed-distance-volume
<surface> - the input surface <refspace> - a volume in the desired output space
(dims, spacing, origin) <outvol> - output - the output volume
[-roi-out] - output an roi volume of where the output has a computed
value <roi-vol> - output - the output roi volume
[-fill-value] - specify a value to put in all voxels that don't get
assigned a distance <value> - value to fill with (default 0)
[-exact-limit] - specify distance for exact output
<dist> - distance in mm (default 5)
[-approx-limit] - specify distance for approximate output
<dist> - distance in mm (default 20)
[-approx-neighborhood] - voxel neighborhood for approximate calculation
<num> - size of neighborhood cube measured from center to face, in
voxels (default 2 = 5x5x5)
[-winding] - winding method for point inside surface test
<method> - name of the method (default EVEN_ODD)
Computes the signed distance function of the surface.
Exact distance is
calculated by finding the closest point on any surface triangle to the center of
the voxel. Approximate distance is calculated starting with these distances, using
dijkstra's method with a neighborhood of voxels. Specifying too small of an exact
distance may produce unexpected results. Valid specifiers for winding methods are
as follows:
EVEN_ODD (default) NEGATIVE NONZERO NORMALS
The NORMALS method uses the normals of triangles and edges, or the closest triangle
hit by a ray from the point. This method may be slightly faster, but is only
reliable for a closed surface that does not cross through itself. All other
methods count entry (positive) and exit (negative) crossings of a vertical ray from
the point, then counts as inside if the total is odd, negative, or nonzero,
respectively.
-estimate-fiber-binghams ESTIMATE FIBER ORIENTATION DISTRIBUTIONS FROM BEDPOSTX SAMPLES
wb_command -estimate-fiber-binghams
<merged_f1samples> - fiber 1 strength samples <merged_th1samples> - fiber 1 theta
samples <merged_ph1samples> - fiber 1 phi samples <merged_f2samples> - fiber 2
strength samples <merged_th2samples> - fiber 2 theta samples <merged_ph2samples> -
fiber 2 phi samples <merged_f3samples> - fiber 3 strength samples
<merged_th3samples> - fiber 3 theta samples <merged_ph3samples> - fiber 3 phi
samples <label-volume> - volume of cifti structure labels <cifti-out> - output -
output cifti fiber distributons file
This command does an estimation of a bingham distribution for each fiber
orientation in each voxel which is labeled a structure identifier. These labelings
come from the <label-volume> argument, which must have labels that match the
following strings:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-fiber-dot-products COMPUTE DOT PRODUCTS OF FIBER ORIENTATIONS WITH SURFACE NORMALS
wb_command -fiber-dot-products
<white-surf> - the white/gray boundary surface <fiber-file> - the fiber orientation
file <max-dist> - the maximum distance from any surface vertex a fiber
population may be, in mm
<direction> - test against surface for whether a fiber population should
be used
<dot-metric> - output - the metric of dot products <f-metric> - output - a metric
of the f values of the fiber distributions
For each vertex, this command finds the closest fiber population that satisfies the
<direction> test, and computes the absolute value of the dot product of the surface
normal and the normalized mean direction of each fiber. The <direction> test must
be one of INSIDE, OUTSIDE, or ANY, which causes the command to only use fiber
populations that are inside the surface, outside the surface, or to not care which
direction it is from the surface. Each fiber population is output in a separate
metric column.
-file-convert CHANGE VERSION OF FILE FORMAT
wb_command -file-convert
[-border-version-convert] - write a border file with a different version
<border-in> - the input border file <out-version> - the format version to write as,
1 or 3 (2 doesn't
exist)
<border-out> - output - the output border file
[-surface] - must be specified if the input is version 1
<surface> - use this surface file for structure and number of
vertices, ignore borders on other structures
[-nifti-version-convert] - write a nifti file with a different version
<input> - the input nifti file <version> - the nifti version to write as <output> -
output - the output nifti file
[-cifti-version-convert] - write a cifti file with a different version
<cifti-in> - the input cifti file <version> - the cifti version to write as
<cifti-out> - output - the output cifti file
You may only specify one top-level option.
-file-information LIST INFORMATION ABOUT A FILE'S CONTENT
wb_command -file-information
<data-file> - data file
[-no-map-info] - do not show map information for files that support maps
[-only-step-interval] - suppress normal output, print the interval
between maps
[-only-number-of-maps] - suppress normal output, print the number of maps
[-only-map-names] - suppress normal output, print the names of all maps
[-only-metadata] - suppress normal output, print file metadata
[-key] - only print the metadata for one key, with no formatting
<key> - the metadata key
[-only-cifti-xml] - suppress normal output, print the cifti xml if the
file type has it
List information about the content of a data file.
Only one -only option
may be specified.
The information listed when no -only option is present
is dependent upon the type of data file.
-foci-create CREATE A FOCI FILE
wb_command -foci-create
<output> - output - the output foci file
[-class] - repeatable - specify class input data
<class-name> - name of class <foci-list-file> - text file containing foci names,
coordinates, and
colors
<surface> - surface file for projection of foci list file
Creates a foci file from names, coordinates, and RGB values in a text file. The
text file must have the following format (2 lines per focus):
<focus-name> <red> <green> <blue> <x> <y> <z> ...
Foci names are specified on a separate line from their coordinates and color, in
order to let foci names contain spaces. Whitespace is trimmed from both ends of
the foci name, but is kept if it is in the middle of a name. The values of <red>,
<green>, <blue> and must be integers from 0 to 255, and will specify the color the
foci is drawn as.
Foci are grouped into classes and the name for the class is specified using the
<class-name> parameter.
All foci within one text file must be associated with the structure contained in
the <surface> parameter and are projected to that surface.
-foci-get-projection-vertex GET PROJECTION VERTEX FOR FOCI
wb_command -foci-get-projection-vertex
<foci> - the foci file <surface> - the surface related to the foci file
<metric-out> - output - the output metric file
[-name] - select a focus by name
<name> - the name of the focus
For each focus, a column is created in <metric-out>, and the vertex with the most
influence on its projection is assigned a value of 1 in that column, with all other
vertices 0. If -name is used, only one focus will be used.
-foci-list-coords OUTPUT FOCI COORDINATES IN A TEXT FILE
wb_command -foci-list-coords
<foci-file> - input foci file <coord-file-out> - output - the output coordinate
text file
[-names-out] - output the foci names
<names-file-out> - output - text file to put foci names in
Output the coordinates for every focus in the foci file, and optionally the focus
names in a second text file.
-foci-resample PROJECT FOCI TO A DIFFERENT SURFACE
wb_command -foci-resample
<foci-in> - the input foci file <foci-out> - output - the output foci file
[-left-surfaces] - the left surfaces for resampling
<current-surf> - the surface the foci are currently projected on <new-surf> - the
surface to project the foci onto
[-right-surfaces] - the right surfaces for resampling
<current-surf> - the surface the foci are currently projected on <new-surf> - the
surface to project the foci onto
[-cerebellum-surfaces] - the cerebellum surfaces for resampling
<current-surf> - the surface the foci are currently projected on <new-surf> - the
surface to project the foci onto
[-discard-distance-from-surface] - ignore the distance the foci are above
or below the current surface
[-restore-xyz] - put the original xyz coordinates into the foci, rather
than the coordinates obtained from unprojection
Unprojects foci from the <current-surf> for the structure, then projects them to
<new-surf>. If the foci have meaningful distances above or below the surface, use
anatomical surfaces. If the foci should be on the surface, use registered spheres
and the options -discard-distance-from-surface and -restore-xyz.
-gifti-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A GIFTI COLUMN
wb_command -gifti-all-labels-to-rois
<label-in> - the input gifti label file <map> - the number or name of the label map
to use <metric-out> - output - the output metric file
The output metric file has a column for each label in the specified input map,
other than the ??? label, each of which contains an ROI of all vertices that are
set to the corresponding label.
-gifti-convert CONVERT A GIFTI FILE TO A DIFFERENT ENCODING
wb_command -gifti-convert
<gifti-encoding> - what the output encoding should be <input-gifti-file> - the
input gifti file <output-gifti-file> - output - the output gifti file
The value of <gifti-encoding> must be one of the following:
ASCII BASE64_BINARY GZIP_BASE64_BINARY EXTERNAL_FILE_BINARY
-gifti-label-add-prefix ADD PREFIX TO ALL LABEL NAMES IN A GIFTI LABEL FILE
wb_command -gifti-label-add-prefix
<label-in> - the input label file <prefix> - the prefix string to add <label-out> -
output - the output label file
For each label other than '???', prepend <prefix> to the label name.
-gifti-label-to-roi MAKE A GIFTI LABEL INTO AN ROI METRIC
wb_command -gifti-label-to-roi
<label-in> - the input gifti label file <metric-out> - output - the output metric
file
[-name] - select label by name
<label-name> - the label name that you want an roi of
[-key] - select label by key
<label-key> - the label key that you want an roi of
[-map] - select a single label map to use
<map> - the map number or name
For each map in <label-in>, a map is created in <metric-out> where all locations
labeled with <label-name> or with a key of <label-key> are given a value of 1, and
all other locations are given 0. Exactly one of -name and -key must be specified.
Specify -map to use only one map from <label-in>.
-label-dilate DILATE A LABEL FILE
wb_command -label-dilate
<label> - the input label <surface> - the surface to dilate on <dilate-dist> -
distance in mm to dilate the labels <label-out> - output - the output label file
[-bad-vertex-roi] - specify an roi of vertices to overwrite, rather than
vertices with the unlabeled key <roi-metric> - metric file, positive values denote
vertices to have
their values replaced
[-column] - select a single column to dilate
<column> - the column number or name
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
Fills in label information for all vertices designated as bad, up to the specified
distance away from other labels. If -bad-vertex-roi is specified, all vertices,
including those with the unlabeled key, are good, except for vertices with a
positive value in the ROI. If it is not specified, only vertices with the
unlabeled key are bad.
-label-erode ERODE A LABEL FILE
wb_command -label-erode
<label> - the input label <surface> - the surface to erode on <erode-dist> -
distance in mm to erode the labels <label-out> - output - the output label file
[-roi] - assume values outside this roi are labeled
<roi-metric> - metric file, positive values denote vertices that have
data
[-column] - select a single column to erode
<column> - the column number or name
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
Around each vertex that is unlabeled, set surrounding vertices to unlabeled. The
surrounding vertices are all immediate neighbors and all vertices within the
specified distance.
Note that the -corrected-areas option uses an approximate correction for distance
along the surface.
-label-export-table EXPORT LABEL TABLE FROM GIFTI AS TEXT
wb_command -label-export-table
<label-in> - the input label file <table-out> - output - the output text file
Takes the label table from the gifti label file, and writes it to a text format
matching what is expected by -metric-label-import.
-label-mask MASK A LABEL FILE
wb_command -label-mask
<label> - the label file to mask <mask> - the mask metric <label-out> - output -
the output label file
[-column] - select a single column
<column> - the column number or name
By default, the output label is a copy of the input label, but with the 'unused'
label wherever the mask metric is zero or negative. if -column is specified, the
output contains only one column, the masked version of the specified input column.
-label-merge MERGE LABEL FILES INTO A NEW FILE
wb_command -label-merge
<label-out> - output - the output label
[-label] - repeatable - specify an input label
<label-in> - a label file to use columns from
[-column] - repeatable - select a single column to use
<column> - the column number or name
[-up-to] - use an inclusive range of columns
<last-column> - the number or name of the last column to include
[-reverse] - use the range in reverse order
Takes one or more label files and constructs a new label file by concatenating
columns from them. The input files must have the same number of vertices and the
same structure.
Example: wb_command -label-merge out.label.gii -label first.label.gii -column 1
-label second.label.gii
This example would take the first column from first.label.gii and all subvolumes
from second.label.gii, and write these to out.label.gii.
-label-modify-keys CHANGE KEY VALUES IN A LABEL FILE
wb_command -label-modify-keys
<label-in> - the input label file <remap-file> - text file with old and new key
values <label-out> - output - output label file
[-column] - select a single column to use
<column> - the column number or name
<remap-file> should have lines of the form 'oldkey newkey', like so:
3 5 5 8 8 2
This would change the current label with key '3' to use the key '5' instead, 5
would use 8, and 8 would use 2. Any collision in key values results in the label
that was not specified in the remap file getting remapped to an otherwise unused
key. Remapping more than one key to the same new key, or the same key to more than
one new key, results in an error. This will not change the appearance of the file
when displayed, as it will change the key values in the data at the same time.
-label-probability FIND FREQUENCY OF SURFACE LABELS
wb_command -label-probability
<label-maps> - label file containing individual label maps from many
subjects
<probability-metric-out> - output - the relative frequencies of each
label at each vertex
[-exclude-unlabeled] - don't make a probability map of the unlabeled key
This command outputs a set of soft ROIs, one for each label in the input, where the
value is how many of the input maps had that label at that vertex, divided by the
number of input maps.
-label-resample RESAMPLE A LABEL FILE TO A DIFFERENT MESH
wb_command -label-resample
<label-in> - the label file to resample <current-sphere> - a sphere surface with
the mesh that the label file is
currently on
<new-sphere> - a sphere surface that is in register with <current-sphere>
and has the desired output mesh
<method> - the method name <label-out> - output - the output label file
[-area-surfs] - specify surfaces to do vertex area correction based on
<current-area> - a relevant anatomical surface with <current-sphere>
mesh
<new-area> - a relevant anatomical surface with <new-sphere> mesh
[-area-metrics] - specify vertex area metrics to do area correction based
on <current-area> - a metric file with vertex areas for <current-sphere>
mesh
<new-area> - a metric file with vertex areas for <new-sphere> mesh
[-current-roi] - use an input roi on the current mesh to exclude non-data
vertices <roi-metric> - the roi, as a metric file
[-valid-roi-out] - output the ROI of vertices that got data from valid
source vertices <roi-out> - output - the output roi as a metric
[-largest] - use only the label of the vertex with the largest weight
Resamples a label file, given two spherical surfaces that are in register. If
ADAP_BARY_AREA is used, exactly one of -area-surfs or -area-metrics must be
specified.
The ADAP_BARY_AREA method is recommended for label data, because it should be
better at resolving vertices that are near multiple labels, or in case of
downsampling. Midthickness surfaces are recommended for the vertex areas for most
data.
The -largest option results in nearest vertex behavior when used with BARYCENTRIC,
as it uses the value of the source vertex that has the largest weight.
When -largest is not specified, the vertex weights are summed according to which
label they correspond to, and the label with the largest sum is used.
The <method> argument must be one of the following:
ADAP_BARY_AREA BARYCENTRIC
-label-to-border DRAW BORDERS AROUND LABELS
wb_command -label-to-border
<surface> - the surface to use for neighbor information <label-in> - the input
label file <border-out> - output - the output border file
[-placement] - set how far along the edge border points are drawn
<fraction> - fraction along edge from inside vertex (default 0.33)
[-column] - select a single column
<column> - the column number or name
For each label, finds all edges on the mesh that cross the boundary of the label,
and draws borders through them. By default, this is done on all columns in the
input file, using the map name as the class name for the border.
-label-to-volume-mapping MAP LABEL FILE TO VOLUME
wb_command -label-to-volume-mapping
<label> - the input label file <surface> - the surface to use coordinates from
<volume-space> - a volume file in the desired output volume space <volume-out> -
output - the output volume file
[-nearest-vertex] - use the label from the vertex closest to the voxel
center <distance> - how far from the surface to map labels to voxels, in mm
[-ribbon-constrained] - use ribbon constrained mapping algorithm
<inner-surf> - the inner surface of the ribbon <outer-surf> - the outer surface of
the ribbon
[-voxel-subdiv] - voxel divisions while estimating voxel weights
<subdiv-num> - number of subdivisions, default 3
[-greedy] - also put labels in voxels with less than 50% partial
volume (legacy behavior)
[-thick-columns] - use overlapping columns (legacy method)
Maps labels from a gifti label file into a volume file.
You must specify
exactly one mapping method option.
The -nearest-vertex method uses the
label from the vertex closest to the voxel center.
The
-ribbon-constrained method uses the same method as in
-volume-to-surface-mapping, then uses the weights in reverse, with
popularity logic to decide on a label to use.
-metadata-remove-provenance REMOVE PROVENANCE INFORMATION FROM FILE METADATA
wb_command -metadata-remove-provenance
<input-file> - the file to remove provenance information from <output-file> -
output - the name to save the modified file as
Removes the provenance metadata fields added by workbench during processing.
-metadata-string-replace REPLACE A STRING IN ALL METADATA OF A FILE
wb_command -metadata-string-replace
<input-file> - the file to replace metadata in <find-string> - the string to find
<replace-string> - the string to replace <find-string> with <output-file> - output
- the name to save the modified file as
[-case-insensitive] - match with case variation also
Replaces all occurrences of <find-string> in the metadata and map names of
<input-file> with <replace-string>.
-metric-convert CONVERT METRIC FILE TO FAKE NIFTI
wb_command -metric-convert
[-to-nifti] - convert metric to nifti
<metric-in> - the metric to convert <nifti-out> - output - the output nifti file
[-from-nifti] - convert nifti to metric
<nifti-in> - the nifti file to convert <surface-in> - surface file to use number of
vertices and structure
from
<metric-out> - output - the output metric file
The purpose of this command is to convert between metric files and nifti1 so that
gifti-unaware programs can operate on the data. You must specify exactly one of
the options.
-metric-dilate DILATE A METRIC FILE
wb_command -metric-dilate
<metric> - the metric to dilate <surface> - the surface to compute on <distance> -
distance in mm to dilate <metric-out> - output - the output metric
[-bad-vertex-roi] - specify an roi of vertices to overwrite, rather than
vertices with value zero <roi-metric> - metric file, positive values denote
vertices to have
their values replaced
[-data-roi] - specify an roi of where there is data
<roi-metric> - metric file, positive values denote vertices that have
data
[-column] - select a single column to dilate
<column> - the column number or name
[-nearest] - use the nearest good value instead of a weighted average
[-linear] - fill in values with linear interpolation along strongest
gradient
[-exponent] - use a different exponent in the weighting function
<exponent> - exponent 'n' to use in (area / (distance ^ n)) as the
weighting function (default 6)
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
[-legacy-cutoff] - use the old method of choosing how many vertices to
use when calulating the dilated value with weighted method
For all metric vertices that are designated as bad, if they neighbor a non-bad
vertex with data or are within the specified distance of such a vertex, replace the
value with a distance-based weighted average of nearby non-bad vertices that have
data, otherwise set the value to zero. No matter how small <distance> is, dilation
will always use at least the immediate neighbor vertices. If -nearest is
specified, it will use the value from the closest non-bad vertex with data within
range instead of a weighted average.
If -bad-vertex-roi is specified, all vertices with a positive ROI value are bad.
If it is not specified, only vertices that have data, with a value of zero, are
bad. If -data-roi is not specified, all vertices are assumed to have data.
Note that the -corrected-areas option uses an approximate correction for the change
in distances along a group average surface.
To get the behavior of version 1.3.2 or earlier, use '-legacy-cutoff -exponent 2'.
-metric-erode ERODE A METRIC FILE
wb_command -metric-erode
<metric> - the metric file to erode <surface> - the surface to compute on
<distance> - distance in mm to erode <metric-out> - output - the output metric
[-roi] - assume values outside this roi are nonzero
<roi-metric> - metric file, positive values denote vertices that have
data
[-column] - select a single column to erode
<column> - the column number or name
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
Around each vertex with a value of zero, set surrounding vertices to zero. The
surrounding vertices are all immediate neighbors and all vertices within the
specified distance.
Note that the -corrected-areas option uses an approximate correction for distance
along the surface.
-metric-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A METRIC FILE
wb_command -metric-estimate-fwhm
<surface> - the surface to use for distance and neighbor information <metric-in> -
the input metric
[-roi] - use only data within an ROI
<roi-metric> - the metric file to use as an ROI
[-column] - select a single column to estimate smoothness of
<column> - the column number or name
[-whole-file] - estimate for the whole file at once, not each column
separately
[-demean] - subtract the mean image before estimating smoothness
Estimates the smoothness of the metric columns, printing the estimates to standard
output. These estimates ignore variation in vertex spacing.
-metric-extrema FIND EXTREMA IN A METRIC FILE
wb_command -metric-extrema
<surface> - the surface to use for distance information <metric-in> - the metric to
find the extrema of <distance> - the minimum distance between identified extrema of
the same
type
<metric-out> - output - the output extrema metric
[-presmooth] - smooth the metric before finding extrema
<kernel> - the sigma for the gaussian smoothing kernel, in mm
[-roi] - ignore values outside the selected area
<roi-metric> - the area to find extrema in, as a metric
[-threshold] - ignore small extrema
<low> - the largest value to consider for being a minimum <high> - the smallest
value to consider for being a maximum
[-sum-columns] - output the sum of the extrema columns instead of each
column separately
[-consolidate-mode] - use consolidation of local minima instead of a
large neighborhood
[-only-maxima] - only find the maxima
[-only-minima] - only find the minima
[-column] - select a single column to find extrema in
<column> - the column number or name
Finds extrema in a metric file, such that no two extrema of the same type are
within <distance> of each other. The extrema are labeled as -1 for minima, 1 for
maxima, 0 otherwise. If -only-maxima or -only-minima is specified, then it will
ignore extrema not of the specified type. These options are mutually exclusive.
If -roi is specified, not only is data outside the roi not used, but any vertex on
the edge of the ROI will never be counted as an extrema, in case the ROI cuts
across a gradient, which would otherwise generate extrema where there should be
none.
If -sum-columns is specified, these extrema columns are summed, and the output has
a single column with this result.
By default, a datapoint is an extrema only if it is more extreme than every other
datapoint that is within <distance> from it. If -consolidate-mode is used, it
instead starts by finding all datapoints that are more extreme than their immediate
neighbors, then while there are any extrema within <distance> of each other, take
the two extrema closest to each other and merge them into one by a weighted average
based on how many original extrema have been merged into each.
By default, all input columns are used with no smoothing, use -column to specify a
single column to use, and -presmooth to smooth the input before finding the
extrema.
-metric-false-correlation COMPARE CORRELATION LOCALLY AND ACROSS/THROUGH SULCI/GYRI
wb_command -metric-false-correlation
<surface> - the surface to compute geodesic and 3D distance with <metric-in> - the
metric to correlate <3D-dist> - maximum 3D distance to check around each vertex
<geo-outer> - maximum geodesic distance to use for neighboring
correlation
<geo-inner> - minimum geodesic distance to use for neighboring
correlation
<metric-out> - output - the output metric
[-roi] - select a region of interest that has data
<roi-metric> - the region, as a metric file
[-dump-text] - dump the raw measures used to a text file
<text-out> - the output text file
For each vertex, compute the average correlation within a range of geodesic
distances that don't cross a sulcus/gyrus, and the correlation to the closest
vertex crossing a sulcus/gyrus. A vertex is considered to cross a sulcus/gyrus if
the 3D distance is less than a third of the geodesic distance. The output file
contains the ratio between these correlations, and some additional maps to help
explain the ratio.
-metric-fill-holes FILL HOLES IN AN ROI METRIC
wb_command -metric-fill-holes
<surface> - the surface to use for neighbor information <metric-in> - the input ROI
metric <metric-out> - output - the output ROI metric
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
Finds all connected areas that are not included in the ROI, and writes ones into
all but the largest one, in terms of surface area.
-metric-find-clusters FILTER CLUSTERS BY SURFACE AREA
wb_command -metric-find-clusters
<surface> - the surface to compute on <metric-in> - the input metric
<value-threshold> - threshold for data values <minimum-area> - threshold for
cluster area, in mm^2 <metric-out> - output - the output metric
[-less-than] - find values less than <value-threshold>, rather than
greater
[-roi] - select a region of interest
<roi-metric> - the roi, as a metric
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
[-column] - select a single column
<column> - the column number or name
[-size-ratio] - ignore clusters smaller than a given fraction of the
largest cluster in map <ratio> - fraction of the largest cluster's area
[-distance] - ignore clusters further than a given distance from the
largest cluster <distance> - how far from the largest cluster a cluster can be,
edge
to edge, in mm
[-start] - start labeling clusters from a value other than 1
<startval> - the value to give the first cluster found
Outputs a metric with nonzero integers for all vertices within a large enough
cluster, and zeros elsewhere. The integers denote cluster membership (by default,
first cluster found will use value 1, second cluster 2, etc). Cluster values are
not reused across maps of the output, but instead keep counting up. By default,
values greater than <value-threshold> are considered to be in a cluster, use
-less-than to test for values less than the threshold. To apply this as a mask to
the data, or to do more complicated thresholding, see -metric-math.
-metric-gradient SURFACE GRADIENT OF A METRIC FILE
wb_command -metric-gradient
<surface> - the surface to compute the gradient on <metric-in> - the metric to
compute the gradient of <metric-out> - output - the magnitude of the gradient
[-presmooth] - smooth the metric before computing the gradient
<kernel> - the sigma for the gaussian smoothing kernel, in mm
[-roi] - select a region of interest to take the gradient of
<roi-metric> - the area to take the gradient within, as a metric
[-match-columns] - for each input column, use the corresponding column
from the roi
[-vectors] - output gradient vectors
<vector-metric-out> - output - the vectors as a metric file
[-column] - select a single column to compute the gradient of
<column> - the column number or name
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
[-average-normals] - average the normals of each vertex with its
neighbors before using them to compute the gradient
At each vertex, the immediate neighbors are unfolded onto a plane tangent to the
surface at the vertex (specifically, perpendicular to the normal). The gradient is
computed using a regression between the unfolded positions of the vertices and
their values. The gradient is then given by the slopes of the regression, and
reconstructed as a 3D gradient vector. By default, takes the gradient of all
columns, with no presmoothing, across the whole surface, without averaging the
normals of the surface among neighbors.
When using -corrected-areas, note that it is an approximate correction. Doing
smoothing on individual surfaces before averaging/gradient is preferred, when
possible, in order to make use of the original surface structure.
Specifying an ROI will restrict the gradient to only use data from where the ROI
metric is positive, and output zeros anywhere the ROI metric is not positive.
By default, the first column of the roi metric is used for all input columns. When
-match-columns is specified to the -roi option, the input and roi metrics must have
the same number of columns, and for each input column's index, the same column
index is used in the roi metric. If the -match-columns option to -roi is used
while the -column option is also used, the number of columns of the roi metric must
match the input metric, and it will use the roi column with the index of the
selected input column.
The vector output metric is organized such that the X, Y, and Z components from a
single input column are consecutive columns.
-metric-label-import IMPORT A GIFTI LABEL FILE FROM A METRIC FILE
wb_command -metric-label-import
<input> - the input metric file <label-list-file> - text file containing the values
and names for labels <output> - output - the output gifti label file
[-discard-others] - set any values not mentioned in the label list to the
??? label
[-unlabeled-value] - set the value that will be interpreted as unlabeled
<value> - the numeric value for unlabeled (default 0)
[-column] - select a single column to import
<column> - the column number or name
[-drop-unused-labels] - remove any unused label values from the label
table
Creates a gifti label file from a metric file with label-like values. You may
specify the empty string (use "") for <label-list-file>, which will be treated as
if it is an empty file. The label list file must have the following format (2
lines per label):
<labelname> <key> <red> <green> <blue> <alpha> ...
Label names are specified on a separate line from their value and color, in order
to let label names contain spaces. Whitespace is trimmed from both ends of the
label name, but is kept if it is in the middle of a label. Do not specify the
"unlabeled" key in the file, it is assumed that 0 means not labeled unless
-unlabeled-value is specified. The value of <key> specifies what value in the
imported file should be used as this label. The values of <red>, <green>, <blue>
and <alpha> must be integers from 0 to 255, and will specify the color the label is
drawn as (alpha of 255 means fully opaque, which is probably what you want).
By default, it will create new label names with names like LABEL_5 for any values
encountered that are not mentioned in the list file, specify -discard-others to
instead set these values to the "unlabeled" key.
-metric-mask MASK A METRIC FILE
wb_command -metric-mask
<metric> - the input metric <mask> - the mask metric <metric-out> - output - the
output metric
[-column] - select a single column
<column> - the column number or name
By default, the output metric is a copy of the input metric, but with zeros
wherever the mask metric is zero or negative. if -column is specified, the output
contains only one column, the masked version of the specified input column.
-metric-math EVALUATE EXPRESSION ON METRIC FILES
wb_command -metric-math
<expression> - the expression to evaluate, in quotes <metric-out> - output - the
output metric
[-fixnan] - replace NaN results with a value
<replace> - value to replace NaN with
[-var] - repeatable - a metric to use as a variable
<name> - the name of the variable, as used in the expression <metric> - the metric
file to use as this variable
[-column] - select a single column
<column> - the column number or name
[-repeat] - reuse a single column for each column of calculation
This command evaluates <expression> at each surface vertex independently. There
must be at least one -var option (to get the structure, number of vertices, and
number of columns from), even if the <name> specified in it isn't used in
<expression>. All metrics must have the same number of vertices. Filenames are
not valid in <expression>, use a variable name and a -var option with matching
<name> to specify an input file. If the -column option is given to any -var
option, only one column is used from that file. If -repeat is specified, the file
must either have only one column, or have the -column option specified. All files
that don't use -repeat must have the same number of columns requested to be used.
The format of <expression> is as follows:
Expressions consist of constants, variables, operators, parentheses, and functions,
in infix notation, such as 'exp(-x + 3) * scale'. Variables are strings of any
length, using the characters a-z, A-Z, 0-9, and _, but may not take the name of a
named constant. Currently, there is only one named constant, PI. The operators
are +, -, *, /, ^, >, <, >=, <=, ==, !=, !, &&, ||. These behave as in C, except
that ^ is exponentiation, i.e. pow(x, y), and takes higher precedence than other
binary operators (also, '-3^-4^-5' means '-(3^(-(4^-5)))'). The <=, >=, ==, and !=
operators are given a small amount of wiggle room, equal to one millionth of the
smaller of the absolute values of the values being compared.
Comparison and logical operators return 0 or 1, you can do masking with expressions
like 'x * (mask > 0)'. For all logical operators, an input is considered true iff
it is greater than 0. The expression '0 < x < 5' is not syntactically wrong, but
it will NOT do what is desired, because it is evaluated left to right, i.e. '((0 <
x) < 5)', which will always return 1, as both possible results of a comparison are
less than 5. A warning is generated if an expression of this type is detected.
Use something like 'x > 0 && x < 5' to get the desired behavior.
Whitespace between elements is ignored, ' sin ( 2 * x ) ' is equivalent to
'sin(2*x)', but 's in(2*x)' is an error. Implied multiplication is not allowed,
the expression '2x' will be parsed as a variable. Parentheses are (), do not use
[] or {}. Functions require parentheses, the expression 'sin x' is an error.
The following functions are supported:
sin: 1 argument, the sine of the argument (units are radians) cos: 1 argument, the
cosine of the argument (units are radians) tan: 1 argument, the tangent of the
argument (units are radians) asin: 1 argument, the inverse of sine of the argument,
in radians acos: 1 argument, the inverse of cosine of the argument, in radians
atan: 1 argument, the inverse of tangent of the argument, in radians atan2: 2
arguments, atan2(y, x) returns the inverse of tangent of
(y/x), in radians, determining quadrant by the sign of both arguments
sinh: 1 argument, the hyperbolic sine of the argument cosh: 1 argument, the
hyperbolic cosine of the argument tanh: 1 argument, the hyperboloc tangent of the
argument asinh: 1 argument, the inverse hyperbolic sine of the argument acosh: 1
argument, the inverse hyperbolic cosine of the argument atanh: 1 argument, the
inverse hyperboloc tangent of the argument ln: 1 argument, the natural logarithm of
the argument exp: 1 argument, the constant e raised to the power of the argument
log: 1 argument, the base 10 logarithm of the argument log2: 1 argument, the base 2
logarithm of the argument sqrt: 1 argument, the square root of the argument abs: 1
argument, the absolute value of the argument floor: 1 argument, the largest integer
not greater than the argument round: 1 argument, the nearest integer, with ties
rounded away from
zero
ceil: 1 argument, the smallest integer not less than the argument min: 2 arguments,
min(x, y) returns y if (x > y), x otherwise max: 2 arguments, max(x, y) returns y
if (x < y), x otherwise mod: 2 arguments, mod(x, y) = x - y * floor(x / y), or 0 if
y == 0 clamp: 3 arguments, clamp(x, low, high) = min(max(x, low), high)
-metric-merge MERGE METRIC FILES INTO A NEW FILE
wb_command -metric-merge
<metric-out> - output - the output metric
[-metric] - repeatable - specify an input metric
<metric-in> - a metric file to use columns from
[-column] - repeatable - select a single column to use
<column> - the column number or name
[-up-to] - use an inclusive range of columns
<last-column> - the number or name of the last column to include
[-reverse] - use the range in reverse order
Takes one or more metric files and constructs a new metric file by concatenating
columns from them. The input metric files must have the same number of vertices
and same structure.
Example: wb_command -metric-merge out.func.gii -metric first.func.gii -column 1
-metric second.func.gii
This example would take the first column from first.func.gii, followed by all
columns from second.func.gii, and write these columns to out.func.gii.
-metric-palette SET THE PALETTE OF A METRIC FILE
wb_command -metric-palette
<metric> - the metric to modify <mode> - the mapping mode
[-column] - select a single column
<column> - the column number or name
[-pos-percent] - percentage min/max for positive data coloring
<pos-min-%> - the percentile for the least positive data <pos-max-%> - the
percentile for the most positive data
[-neg-percent] - percentage min/max for negative data coloring
<neg-min-%> - the percentile for the least negative data <neg-max-%> - the
percentile for the most negative data
[-pos-user] - user min/max values for positive data coloring
<pos-min-user> - the value for the least positive data <pos-max-user> - the value
for the most positive data
[-neg-user] - user min/max values for negative data coloring
<neg-min-user> - the value for the least negative data <neg-max-user> - the value
for the most negative data
[-interpolate] - interpolate colors
<interpolate> - boolean, whether to interpolate
[-disp-pos] - display positive data
<display> - boolean, whether to display
[-disp-neg] - display positive data
<display> - boolean, whether to display
[-disp-zero] - display data closer to zero than the min cutoff
<display> - boolean, whether to display
[-palette-name] - set the palette used
<name> - the name of the palette
[-thresholding] - set the thresholding
<type> - thresholding setting <test> - show values inside or outside thresholds
<min> - lower threshold <max> - upper threshold
[-inversion] - specify palette inversion
<type> - the type of inversion
The original metric file is overwritten with the modified version.
By
default, all columns of the metric file are adjusted to the new settings, use the
-column option to change only one column. Mapping settings not specified in
options will be taken from the first column. The <mode> argument must be one of
the following:
MODE_AUTO_SCALE MODE_AUTO_SCALE_ABSOLUTE_PERCENTAGE MODE_AUTO_SCALE_PERCENTAGE
MODE_USER_SCALE
The <name> argument to -palette-name must be one of the following:
ROY-BIG-BL videen_style Gray_Interp_Positive Gray_Interp PSYCH-FIXED RBGYR20
RBGYR20P RYGBR4_positive RGRBR_mirror90_pos Orange-Yellow POS_NEG_ZERO red-yellow
blue-lightblue FSL power_surf fsl_red fsl_green fsl_blue fsl_yellow RedWhiteBlue
cool-warm spectral RY-BC-BL magma JET256 PSYCH PSYCH-NO-NONE ROY-BIG clear_brain
fidl raich4_clrmid raich6_clrmid HSB8_clrmid POS_NEG
The <type> argument to -thresholding must be one of the following:
THRESHOLD_TYPE_OFF THRESHOLD_TYPE_NORMAL THRESHOLD_TYPE_FILE
The <test> argument to -thresholding must be one of the following:
THRESHOLD_TEST_SHOW_OUTSIDE THRESHOLD_TEST_SHOW_INSIDE
The <type> argument to -inversion must be one of the following:
OFF POSITIVE_WITH_NEGATIVE POSITIVE_NEGATIVE_SEPARATE
-metric-reduce PERFORM REDUCTION OPERATION ACROSS METRIC COLUMNS
wb_command -metric-reduce
<metric-in> - the metric to reduce <operation> - the reduction operator to use
<metric-out> - output - the output metric
[-exclude-outliers] - exclude non-numeric values and outliers by standard
deviation <sigma-below> - number of standard deviations below the mean to
include
<sigma-above> - number of standard deviations above the mean to
include
[-only-numeric] - exclude non-numeric values
For each surface vertex, takes the data across columns as a vector, and performs
the specified reduction on it, putting the result into the single output column at
that vertex. The reduction operators are as follows:
MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based index of the
maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all values
PRODUCT: multiply all values MEAN: the mean of the data STDEV: the standard
deviation (N denominator) SAMPSTDEV: the sample standard deviation (N-1
denominator) VARIANCE: the variance of the data TSNR: mean divided by sample
standard deviation (N-1 denominator) COV: sample standard deviation (N-1
denominator) divided by mean L2NORM: square root of sum of squares MEDIAN: the
median of the data MODE: the mode of the data COUNT_NONZERO: the number of nonzero
elements in the data
-metric-regression REGRESS METRICS OUT OF A METRIC FILE
wb_command -metric-regression
<metric-in> - the metric to regress from <metric-out> - output - the output metric
[-roi] - only regress inside an roi
<roi-metric> - the area to use for regression, as a metric
[-column] - select a single column to regress from
<column> - the column number or name
[-remove] - repeatable - specify a metric to regress out
<metric> - the metric file to use
[-remove-column] - select a column to use, rather than all
<column> - the column number or name
[-keep] - repeatable - specify a metric to include in regression, but not
remove <metric> - the metric file to use
[-keep-column] - select a column to use, rather than all
<column> - the column number or name
For each regressor, its mean across the surface is subtracted from its data. Each
input map is then regressed against these, and a constant term. The resulting
regressed slopes of all regressors specified with -remove are multiplied with their
respective regressor maps, and these are subtracted from the input map.
-metric-remove-islands REMOVE ISLANDS FROM AN ROI METRIC
wb_command -metric-remove-islands
<surface> - the surface to use for neighbor information <metric-in> - the input ROI
metric <metric-out> - output - the output ROI metric
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
Finds all connected areas in the ROI, and zeros out all but the largest one, in
terms of surface area.
-metric-resample RESAMPLE A METRIC FILE TO A DIFFERENT MESH
wb_command -metric-resample
<metric-in> - the metric file to resample <current-sphere> - a sphere surface with
the mesh that the metric is
currently on
<new-sphere> - a sphere surface that is in register with <current-sphere>
and has the desired output mesh
<method> - the method name <metric-out> - output - the output metric
[-area-surfs] - specify surfaces to do vertex area correction based on
<current-area> - a relevant anatomical surface with <current-sphere>
mesh
<new-area> - a relevant anatomical surface with <new-sphere> mesh
[-area-metrics] - specify vertex area metrics to do area correction based
on <current-area> - a metric file with vertex areas for <current-sphere>
mesh
<new-area> - a metric file with vertex areas for <new-sphere> mesh
[-current-roi] - use an input roi on the current mesh to exclude non-data
vertices <roi-metric> - the roi, as a metric file
[-valid-roi-out] - output the ROI of vertices that got data from valid
source vertices <roi-out> - output - the output roi as a metric
[-largest] - use only the value of the vertex with the largest weight
Resamples a metric file, given two spherical surfaces that are in register. If
ADAP_BARY_AREA is used, exactly one of -area-surfs or -area-metrics must be
specified.
The ADAP_BARY_AREA method is recommended for ordinary metric data, because it
should use all data while downsampling, unlike BARYCENTRIC. The recommended areas
option for most data is individual midthicknesses for individual data, and averaged
vertex area metrics from individual midthicknesses for group average data.
The -current-roi option only masks the input, the output may be slightly dilated in
comparison, consider using -metric-mask on the output when using -current-roi.
The -largest option results in nearest vertex behavior when used with BARYCENTRIC.
When resampling a binary metric, consider thresholding at 0.5 after resampling
rather than using -largest.
The <method> argument must be one of the following:
ADAP_BARY_AREA BARYCENTRIC
-metric-rois-from-extrema CREATE METRIC ROI MAPS FROM EXTREMA MAPS
wb_command -metric-rois-from-extrema
<surface> - the surface to use for geodesic distance <metric> - the input metric
file <limit> - geodesic distance limit from vertex, in mm <metric-out> - output -
the output metric file
[-gaussian] - generate a gaussian kernel instead of a flat ROI
<sigma> - the sigma for the gaussian kernel, in mm
[-roi] - select a region of interest to use
<roi-metric> - the area to use, as a metric
[-overlap-logic] - how to handle overlapping ROIs, default ALLOW
<method> - the method of resolving overlaps
[-column] - select a single input column to use
<column> - the column number or name
For each nonzero value in each map, make a map with an ROI around that location.
If the -gaussian option is specified, then normalized gaussian kernels are output
instead of ROIs. The <method> argument to -overlap-logic must be one of ALLOW,
CLOSEST, or EXCLUDE. ALLOW is the default, and means that ROIs are treated
independently and may overlap. CLOSEST means that ROIs may not overlap, and that
no ROI contains vertices that are closer to a different seed vertex. EXCLUDE means
that ROIs may not overlap, and that any vertex within range of more than one ROI
does not belong to any ROI.
-metric-rois-to-border DRAW BORDERS AROUND METRIC ROIS
wb_command -metric-rois-to-border
<surface> - the surface to use for neighbor information <metric> - the input metric
containing ROIs <class-name> - the name to use for the class of the output borders
<border-out> - output - the output border file
[-placement] - set how far along the edge border points are drawn
<fraction> - fraction along edge from inside vertex (default 0.33)
[-column] - select a single column
<column> - the column number or name
For each ROI column, finds all edges on the mesh that cross the boundary of the
ROI, and draws borders through them. By default, this is done on all columns in
the input file, using the map name as the name for the border.
-metric-smoothing SMOOTH A METRIC FILE
wb_command -metric-smoothing
<surface> - the surface to smooth on <metric-in> - the metric to smooth
<smoothing-kernel> - the sigma for the gaussian kernel function, in mm <metric-out>
- output - the output metric
[-roi] - select a region of interest to smooth
<roi-metric> - the roi to smooth within, as a metric
[-match-columns] - for each input column, use the corresponding column
from the roi
[-fix-zeros] - treat zero values as not being data
[-column] - select a single column to smooth
<column> - the column number or name
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
[-method] - select smoothing method, default GEO_GAUSS_AREA
<method> - the name of the smoothing method
Smooth a metric file on a surface.
By default, smooths all input columns
on the entire surface, specify -column to use only one input column, and -roi to
smooth only where the roi metric is greater than 0, outputting zeros elsewhere.
When using -roi, input data outside the ROI is not used to compute the smoothed
values. By default, the first column of the roi metric is used for all input
columns. When -match-columns is specified to the -roi option, the input and roi
metrics must have the same number of columns, and for each input column's index,
the same column index is used in the roi metric. If the -match-columns option to
-roi is used while the -column option is also used, the number of columns must
match between the roi and input metric, and it will use the roi column with the
index of the selected input column.
The -fix-zeros option causes the smoothing to not use an input value if it is zero,
but still write a smoothed value to the vertex. This is useful for zeros that
indicate lack of information, preventing them from pulling down the intensity of
nearby vertices, while giving the zero an extrapolated value.
The -corrected-areas option is intended for when it is unavoidable to smooth on a
group average surface, it is only an approximate correction for the reduction of
structure in a group average surface. It is better to smooth the data on
individuals before averaging, when feasible.
Valid values for <method> are:
GEO_GAUSS_AREA - uses a geodesic gaussian kernel, and normalizes based on vertex
area in order to work more reliably on irregular surfaces
GEO_GAUSS_EQUAL - uses a geodesic gaussian kernel, and normalizes assuming each
vertex has equal importance
GEO_GAUSS - matches geodesic gaussian smoothing from caret5, but does not check
kernels for having unequal importance
The GEO_GAUSS_AREA method is the default because it is usually the correct choice.
GEO_GAUSS_EQUAL may be the correct choice when the sum of vertex values is more
meaningful then the surface integral (sum of values .* areas), for instance when
smoothing vertex areas (the sum is the total surface area, while the surface
integral is the sum of squares of the vertex areas). The GEO_GAUSS method is not
recommended, it exists mainly to replicate methods of studies done with caret5's
geodesic smoothing.
-metric-stats SPATIAL STATISTICS ON A METRIC FILE
wb_command -metric-stats
<metric-in> - the input metric
[-reduce] - use a reduction operation
<operation> - the reduction operation
[-percentile] - give the value at a percentile
<percent> - the percentile to find
[-column] - only display output for one column
<column> - the column number or name
[-roi] - only consider data inside an roi
<roi-metric> - the roi, as a metric file
[-match-maps] - each column of input uses the corresponding column
from the roi file
[-show-map-name] - print map index and name before each output
For each column of the input, a single number is printed, resulting from the
specified reduction or percentile operation. Use -column to only give output for a
single column. Use -roi to consider only the data within a region. Exactly one of
-reduce or -percentile must be specified.
The argument to the -reduce option must be one of the following:
MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based index of the
maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all values
PRODUCT: multiply all values MEAN: the mean of the data STDEV: the standard
deviation (N denominator) SAMPSTDEV: the sample standard deviation (N-1
denominator) VARIANCE: the variance of the data TSNR: mean divided by sample
standard deviation (N-1 denominator) COV: sample standard deviation (N-1
denominator) divided by mean L2NORM: square root of sum of squares MEDIAN: the
median of the data MODE: the mode of the data COUNT_NONZERO: the number of nonzero
elements in the data
-metric-tfce DO TFCE ON A METRIC FILE
wb_command -metric-tfce
<surface> - the surface to compute on <metric-in> - the metric to run TFCE on
<metric-out> - output - the output metric
[-presmooth] - smooth the metric before running TFCE
<kernel> - the sigma for the gaussian smoothing kernel, in mm
[-roi] - select a region of interest to run TFCE on
<roi-metric> - the area to run TFCE on, as a metric
[-parameters] - set parameters for TFCE integral
<E> - exponent for cluster area (default 1.0) <H> - exponent for threshold value
(default 2.0)
[-column] - select a single column
<column> - the column number or name
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
Threshold-free cluster enhancement is a method to increase the relative value of
regions that would form clusters in a standard thresholding test. This is
accomplished by evaluating the integral of:
e(h, p)^E * h^H * dh
at each vertex p, where h ranges from 0 to the maximum value in the data, and e(h,
p) is the extent of the cluster containing vertex p at threshold h. Negative
values are similarly enhanced by negating the data, running the same process, and
negating the result.
When using -presmooth with -corrected-areas, note that it is an approximate
correction within the smoothing algorithm (the TFCE correction is exact). Doing
smoothing on individual surfaces before averaging/TFCE is preferred, when possible,
in order to better tie the smoothing kernel size to the original feature size.
The TFCE method is explained in: Smith SM, Nichols TE., "Threshold-free cluster
enhancement: addressing problems of smoothing, threshold dependence and
localisation in cluster inference." Neuroimage. 2009 Jan 1;44(1):83-98. PMID:
18501637
-metric-to-volume-mapping MAP METRIC FILE TO VOLUME
wb_command -metric-to-volume-mapping
<metric> - the input metric file <surface> - the surface to use coordinates from
<volume-space> - a volume file in the desired output volume space <volume-out> -
output - the output volume file
[-nearest-vertex] - use the value from the vertex closest to the voxel
center <distance> - how far from the surface to map values to voxels, in mm
[-ribbon-constrained] - use ribbon constrained mapping algorithm
<inner-surf> - the inner surface of the ribbon <outer-surf> - the outer surface of
the ribbon
[-voxel-subdiv] - voxel divisions while estimating voxel weights
<subdiv-num> - number of subdivisions, default 3
[-greedy] - instead of antialiasing partial-volumed voxels, put full
metric values (legacy behavior)
[-thick-columns] - use overlapping columns (legacy method)
Maps values from a metric file into a volume file.
You must specify
exactly one mapping method option.
The -nearest-vertex method uses the
value from the vertex closest to the voxel center (useful for integer values). The
-ribbon-constrained method uses the same method as in -volume-to-surface-mapping,
then uses the weights in reverse. Mapping to lower resolutions than the mesh may
require a larger -voxel-subdiv value in order to have all of the surface data
participate.
-metric-vector-operation DO A VECTOR OPERATION ON METRIC FILES
wb_command -metric-vector-operation
<vectors-a> - first vector input file <vectors-b> - second vector input file
<operation> - what vector operation to do <metric-out> - output - the output file
[-normalize-a] - normalize vectors of first input
[-normalize-b] - normalize vectors of second input
[-normalize-output] - normalize output vectors (not valid for dot
product)
[-magnitude] - output the magnitude of the result (not valid for dot
product)
Does a vector operation on two metric files (that must have a multiple of 3
columns). Either of the inputs may have multiple vectors (more than 3 columns),
but not both (at least one must have exactly 3 columns). The -magnitude and
-normalize-output options may not be specified together, or with an operation that
returns a scalar (dot product). The <operation> parameter must be one of the
following:
DOT CROSS ADD SUBTRACT
-metric-vector-toward-roi FIND IF VECTORS POINT TOWARD AN ROI
wb_command -metric-vector-toward-roi
<surface> - the surface to compute on <target-roi> - the roi to find the shortest
path to <metric-out> - output - the output metric
[-roi] - don't compute for vertices outside an roi
<roi-metric> - the region to compute inside, as a metric
At each vertex, compute the vector along the start of the shortest path to the ROI.
-metric-weighted-stats WEIGHTED SPATIAL STATISTICS ON A METRIC FILE
wb_command -metric-weighted-stats
<metric-in> - the input metric
[-area-surface] - use vertex areas as weights
<area-surface> - the surface to use for vertex areas
[-weight-metric] - use weights from a metric file
<weight-metric> - metric file containing the weights
[-column] - only display output for one column
<column> - the column number or name
[-roi] - only consider data inside an roi
<roi-metric> - the roi, as a metric file
[-match-maps] - each column of input uses the corresponding column
from the roi file
[-mean] - compute weighted mean
[-stdev] - compute weighted standard deviation
[-sample] - estimate population stdev from the sample
[-percentile] - compute weighted percentile
<percent> - the percentile to find
[-sum] - compute weighted sum
[-show-map-name] - print map index and name before each output
For each column of the input, a single number is printed, resulting from the
specified operation. You must specify exactly one of -area-surface or
-weight-metric. Use -column to only give output for a single column. Use -roi to
consider only the data within a region. Exactly one of -mean, -stdev, -percentile
or -sum must be specified.
Using -sum with -area-surface (or -weight-metric with a metric containing similar
data) is equivalent to integrating with respect to surface area. For example, if
you want to find the surface area within an roi, do this:
$ wb_command -metric-weighted-stats roi.func.gii -sum -area-surface
midthickness.surf.gii
-nifti-information DISPLAY INFORMATION ABOUT A NIFTI/CIFTI FILE
wb_command -nifti-information
<nifti-file> - the nifti/cifti file to examine
[-print-header] - display the header contents
[-allow-truncated] - print the header even if the data is truncated
[-print-matrix] - output the values in the matrix (cifti only)
[-print-xml] - print the cifti XML (cifti only)
[-version] - convert the XML to a specific CIFTI version (default is
the file's cifti version) <version> - the CIFTI version to use
You must specify at least one -print-* option.
-probtrackx-dot-convert CONVERT A .DOT FILE FROM PROBTRACKX TO CIFTI
wb_command -probtrackx-dot-convert
<dot-file> - input .dot file <cifti-out> - output - output cifti file
[-row-voxels] - the output mapping along a row will be voxels
<voxel-list-file> - a text file containing IJK indices for the voxels
used
<label-vol> - a label volume with the dimensions and sform used, with
structure labels
[-row-surface] - the output mapping along a row will be surface vertices
<roi-metric> - a metric file with positive values on all vertices used
[-row-cifti] - take the mapping along a row from a cifti file
<cifti> - the cifti file to take the mapping from <direction> - which dimension to
take the mapping along, ROW or COLUMN
[-col-voxels] - the output mapping along a column will be voxels
<voxel-list-file> - a text file containing IJK indices for the voxels
used
<label-vol> - a label volume with the dimensions and sform used, with
structure labels
[-col-surface] - the output mapping along a column will be surface
vertices <roi-metric> - a metric file with positive values on all vertices used
[-col-cifti] - take the mapping along a column from a cifti file
<cifti> - the cifti file to take the mapping from <direction> - which dimension to
take the mapping along, ROW or COLUMN
[-transpose] - transpose the input matrix
[-make-symmetric] - transform half-square input into full matrix output
NOTE: exactly one -row option and one -col option must be used.
If the input file does not have its indexes sorted in the correct ordering, this
command may take longer than expected. Specifying -transpose will transpose the
input matrix before trying to put its values into the cifti file, which is
currently needed for at least matrix2 in order to display it as intended. How the
cifti file is displayed is based on which -row option is specified: if -row-voxels
is specified, then it will display data on volume slices. The label names in the
label volume(s) must have the following names, other names are ignored:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
-scene-file-merge REARRANGE SCENES INTO A NEW FILE
wb_command -scene-file-merge
<scene-file-out> - output - the output scene file
[-scene-file] - repeatable - specify a scene file to use scenes from
<scene-file> - the input scene file
[-scene] - repeatable - specify a scene to use
<scene> - the scene number or name
[-up-to] - use an inclusive range of scenes
<last-column> - the number or name of the last scene to include
[-reverse] - use the range in reverse order
Takes one or more scene files and constructs a new scene file by concatenating
specified scenes from them.
Example: wb_command -scene-file-merge out.scene -scene-file first.scene -scene 1
-scene-file second.scene
This example would take the first scene from first.scene, followed by all scenes
from second.scene, and write these scenes to out.scene.
-scene-file-relocate RECREATE SCENE FILE IN NEW LOCATION
wb_command -scene-file-relocate
<input-scene> - the scene file to use <output-scene> - output - the new scene file
to create
Scene files contain internal relative paths, such that moving or copying a scene
file will cause it to lose track of the files it refers to. This command makes a
modified copy of the scene file, changing the relative paths to refer to the new
relative locations of the files.
-set-map-names SET THE NAME OF ONE OR MORE MAPS IN A FILE
wb_command -set-map-names
<data-file> - the file to set the map names of
[-name-file] - use a text file to replace all map names
<file> - text file containing map names, one per line
[-map] - repeatable - specify a map to set the name of
<index> - the map index to change the name of <new-name> - the name to set for the
map
Sets the name of one or more maps for metric, shape, label, volume, cifti scalar or
cifti label files. If the -name-file option is not specified, the -map option must
be specified at least once. The -map option cannot be used when -name-file is
specified.
-set-structure SET STRUCTURE OF A DATA FILE
wb_command -set-structure
<data-file> - the file to set the structure of <structure> - the structure to set
the file to
[-surface-type] - set the type of a surface (only used if file is a
surface file) <type> - name of surface type
[-surface-secondary-type] - set the secondary type of a surface (only
used if file is a surface file) <secondary type> - name of surface secondary type
The existing file is modified and rewritten to the same filename.
Valid
values for the structure name are:
CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_LEFT
CEREBELLUM_RIGHT CEREBRAL_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT CORTEX
DIENCEPHALON_VENTRAL_LEFT DIENCEPHALON_VENTRAL_RIGHT HIPPOCAMPUS_LEFT
HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT
Valid names for the surface type are:
UNKNOWN RECONSTRUCTION ANATOMICAL INFLATED VERY_INFLATED SPHERICAL SEMI_SPHERICAL
ELLIPSOID FLAT HULL
Valid names for the surface secondary type are:
INVALID GRAY_WHITE MIDTHICKNESS PIAL
-show-scene OFFSCREEN RENDERING OF SCENE TO AN IMAGE FILE
wb_command -show-scene
<scene-file> - scene file <scene-name-or-number> - name or number (starting at one)
of the scene in
the scene file
<image-file-name> - output image file name <image-width> - width of output
image(s), in pixels <image-height> - height of output image(s), in pixels
[-use-window-size] - Override image size with window size
[-no-scene-colors] - Do not use background and foreground colors in scene
[-set-map-yoke] - Override selected map index for a map yoking group.
<Map Yoking Roman Numeral> - Roman numeral identifying the map yoking
group (I, II, III, IV, V, VI, VII, VIII, IX, X)
<Map Index> - Map index for yoking group.
Indices start at 1 (one)
[-conn-db-login] - Login for scenes with files in Connectome Database
<Username> - Connectome DB Username <Password> - Connectome DB Password
Render content of browser windows displayed in a scene into image file(s). The
image file name should be similar to "capture.png". If there is only one image to
render, the image name will not change. If there is more than one image to render,
an index will be inserted into the image name: "capture_01.png", "capture_02.png"
etc.
If the scene references files in the Connectome Database, the "-conn-db-login"
option is available for providing the username and password. If this options is
not specified, the username and password stored in the user's preferences is used.
The image format is determined by the image file extension. The available image
formats may vary by operating system. Image formats available on this system are:
bmp cur ico jpeg jpg pbm pgm png ppm xbm xpm
The result of using the "-use-window-size" option is dependent upon the version
used to create the scene.
* Versions 1.2 and newer contain the width and
height of the graphics region.
The output image
will be the width and height from the scene and the image width and height
specified on the command line is ignored.
* If the scene does not contain the width and height
of the graphics region, the width and height specified on the command line is used
for the size of the output image.
-signed-distance-to-surface COMPUTE SIGNED DISTANCE FROM ONE SURFACE TO ANOTHER
wb_command -signed-distance-to-surface
<surface-comp> - the comparison surface to measure the signed distance on
<surface-ref> - the reference surface that defines the signed distance
function
<metric> - output - the output metric
[-winding] - winding method for point inside surface test
<method> - name of the method (default EVEN_ODD)
Compute the signed distance function of the reference surface at every vertex on
the comparison surface. NOTE: this relation is NOT symmetric, the line from a
vertex to the closest point on the 'ref' surface (the one that defines the signed
distance function) will only align with the normal of the 'ref' surface. Valid
specifiers for winding methods are as follows:
EVEN_ODD (default) NEGATIVE NONZERO NORMALS
The NORMALS method uses the normals of triangles and edges, or the closest triangle
hit by a ray from the point. This method may be slightly faster, but is only
reliable for a closed surface that does not cross through itself. All other
methods count entry (positive) and exit (negative) crossings of a vertical ray from
the point, then counts as inside if the total is odd, negative, or nonzero,
respectively.
-spec-file-merge MERGE TWO SPEC FILES INTO ONE
wb_command -spec-file-merge
<spec-1> - first spec file to merge <spec-2> - second spec file to merge <out-spec>
- output - output spec file
The output spec file contains every file that is in either of the input spec files.
-spec-file-relocate RECREATE SPEC FILE IN NEW LOCATION
wb_command -spec-file-relocate
<input-spec> - the spec file to use <output-spec> - output - the new spec file to
create
Spec files contain internal relative paths, such that moving or copying a spec file
will cause it to lose track of the files it refers to. This command makes a
modified copy of the spec file, changing the relative paths to refer to the new
relative locations of the files.
-surface-affine-regression REGRESS THE AFFINE TRANSFORM BETWEEN SURFACES ON THE SAME MESH
wb_command -surface-affine-regression
<source> - the surface to warp <target> - the surface to match the coordinates of
<affine-out> - output - the output affine file
Use linear regression to compute an affine that minimizes the sum of squares of the
coordinate differences between the target surface and the warped source surface.
Note that this has a bias to shrink the surface that is being warped. The output
is written as a NIFTI 'world' matrix, see -convert-affine to convert it for use in
other software.
-surface-apply-affine APPLY AFFINE TRANSFORM TO SURFACE FILE
wb_command -surface-apply-affine
<in-surf> - the surface to transform <affine> - the affine file <out-surf> - output
- the output transformed surface
[-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
For flirt matrices, you must use the -flirt option, because flirt matrices are not
a complete description of the coordinate transform they represent. If the -flirt
option is not present, the affine must be a nifti 'world' affine, which can be
obtained with the -convert-affine command, or aff_conv from the 4dfp suite.
-surface-apply-warpfield APPLY WARPFIELD TO SURFACE FILE
wb_command -surface-apply-warpfield
<in-surf> - the surface to transform <warpfield> - the INVERSE warpfield <out-surf>
- output - the output transformed surface
[-fnirt] - MUST be used if using a fnirt warpfield
<forward-warp> - the forward warpfield
NOTE: warping a surface requires the INVERSE of the warpfield used to warp the
volume it lines up with. The header of the forward warp is needed by the -fnirt
option in order to correctly interpret the displacements in the fnirt warpfield.
If the -fnirt option is not present, the warpfield must be a nifti 'world'
warpfield, which can be obtained with the -convert-warpfield command.
-surface-average AVERAGE SURFACE FILES TOGETHER
wb_command -surface-average
<surface-out> - output - the output averaged surface
[-stddev] - compute 3D sample standard deviation
<stddev-metric-out> - output - the output metric for 3D sample
standard deviation
[-uncertainty] - compute caret5 'uncertainty'
<uncert-metric-out> - output - the output metric for uncertainty
[-surf] - repeatable - specify a surface to include in the average
<surface> - a surface file to average
[-weight] - specify a weighted average
<weight> - the weight to use (default 1)
The 3D sample standard deviation is computed as 'sqrt(sum(squaredlength(xyz -
mean(xyz)))/(n - 1))'.
Uncertainty is a legacy measure used in caret5, and is computed as 'sum(length(xyz
- mean(xyz)))/n'.
When weights are used, the 3D sample standard deviation treats them as reliability
weights.
-surface-closest-vertex FIND CLOSEST SURFACE VERTEX TO COORDINATES
wb_command -surface-closest-vertex
<surface> - the surface to use <coord-list-file> - text file with coordinates
<vertex-list-out> - output - the output text file with vertex numbers
For each coordinate XYZ triple, find the closest vertex in the surface, and output
its vertex number into a text file. The input file should only use whitespace to
separate coordinates (spaces, newlines, tabs), for instance:
20 30 25 30 -20 10
-surface-coordinates-to-metric MAKE METRIC FILE OF SURFACE COORDINATES
wb_command -surface-coordinates-to-metric
<surface> - the surface to use the coordinates of <metric-out> - output - the
output metric
Puts the coordinates of the surface into a 3-map metric file, as x, y, z.
-surface-cortex-layer CREATE SURFACE APPROXIMATING A CORTICAL LAYER
wb_command -surface-cortex-layer
<white-surface> - the white matter surface <pial-surface> - the pial surface
<location> - what volume fraction to place the layer at <out-surface> - output -
the output surface
[-placement-out] - output the placement as a distance fraction from pial
to white <placement-metric> - output - output metric
The input surfaces must have vertex correspondence.
The output surface
is generated by placing vertices between the two surfaces such that the enclosed
volume within any small patch of the new and white surfaces is the given fraction
of the volume of the same patch between the pial and white surfaces (i.e.,
specifying 0 would give the white surface, 1 would give the pial surface).
-surface-create-sphere GENERATE A SPHERE WITH CONSISTENT VERTEX AREAS
wb_command -surface-create-sphere
<num-vertices> - desired number of vertices <sphere-out> - output - the output
sphere
Generates a sphere by regularly dividing the triangles of an icosahedron, to come
as close to the desired number of vertices as possible, and modifying it to have
very similar vertex areas for all vertices. To generate a pair of vertex-matched
left and right spheres, use this command, then -surface-flip-lr to generate the
other sphere, then -set-structure on each. For example:
$ wb_command -surface-create-sphere 6000 Sphere.6k.R.surf.gii
$ wb_command -surface-flip-lr Sphere.6k.R.surf.gii Sphere.6k.L.surf.gii
$ wb_command -set-structure Sphere.6k.R.surf.gii CORTEX_RIGHT
$ wb_command -set-structure Sphere.6k.L.surf.gii CORTEX_LEFT
-surface-curvature CALCULATE CURVATURE OF SURFACE
wb_command -surface-curvature
<surface> - the surface to compute the curvature of
[-mean] - output mean curvature
<mean-out> - output - mean curvature metric
[-gauss] - output gaussian curvature
<gauss-out> - output - gaussian curvature metric
Compute the curvature of the surface, using the method from: Interactive Texture
Mapping by J. Maillot, Yahia, and Verroust, 1993. ACM-0-98791-601-8/93/008
-surface-cut-resample RESAMPLE A CUT SURFACE
wb_command -surface-cut-resample
<surface-in> - the surface file to resample <current-sphere> - a sphere surface
with the mesh that the input surface
is currently on
<new-sphere> - a sphere surface that is in register with <current-sphere>
and has the desired output mesh
<surface-out> - output - the output surface file
Resamples a surface file, given two spherical surfaces that are in register.
Barycentric resampling is used, because it is usually better for resampling
surfaces, and because it is needed to figure out the new topology anyway.
-surface-distortion MEASURE DISTORTION BETWEEN SURFACES
wb_command -surface-distortion
<surface-reference> - the reference surface <surface-distorted> - the distorted
surface <metric-out> - output - the output distortion metric
[-smooth] - smooth the area data
<sigma> - the smoothing kernel sigma in mm
[-caret5-method] - use the surface distortion method from caret5
[-edge-method] - calculate distortion of edge lengths rather than areas
[-local-affine-method] - calculate distortion by the local affines
between triangles
[-log2] - apply base-2 log transform
This command, when not using -caret5-method, -edge-method, or -local-affine-method,
is equivalent to using -surface-vertex-areas on each surface, smoothing both output
metrics with the GEO_GAUSS_EQUAL method on the surface they came from if -smooth is
specified, and then using the formula 'ln(distorted/reference)/ln(2)' on the
smoothed results.
When using -caret5-method, it uses the surface distortion method from caret5, which
takes the base 2 log of the ratio of tile areas, then averages those results at
each vertex, and then smooths the result on the reference surface.
When using -edge-method, the -smooth option is ignored, and the output at each
vertex is the average of 'abs(ln(refEdge/distortEdge)/ln(2))' over all edges
connected to the vertex.
When using -local-affine-method, the -smooth option is ignored.
The
output is two columns, the first is the area distortion ratio, and the second is
anisotropic strain. These are calculated by an affine transform between matching
triangles, and then averaged across the triangles of a vertex.
-surface-flip-lr MIRROR A SURFACE THROUGH THE YZ PLANE
wb_command -surface-flip-lr
<surface> - the surface to flip <surface-out> - output - the output flipped surface
This command negates the x coordinate of each vertex, and flips the surface
normals, so that you have a surface of opposite handedness with the same features
and vertex correspondence, with normals consistent with the original surface. That
is, if the input surface has normals facing outward, the output surface will also
have normals facing outward.
-surface-flip-normals FLIP ALL TILES ON A SURFACE
wb_command -surface-flip-normals
<surface> - the surface to flip the normals of <surface-out> - output - the output
surface
Flips all triangles on a surface, resulting in surface normals being flipped the
other direction (inward vs outward). If you transform a surface with an affine
that has negative determinant, or a warpfield that similarly flips the surface, you
may end up with a surface that has normals pointing inwards, which may have display
problems. Using this command will solve that problem.
-surface-generate-inflated SURFACE GENERATE INFLATED
wb_command -surface-generate-inflated
<anatomical-surface-in> - the anatomical surface <inflated-surface-out> - output -
the output inflated surface <very-inflated-surface-out> - output - the output very
inflated surface
[-iterations-scale] - optional iterations scaling
<iterations-scale-value> - iterations-scale value
Generate inflated and very inflated surfaces. The output surfaces are 'matched'
(have same XYZ range) to the anatomical surface. In most cases, an iterations-scale
of 1.0 (default) is sufficient. However, if the surface contains a large number of
vertices (150,000), try an iterations-scale of 2.5.
-surface-geodesic-distance COMPUTE GEODESIC DISTANCE FROM ONE VERTEX TO THE ENTIRE SURFACE
wb_command -surface-geodesic-distance
<surface> - the surface to compute on <vertex> - the vertex to compute geodesic
distance from <metric-out> - output - the output metric
[-naive] - use only neighbors, don't crawl triangles (not recommended)
[-limit] - stop at a certain distance
<limit-mm> - distance in mm to stop at
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
Unless -limit is specified, computes the geodesic distance from the specified
vertex to all others. The result is output as a single column metric file, with a
value of -1 for vertices that the distance was not computed for.
The -corrected-areas option should be used when the input is a group average
surface - group average surfaces have significantly less surface area than
individual surfaces do, and therefore distances measured on them would be smaller
than measuring them on individual surfaces. In this case, the input to this option
should be a group average of the output of -surface-vertex-areas for each subject.
If -naive is not specified, the algorithm uses not just immediate neighbors, but
also neighbors derived from crawling across pairs of triangles that share an edge.
-surface-geodesic-distance-all-to-all COMPUTE GEODESIC DISTANCES FROM ALL VERTICES
wb_command -surface-geodesic-distance-all-to-all
<surface> - the surface to compute on <cifti-out> - output - single-hemisphere
dconn containing the distances
[-roi] - only output distances for vertices inside an ROI
<roi-metric> - the ROI as a metric file
[-limit] - stop at a specified distance
<limit-mm> - distance in mm to stop at
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
[-naive] - use only neighbors, don't crawl triangles (not recommended)
Computes geodesic distance from every vertex to every vertex, outputting a
single-hemisphere dconn file. If you are only interested in a few vertices, see
-surface-geodesic-distance. When -limit is specified, any vertex beyond the limit
is assigned the value -1.
The -roi option makes the output file smaller by not outputting distances to or
from vertices outside the ROI, but paths are still allowed to go outside the ROI
when finding distances to other vertices.
The -corrected-areas option should be used when the input is a group average
surface - group average surfaces have significantly less surface area than
individual surfaces do, and therefore distances measured on them would be smaller
than measuring them on individual surfaces. In this case, the input to this option
should be a group average of the output of -surface-vertex-areas for each subject.
If -naive is not specified, the algorithm uses not just immediate neighbors, but
also neighbors derived from crawling across pairs of triangles that share an edge.
-surface-geodesic-rois DRAW GEODESIC LIMITED ROIS AT VERTICES
wb_command -surface-geodesic-rois
<surface> - the surface to draw on <limit> - geodesic distance limit from vertex,
in mm <vertex-list-file> - a text file containing the vertices to draw ROIs
around
<metric-out> - output - the output metric
[-gaussian] - generate a gaussian kernel instead of a flat ROI
<sigma> - the sigma for the gaussian kernel, in mm
[-overlap-logic] - how to handle overlapping ROIs, default ALLOW
<method> - the method of resolving overlaps
[-names] - name the columns from text file
<name-list-file> - a text file containing column names, one per line
[-corrected-areas] - vertex areas to use instead of computing them from
the surface <area-metric> - the corrected vertex areas, as a metric
For each vertex in the list file, a column in the output metric is created, and an
ROI around that vertex is drawn in that column. Each metric column will have zeros
outside the geodesic distance spacified by <limit>, and by default will have a
value of 1.0 inside it. If the -gaussian option is specified, the values inside
the ROI will instead form a gaussian with the specified value of sigma, normalized
so that the sum of the nonzero values in the metric column is 1.0. The <method>
argument to -overlap-logic must be one of ALLOW, CLOSEST, or EXCLUDE. ALLOW is the
default, and means that ROIs are treated independently and may overlap. CLOSEST
means that ROIs may not overlap, and that no ROI contains vertices that are closer
to a different seed vertex. EXCLUDE means that ROIs may not overlap, and that any
vertex within range of more than one ROI does not belong to any ROI.
-surface-inflation SURFACE INFLATION
wb_command -surface-inflation
<anatomical-surface-in> - the anatomical surface <surface-in> - the surface file to
inflate <number-of-smoothing-cycles> - number of smoothing cycles
<smoothing-strength> - smoothing strength (ranges [0.0 - 1.0])
<smoothing-iterations> - smoothing iterations <inflation-factor> - inflation factor
<surface-out> - output - output surface file
Inflate a surface by performing cycles that consist of smoothing followed by
inflation (to correct shrinkage caused by smoothing).
-surface-information DISPLAY INFORMATION ABOUT A SURFACE
wb_command -surface-information
<Surface File> - Surface for which information is displayed
Information about surface is displayed including vertices, triangles, bounding box,
and spacing.
-surface-match SURFACE MATCH
wb_command -surface-match
<Match Surface File> - Match (Reference) Surface <Input Surface File> - File
containing surface that will be transformed <Output Surface Name> - Surface File
after transformation
The Input Surface File will be transformed so that its coordinate ranges (bounding
box) match that of the Match Surface File
-surface-modify-sphere CHANGE RADIUS AND OPTIONALLY RECENTER A SPHERE
wb_command -surface-modify-sphere
<sphere-in> - the sphere to modify <radius> - the radius the output sphere should
have <sphere-out> - output - the output sphere
[-recenter] - recenter the sphere by means of the bounding box
This command may be useful if you have used -surface-resample to resample a sphere,
which can suffer from problems generally not present in
-surface-sphere-project-unproject. If the sphere should already be centered around
the origin, using -recenter may still shift it slightly before changing the radius,
which is likely to be undesireable.
If <sphere-in> is not close to spherical, or not centered around the origin and
-recenter is not used, a warning is printed.
-surface-normals OUTPUT VERTEX NORMALS AS METRIC FILE
wb_command -surface-normals
<surface> - the surface to output the normals of <metric-out> - output - the normal
vectors
Computes the normal vectors of the surface file, and outputs them as a 3 column
metric file.
-surface-resample RESAMPLE A SURFACE TO A DIFFERENT MESH
wb_command -surface-resample
<surface-in> - the surface file to resample <current-sphere> - a sphere surface
with the mesh that the input surface
is currently on
<new-sphere> - a sphere surface that is in register with <current-sphere>
and has the desired output mesh
<method> - the method name <surface-out> - output - the output surface file
[-area-surfs] - specify surfaces to do vertex area correction based on
<current-area> - a relevant surface with <current-sphere> mesh <new-area> - a
relevant surface with <new-sphere> mesh
[-area-metrics] - specify vertex area metrics to do area correction based
on <current-area> - a metric file with vertex areas for <current-sphere>
mesh
<new-area> - a metric file with vertex areas for <new-sphere> mesh
Resamples a surface file, given two spherical surfaces that are in register. If
ADAP_BARY_AREA is used, exactly one of -area-surfs or -area-metrics must be
specified. This method is not generally recommended for surface resampling, but is
provided for completeness.
The BARYCENTRIC method is generally recommended for anatomical surfaces, in order
to minimize smoothing.
For cut surfaces (including flatmaps), use -surface-cut-resample.
Instead of resampling a spherical surface, the -surface-sphere-project-unproject
command is recommended.
The <method> argument must be one of the following:
ADAP_BARY_AREA BARYCENTRIC
-surface-set-coordinates MODIFY COORDINATES OF A SURFACE
wb_command -surface-set-coordinates
<surface-in> - the surface to use for the topology <coord-metric> - the new
coordinates, as a 3-column metric file <surface-out> - output - the new surface
Takes the topology from an existing surface file, and uses values from a metric
file as coordinates to construct a new surface file.
See -surface-coordinates-to-metric for how to get surface coordinates as a metric
file, such that you can then modify them via metric commands, etc.
-surface-smoothing SURFACE SMOOTHING
wb_command -surface-smoothing
<surface-in> - the surface file to smooth <smoothing-strength> - smoothing strength
(ranges [0.0 - 1.0]) <smoothing-iterations> - smoothing iterations <surface-out> -
output - output surface file
Smooths a surface by averaging vertex coordinates with those of the neighboring
vertices.
-surface-sphere-project-unproject COPY REGISTRATION DEFORMATIONS TO DIFFERENT SPHERE
wb_command -surface-sphere-project-unproject
<sphere-in> - a sphere with the desired output mesh <sphere-project-to> - a sphere
that aligns with sphere-in <sphere-unproject-from> - <sphere-project-to> deformed
to the desired
output space
<sphere-out> - output - the output sphere
Background: A surface registration starts with an input sphere, and moves its
vertices around on the sphere until it matches the template data. This means that
the registration deformation is actually represented as the difference between two
separate files - the starting sphere, and the registered sphere. Since the
starting sphere of the registration may not have vertex correspondence to any other
sphere (often, it is a native sphere), it can be inconvenient to manipulate or
compare these deformations across subjects, etc.
The purpose of this command is to be able to apply these deformations onto a new
sphere of the user's choice, to make it easier to compare or manipulate them.
Common uses are to concatenate two successive separate registrations (e.g. Human to
Chimpanzee, and then Chimpanzee to Macaque) or inversion (for dedrifting or
symmetric registration schemes).
<sphere-in> must already be considered to be in alignment with one of the two ends
of the registration (if your registration is Human to Chimpanzee, <sphere-in> must
be in register with either Human or Chimpanzee). The 'project-to' sphere must be
the side of the registration that is aligned with <sphere-in> (if your registration
is Human to Chimpanzee, and <sphere-in> is aligned with Human, then 'project-to'
should be the original Human sphere). The 'unproject-from' sphere must be the
remaining sphere of the registration (original vs deformed/registered). The output
is as if you had run the same registration with <sphere-in> as the starting sphere,
in the direction of deforming the 'project-to' sphere to create the
'unproject-from' sphere.
Note that this command cannot check for you what spheres are aligned with other
spheres, and using the wrong spheres or in the incorrect order will not necessarily
cause an error message. In some cases, it may be useful to use a new, arbitrary
sphere as the input, which can be created with the -surface-create-sphere command.
Example 1: You have a Human to Chimpanzee registration, and a Chimpanzee to Macaque
registration, and want to combine them. If you use the Human sphere registered to
Chimpanzee as sphere-in, the Chimpanzee standard sphere as project-to, and the
Chimpanzee sphere registered to Macaque as unproject-from, the output will be the
Human sphere in register with the Macaque.
Example 2: You have a Human to Chimpanzee registration, but what you really want is
the inverse, that is, the sphere as if you had run the registration from Chimpanzee
to Human. If you use the Chimpanzee standard sphere as sphere-in, the Human sphere
registered to Chimpanzee as project-to, and the standard Human sphere as
unproject-from, the output will be the Chimpanzee sphere in register with the
Human.
Technical details: Each vertex of <sphere-in> is projected to a triangle of
<sphere-project-to>, and its new position is determined by the position of the
corresponding triangle in <sphere-unproject-from>. The output is a sphere with the
topology of <sphere-in>, but coordinates shifted by the deformation from
<sphere-project-to> to <sphere-unproject-from>. <sphere-project-to> and
<sphere-unproject-from> must have the same topology as each other, but <sphere-in>
may have any topology.
-surface-to-surface-3d-distance COMPUTE DISTANCE BETWEEN CORRESPONDING VERTICES
wb_command -surface-to-surface-3d-distance
<surface-comp> - the surface to compare to the reference <surface-ref> - the
surface to use as the reference <dists-out> - output - the output distances
[-vectors] - output the displacement vectors
<vectors-out> - output - the output vectors
Computes the vector difference between the vertices of each surface with the same
index, as (comp - ref), and output the magnitudes, and optionally the displacement
vectors.
-surface-vertex-areas MEASURE SURFACE AREA EACH VERTEX IS RESPONSIBLE FOR
wb_command -surface-vertex-areas
<surface> - the surface to measure <metric> - output - the output metric
Each vertex gets one third of the area of each triangle it is a part of. Units are
mm^2.
-surface-wedge-volume MEASURE PER-VERTEX VOLUME BETWEEN SURFACES
wb_command -surface-wedge-volume
<inner-surface> - the inner surface <outer-surface> - the outer surface <metric> -
output - the output metric
Compute the volume of each vertex's area from one surface to another. The surfaces
must have vertex correspondence, and have consistent triangle orientation.
-unit-test
-volume-affine-resample RESAMPLE VOLUME USING AFFINE TRANSFORM
wb_command -volume-affine-resample
<volume-in> - volume to resample <affine> - the affine file to apply <volume-space>
- a volume file in the volume space you want for the
output
<method> - the resampling method <volume-out> - output - the output volume
[-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
Resample a volume file with an affine transformation.
The recommended
methods are CUBIC (cubic spline) for most data, and ENCLOSING_VOXEL for label data.
The parameter <method> must be one of:
CUBIC ENCLOSING_VOXEL TRILINEAR
-volume-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A VOLUME FRAME
wb_command -volume-all-labels-to-rois
<label-in> - the input volume label file <map> - the number or name of the label
map to use <volume-out> - output - the output volume file
The output volume has a frame for each label in the specified input frame, other
than the ??? label, each of which contains an ROI of all voxels that are set to the
corresponding label.
-volume-capture-plane INTERPOLATE IMAGE FROM PLANE THROUGH VOLUME
wb_command -volume-capture-plane
<volume> - the volume file to interpolate from <subvolume> - the name or number of
the subvolume to use <interp> - interpolation type <h-dim> - width of output image,
in pixels <v-dim> - height of output image, in pixels <scale-min> - value to render
as black <scale-max> - value to render as white <bottom-left-x> - x-coordinate of
the bottom left of the output image <bottom-left-y> - y-coordinate of the bottom
left of the output image <bottom-left-z> - z-coordinate of the bottom left of the
output image <bottom-right-x> - x-coordinate of the bottom right of the output
image <bottom-right-y> - y-coordinate of the bottom right of the output image
<bottom-right-z> - z-coordinate of the bottom right of the output image
<top-left-x> - x-coordinate of the top left of the output image <top-left-y> -
y-coordinate of the top left of the output image <top-left-z> - z-coordinate of the
top left of the output image <image> - output - the output image
NOTE: If you want to generate an image with all of the capabilities of the GUI
rendering, see -show-scene.
Renders an image of an arbitrary plane through the volume file, with a simple
linear grayscale palette. The parameter <interp> must be one of:
CUBIC ENCLOSING_VOXEL TRILINEAR
-volume-copy-extensions COPY EXTENDED DATA TO ANOTHER VOLUME FILE
wb_command -volume-copy-extensions
<data-volume> - the volume file containing the voxel data to use <extension-volume>
- the volume file containing the extensions to use <volume-out> - output - the
output volume
[-drop-unknown] - don't copy extensions that workbench doesn't understand
This command copies the information in a volume file that isn't a critical part of
the standard header or data matrix, e.g. map names, palette settings, label tables.
If -drop-unknown is not specified, it also copies similar kinds of information set
by other software.
-volume-create CREATE A BLANK VOLUME FILE
wb_command -volume-create
<i-dim> - length of first dimension <j-dim> - length of second dimension <k-dim> -
length of third dimension <volume-out> - output - the output volume
[-plumb] - set via axis order and spacing/offset
<axis-order> - a string like 'XYZ' that specifies which index is along
which spatial dimension
<x-spacing> - change in x-coordinate from incrementing the relevant
index
<y-spacing> - change in y-coordinate from incrementing the relevant
index
<z-spacing> - change in z-coordinate from incrementing the relevant
index
<x-offset> - the x-coordinate of the center of the first voxel <y-offset> - the
y-coordinate of the center of the first voxel <z-offset> - the z-coordinate of the
center of the first voxel
[-sform] - set via a nifti sform
<xi-spacing> - increase in x coordinate from incrementing the i index <xj-spacing>
- increase in x coordinate from incrementing the j index <xk-spacing> - increase in
x coordinate from incrementing the k index <x-offset> - x coordinate of first voxel
<yi-spacing> - increase in y coordinate from incrementing the i index <yj-spacing>
- increase in y coordinate from incrementing the j index <yk-spacing> - increase in
y coordinate from incrementing the k index <y-offset> - y coordinate of first voxel
<zi-spacing> - increase in z coordinate from incrementing the i index <zj-spacing>
- increase in z coordinate from incrementing the j index <zk-spacing> - increase in
z coordinate from incrementing the k index <z-offset> - z coordinate of first voxel
Creates a volume file full of zeros.
Exactly one of -plumb or -sform
must be specified.
-volume-dilate DILATE A VOLUME FILE
wb_command -volume-dilate
<volume> - the volume to dilate <distance> - distance in mm to dilate <method> -
dilation method to use <volume-out> - output - the output volume
[-exponent] - use a different exponent in the weighting function
<exponent> - exponent 'n' to use in (1 / (distance ^ n)) as the
weighting function (default 7)
[-bad-voxel-roi] - specify an roi of voxels to overwrite, rather than
voxels with value zero <roi-volume> - volume file, positive values denote voxels to
have
their values replaced
[-data-roi] - specify an roi of where there is data
<roi-volume> - volume file, positive values denote voxels that have
data
[-subvolume] - select a single subvolume to dilate
<subvol> - the subvolume number or name
[-legacy-cutoff] - use the old method of excluding voxels further than
the dilation distance when calculating the dilated value
For all voxels that are designated as bad, if they neighbor a non-bad voxel with
data or are within the specified distance of such a voxel, replace the value in the
bad voxel with a value calculated from nearby non-bad voxels that have data,
otherwise set the value to zero. No matter how small <distance> is, dilation will
always use at least the face neighbor voxels.
By default, voxels that have data with the value 0 are bad, specify -bad-voxel-roi
to only count voxels as bad if they are selected by the roi. If -data-roi is not
specified, all voxels are assumed to have data.
To get the behavior of version 1.3.2 or earlier, use '-legacy-cutoff -exponent 2'.
Valid values for <method> are:
NEAREST - use the value from the nearest good voxel WEIGHTED - use a weighted
average based on distance
-volume-distortion CALCULATE VOLUME WARPFIELD DISTORTION
wb_command -volume-distortion
<warpfield> - the warpfield to compute the distortion of <volume-out> - output -
the output distortion measures
[-fnirt] - MUST be used if using a fnirt warpfield
<source-volume> - the source volume used when generating the warpfield
[-circular] - use the circle-based formula for the anisotropic measure
[-log2] - apply base-2 log transform
Calculates isotropic and anisotropic distortions in the volume warpfield. At each
voxel, the gradient of the absolute warpfield is computed to obtain the local
affine transforms for each voxel (jacobian matrices), and strain tensors are
derived from them. The isotropic component (volumetric expansion ratio) is the
product of the three principal strains. The default measure ('elongation') for the
anisotropic component is the largest principal strain divided by the smallest.
The -circular option instead calculates the anisotropic component by transforming
the principal strains into log space, considering them as x-values of points on a
circle 120 degrees apart, finds the circle's diameter, and transforms that back to
a ratio.
-volume-erode ERODE A VOLUME FILE
wb_command -volume-erode
<volume> - the volume to erode <distance> - distance in mm to erode <volume-out> -
output - the output volume
[-roi] - assume voxels outside this roi are nonzero
<roi-volume> - volume file, positive values denote voxels that have
data
[-subvolume] - select a single subvolume to dilate
<subvol> - the subvolume number or name
Around each voxel with a value of zero, set surrounding voxels to zero. The
surrounding voxels are all face neighbors and all voxels within the specified
distance (center to center).
-volume-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A VOLUME
wb_command -volume-estimate-fwhm
<volume> - the input volume
[-roi] - use only data within an ROI
<roivol> - the volume to use as an ROI
[-subvolume] - select a single subvolume to estimate smoothness of
<subvol> - the subvolume number or name
[-whole-file] - estimate for the whole file at once, not each subvolume
separately
[-demean] - subtract the mean image before estimating smoothness
Estimates the smoothness of the input volume in X, Y, and Z directions separately,
printing the estimates to standard output, in mm as FWHM. If -subvolume or
-whole-file are not specified, each subvolume is estimated and displayed
separately.
-volume-extrema FIND EXTREMA IN A VOLUME FILE
wb_command -volume-extrema
<volume-in> - volume file to find the extrema of <distance> - the minimum distance
between identified extrema of the same
type
<volume-out> - output - the output extrema volume
[-presmooth] - smooth the volume before finding extrema
<kernel> - the sigma for the gaussian smoothing kernel, in mm
[-roi] - ignore values outside the selected area
<roi-volume> - the area to find extrema in
[-threshold] - ignore small extrema
<low> - the largest value to consider for being a minimum <high> - the smallest
value to consider for being a maximum
[-sum-subvols] - output the sum of the extrema subvolumes instead of each
subvolume separately
[-consolidate-mode] - use consolidation of local minima instead of a
large neighborhood
[-only-maxima] - only find the maxima
[-only-minima] - only find the minima
[-subvolume] - select a single subvolume to find extrema in
<subvolume> - the subvolume number or name
Finds extrema in a volume file, such that no two extrema of the same type are
within <distance> of each other. The extrema are labeled as -1 for minima, 1 for
maxima, 0 otherwise. If -only-maxima or -only-minima is specified, then it will
ignore extrema not of the specified type. These options are mutually exclusive.
If -sum-subvols is specified, these extrema subvolumes are summed, and the output
has a single subvolume with this result.
By default, a datapoint is an extrema only if it is more extreme than every other
datapoint that is within <distance> from it. If -consolidate-mode is used, it
instead starts by finding all datapoints that are more extreme than their immediate
neighbors, then while there are any extrema within <distance> of each other, take
the two extrema closest to each other and merge them into one by a weighted average
based on how many original extrema have been merged into each.
By default, all input subvolumes are used with no smoothing, use -subvolume to
specify a single subvolume to use, and -presmooth to smooth the input before
finding the extrema.
-volume-fill-holes FILL HOLES IN AN ROI VOLUME
wb_command -volume-fill-holes
<volume-in> - the input ROI volume <volume-out> - output - the output ROI volume
Finds all face-connected parts that are not included in the ROI, and fills all but
the largest one with ones.
-volume-find-clusters FILTER CLUSTERS BY VOLUME
wb_command -volume-find-clusters
<volume-in> - the input volume <value-threshold> - threshold for data values
<minimum-volume> - threshold for cluster volume, in mm^3 <volume-out> - output -
the output volume
[-less-than] - find values less than <value-threshold>, rather than
greater
[-roi] - select a region of interest
<roi-volume> - the roi, as a volume file
[-subvolume] - select a single subvolume
<subvol> - the subvolume number or name
[-size-ratio] - ignore clusters smaller than a given fraction of the
largest cluster in map <ratio> - fraction of the largest cluster's volume
[-distance] - ignore clusters further than a given distance from the
largest cluster <distance> - how far from the largest cluster a cluster can be,
edge
to edge, in mm
[-start] - start labeling clusters from a value other than 1
<startval> - the value to give the first cluster found
Outputs a volume with nonzero integers for all voxels within a large enough
cluster, and zeros elsewhere. The integers denote cluster membership (by default,
first cluster found will use value 1, second cluster 2, etc). Cluster values are
not reused across frames of the output, but instead keep counting up. By default,
values greater than <value-threshold> are considered to be in a cluster, use
-less-than to test for values less than the threshold. To apply this as a mask to
the data, or to do more complicated thresholding, see -volume-math.
-volume-gradient GRADIENT OF A VOLUME FILE
wb_command -volume-gradient
<volume-in> - the input volume <volume-out> - output - the output gradient
magnitude volume
[-presmooth] - smooth the volume before computing the gradient
<kernel> - sigma for gaussian weighting function, in mm
[-roi] - select a region of interest to take the gradient of
<roi-volume> - the region to take the gradient within
[-vectors] - output vectors
<vector-volume-out> - output - the vectors as a volume file
[-subvolume] - select a single subvolume to take the gradient of
<subvol> - the subvolume number or name
Computes the gradient of the volume by doing linear regressions for each voxel,
considering only its face neighbors unless too few face neighbors exist. The
gradient vector is constructed from the partial derivatives of the resulting linear
function, and the magnitude of this vector is the output. If specified, the volume
vector output is arranged with the x, y, and z components from a subvolume as
consecutive subvolumes.
-volume-label-export-table EXPORT LABEL TABLE FROM VOLUME AS TEXT
wb_command -volume-label-export-table
<label-in> - the input volume label file <map> - the number or name of the label
map to use <table-out> - output - the output text file
Takes the label table from the volume label map, and writes it to a text format
matching what is expected by -volume-label-import.
-volume-label-import IMPORT A LABEL VOLUME TO WORKBENCH FORMAT
wb_command -volume-label-import
<input> - the input volume file <label-list-file> - text file containing the values
and names for labels <output> - output - the output workbench label volume
[-discard-others] - set any voxels with values not mentioned in the label
list to the ??? label
[-unlabeled-value] - set the value that will be interpreted as unlabeled
<value> - the numeric value for unlabeled (default 0)
[-subvolume] - select a single subvolume to import
<subvol> - the subvolume number or name
[-drop-unused-labels] - remove any unused label values from the label
table
Creates a label volume from an integer-valued volume file.
The label
name and color information is stored in the volume header in a nifti extension,
with a similar format as in caret5, see -volume-help. You may specify the empty
string (use "") for <label-list-file>, which will be treated as if it is an empty
file. The label list file must have the following format (2 lines per label):
<labelname> <key> <red> <green> <blue> <alpha> ...
Label names are specified on a separate line from their value and color, in order
to let label names contain spaces. Whitespace is trimmed from both ends of the
label name, but is kept if it is in the middle of a label. Do not specify the
"unlabeled" key in the file, it is assumed that 0 means not labeled unless
-unlabeled-value is specified. The value of <key> specifies what value in the
imported file should be used as this label. The values of <red>, <green>, <blue>
and <alpha> must be integers from 0 to 255, and will specify the color the label is
drawn as (alpha of 255 means fully opaque, which is probably what you want).
By default, it will create new label names with names like LABEL_5 for any values
encountered that are not mentioned in the list file, specify -discard-others to
instead set these values to the "unlabeled" key.
-volume-label-modify-keys CHANGE KEY VALUES IN A VOLUME LABEL FILE
wb_command -volume-label-modify-keys
<volume-in> - the input volume label file <remap-file> - text file with old and new
key values <volume-out> - output - the output volume label file
[-subvolume] - select a single subvolume
<subvolume> - the subvolume number or name
<remap-file> should have lines of the form 'oldkey newkey', like so:
3 5 5 8 8 2
This would change the current label with key '3' to use the key '5' instead, 5
would use 8, and 8 would use 2. Any collision in key values results in the label
that was not specified in the remap file getting remapped to an otherwise unused
key. Remapping more than one key to the same new key, or the same key to more than
one new key, results in an error. This will not change the appearance of the file
when displayed, as it will change the key values in the data at the same time.
-volume-label-probability FIND FREQUENCY OF VOLUME LABELS
wb_command -volume-label-probability
<label-maps> - volume label file containing individual label maps from
many subjects
<probability-out> - output - the relative frequencies of each label at
each voxel
[-exclude-unlabeled] - don't make a probability map of the unlabeled key
This command outputs a set of soft ROIs, one for each label in the input, where the
value is how many of the input maps had that label at that voxel, divided by the
number of input maps.
-volume-label-to-roi MAKE A VOLUME LABEL INTO AN ROI VOLUME
wb_command -volume-label-to-roi
<label-in> - the input volume label file <volume-out> - output - the output volume
file
[-name] - select label by name
<label-name> - the label name that you want an roi of
[-key] - select label by key
<label-key> - the label key that you want an roi of
[-map] - select a single label map to use
<map> - the map number or name
For each map in <label-in>, a map is created in <volume-out> where all locations
labeled with <label-name> or with a key of <label-key> are given a value of 1, and
all other locations are given 0. Exactly one of -name and -key must be specified.
Specify -map to use only one map from <label-in>.
-volume-label-to-surface-mapping MAP A LABEL VOLUME TO A SURFACE LABEL FILE
wb_command -volume-label-to-surface-mapping
<volume> - the volume to map data from <surface> - the surface to map the data onto
<label-out> - output - the output gifti label file
[-ribbon-constrained] - use ribbon constrained mapping algorithm
<inner-surf> - the inner surface of the ribbon <outer-surf> - the outer surface of
the ribbon
[-volume-roi] - use a volume roi
<roi-volume> - the volume file
[-voxel-subdiv] - voxel divisions while estimating voxel weights
<subdiv-num> - number of subdivisions, default 3
[-thin-columns] - use non-overlapping polyhedra
[-subvol-select] - select a single subvolume to map
<subvol> - the subvolume number or name
Map label volume data to a surface.
If -ribbon-constrained is not
specified, uses the enclosing voxel method.
The ribbon mapping method
constructs a polyhedron from the vertex's neighbors on each surface, and estimates
the amount of this polyhedron's volume that falls inside any nearby voxels, to use
as the weights for a popularity comparison. If -thin-columns is specified, the
polyhedron uses the edge midpoints and triangle centroids, so that neighboring
vertices do not have overlapping polyhedra. This may require increasing
-voxel-subdiv to get enough samples in each voxel to reliably land inside these
smaller polyhedra. The volume ROI is useful to exclude partial volume effects of
voxels the surfaces pass through, and will cause the mapping to ignore voxels that
don't have a positive value in the mask. The subdivision number specifies how it
approximates the amount of the volume the polyhedron intersects, by splitting each
voxel into NxNxN pieces, and checking whether the center of each piece is inside
the polyhedron. If you have very large voxels, consider increasing this if you get
unexpected unlabeled vertices in your output.
-volume-math EVALUATE EXPRESSION ON VOLUME FILES
wb_command -volume-math
<expression> - the expression to evaluate, in quotes <volume-out> - output - the
output volume
[-fixnan] - replace NaN results with a value
<replace> - value to replace NaN with
[-var] - repeatable - a volume file to use as a variable
<name> - the name of the variable, as used in the expression <volume> - the volume
file to use as this variable
[-subvolume] - select a single subvolume
<subvol> - the subvolume number or name
[-repeat] - reuse a single subvolume for each subvolume of calculation
This command evaluates <expression> at each voxel independently.
There
must be at least one -var option (to get the volume space from), even if the <name>
specified in it isn't used in <expression>. All volumes must have the same volume
space. Filenames are not valid in <expression>, use a variable name and a -var
option with matching <name> to specify an input file. If the -subvolume option is
given to any -var option, only one subvolume is used from that file. If -repeat is
specified, the file must either have only one subvolume, or have the -subvolume
option specified. All files that don't use -repeat must have the same number of
subvolumes requested to be used. The format of <expression> is as follows:
Expressions consist of constants, variables, operators, parentheses, and functions,
in infix notation, such as 'exp(-x + 3) * scale'. Variables are strings of any
length, using the characters a-z, A-Z, 0-9, and _, but may not take the name of a
named constant. Currently, there is only one named constant, PI. The operators
are +, -, *, /, ^, >, <, >=, <=, ==, !=, !, &&, ||. These behave as in C, except
that ^ is exponentiation, i.e. pow(x, y), and takes higher precedence than other
binary operators (also, '-3^-4^-5' means '-(3^(-(4^-5)))'). The <=, >=, ==, and !=
operators are given a small amount of wiggle room, equal to one millionth of the
smaller of the absolute values of the values being compared.
Comparison and logical operators return 0 or 1, you can do masking with expressions
like 'x * (mask > 0)'. For all logical operators, an input is considered true iff
it is greater than 0. The expression '0 < x < 5' is not syntactically wrong, but
it will NOT do what is desired, because it is evaluated left to right, i.e. '((0 <
x) < 5)', which will always return 1, as both possible results of a comparison are
less than 5. A warning is generated if an expression of this type is detected.
Use something like 'x > 0 && x < 5' to get the desired behavior.
Whitespace between elements is ignored, ' sin ( 2 * x ) ' is equivalent to
'sin(2*x)', but 's in(2*x)' is an error. Implied multiplication is not allowed,
the expression '2x' will be parsed as a variable. Parentheses are (), do not use
[] or {}. Functions require parentheses, the expression 'sin x' is an error.
The following functions are supported:
sin: 1 argument, the sine of the argument (units are radians) cos: 1 argument, the
cosine of the argument (units are radians) tan: 1 argument, the tangent of the
argument (units are radians) asin: 1 argument, the inverse of sine of the argument,
in radians acos: 1 argument, the inverse of cosine of the argument, in radians
atan: 1 argument, the inverse of tangent of the argument, in radians atan2: 2
arguments, atan2(y, x) returns the inverse of tangent of
(y/x), in radians, determining quadrant by the sign of both arguments
sinh: 1 argument, the hyperbolic sine of the argument cosh: 1 argument, the
hyperbolic cosine of the argument tanh: 1 argument, the hyperboloc tangent of the
argument asinh: 1 argument, the inverse hyperbolic sine of the argument acosh: 1
argument, the inverse hyperbolic cosine of the argument atanh: 1 argument, the
inverse hyperboloc tangent of the argument ln: 1 argument, the natural logarithm of
the argument exp: 1 argument, the constant e raised to the power of the argument
log: 1 argument, the base 10 logarithm of the argument log2: 1 argument, the base 2
logarithm of the argument sqrt: 1 argument, the square root of the argument abs: 1
argument, the absolute value of the argument floor: 1 argument, the largest integer
not greater than the argument round: 1 argument, the nearest integer, with ties
rounded away from
zero
ceil: 1 argument, the smallest integer not less than the argument min: 2 arguments,
min(x, y) returns y if (x > y), x otherwise max: 2 arguments, max(x, y) returns y
if (x < y), x otherwise mod: 2 arguments, mod(x, y) = x - y * floor(x / y), or 0 if
y == 0 clamp: 3 arguments, clamp(x, low, high) = min(max(x, low), high)
-volume-merge MERGE VOLUME FILES INTO A NEW FILE
wb_command -volume-merge
<volume-out> - output - the output volume file
[-volume] - repeatable - specify an input volume file
<volume-in> - a volume file to use subvolumes from
[-subvolume] - repeatable - select a single subvolume to use
<subvol> - the subvolume number or name
[-up-to] - use an inclusive range of subvolumes
<last-subvol> - the number or name of the last subvolume to
include
[-reverse] - use the range in reverse order
Takes one or more volume files and constructs a new volume file by concatenating
subvolumes from them. The input volume files must have the same volume space.
Example: wb_command -volume-merge out.nii -volume first.nii -subvolume 1 -volume
second.nii
This example would take the first subvolume from first.nii, followed by all
subvolumes from second.nii, and write these to out.nii.
-volume-palette SET THE PALETTE OF A VOLUME FILE
wb_command -volume-palette
<volume> - the volume file to modify <mode> - the mapping mode
[-subvolume] - select a single subvolume
<subvolume> - the subvolume number or name
[-pos-percent] - percentage min/max for positive data coloring
<pos-min-%> - the percentile for the least positive data <pos-max-%> - the
percentile for the most positive data
[-neg-percent] - percentage min/max for negative data coloring
<neg-min-%> - the percentile for the least negative data <neg-max-%> - the
percentile for the most negative data
[-pos-user] - user min/max values for positive data coloring
<pos-min-user> - the value for the least positive data <pos-max-user> - the value
for the most positive data
[-neg-user] - user min/max values for negative data coloring
<neg-min-user> - the value for the least negative data <neg-max-user> - the value
for the most negative data
[-interpolate] - interpolate colors
<interpolate> - boolean, whether to interpolate
[-disp-pos] - display positive data
<display> - boolean, whether to display
[-disp-neg] - display positive data
<display> - boolean, whether to display
[-disp-zero] - display data closer to zero than the min cutoff
<display> - boolean, whether to display
[-palette-name] - set the palette used
<name> - the name of the palette
[-thresholding] - set the thresholding
<type> - thresholding setting <test> - show values inside or outside thresholds
<min> - lower threshold <max> - upper threshold
[-inversion] - specify palette inversion
<type> - the type of inversion
The original volume file is overwritten with the modified version.
By
default, all columns of the volume file are adjusted to the new settings, use the
-subvolume option to change only one subvolume. Mapping settings not specified in
options will be taken from the first subvolume. The <mode> argument must be one of
the following:
MODE_AUTO_SCALE MODE_AUTO_SCALE_ABSOLUTE_PERCENTAGE MODE_AUTO_SCALE_PERCENTAGE
MODE_USER_SCALE
The <name> argument to -palette-name must be one of the following:
ROY-BIG-BL videen_style Gray_Interp_Positive Gray_Interp PSYCH-FIXED RBGYR20
RBGYR20P RYGBR4_positive RGRBR_mirror90_pos Orange-Yellow POS_NEG_ZERO red-yellow
blue-lightblue FSL power_surf fsl_red fsl_green fsl_blue fsl_yellow RedWhiteBlue
cool-warm spectral RY-BC-BL magma JET256 PSYCH PSYCH-NO-NONE ROY-BIG clear_brain
fidl raich4_clrmid raich6_clrmid HSB8_clrmid POS_NEG
The <type> argument to -thresholding must be one of the following:
THRESHOLD_TYPE_OFF THRESHOLD_TYPE_NORMAL THRESHOLD_TYPE_FILE
The <test> argument to -thresholding must be one of the following:
THRESHOLD_TEST_SHOW_OUTSIDE THRESHOLD_TEST_SHOW_INSIDE
The <type> argument to -inversion must be one of the following:
OFF POSITIVE_WITH_NEGATIVE POSITIVE_NEGATIVE_SEPARATE
-volume-parcel-resampling SMOOTH AND RESAMPLE VOLUME PARCELS
wb_command -volume-parcel-resampling
<volume-in> - the input data volume <cur-parcels> - label volume of where the
parcels currently are <new-parcels> - label volume of where the parcels should be
<kernel> - gaussian kernel sigma to smooth by during resampling <volume-out> -
output - output volume
[-fix-zeros] - treat zero values as not being data
[-subvolume] - select a single subvolume as input
<subvol> - the subvolume number or name
Smooths and resamples the region inside each label in cur-parcels to the region of
the same label name in new-parcels. Any voxels in the output label region but
outside the input label region will be extrapolated from nearby data. The
-fix-zeros option causes the smoothing to not use an input value if it is zero, but
still write a smoothed value to the voxel, and after smoothing is complete, it will
check for any remaining values of zero, and fill them in with extrapolated values.
Note: all volumes must have the same dimensions and spacing.
To use a
different output space, see -volume-parcel-resampling-generic.
-volume-parcel-resampling-generic SMOOTH AND RESAMPLE VOLUME PARCELS FROM DIFFERENT VOLUME
SPACE
wb_command -volume-parcel-resampling-generic
<volume-in> - the input data volume <cur-parcels> - label volume of where the
parcels currently are <new-parcels> - label volume of where the parcels should be
<kernel> - gaussian kernel sigma to smooth by during resampling <volume-out> -
output - output volume
[-fix-zeros] - treat zero values as not being data
[-subvolume] - select a single subvolume as input
<subvol> - the subvolume number or name
Smooths and resamples the region inside each label in cur-parcels to the region of
the same label name in new-parcels. Any voxels in the output label region but
outside the input label region will be extrapolated from nearby data. The
-fix-zeros option causes the smoothing to not use an input value if it is zero, but
still write a smoothed value to the voxel, and after smoothing is complete, it will
check for any remaining values of zero, and fill them in with extrapolated values.
The output volume will use the volume space of new-parcels, which does not need to
be in the same volume space as the input.
-volume-parcel-smoothing SMOOTH PARCELS IN A VOLUME SEPARATELY
wb_command -volume-parcel-smoothing
<data-volume> - the volume to smooth <label-volume> - a label volume containing the
parcels to smooth <kernel> - the gaussian smoothing kernel sigma, in mm
<volume-out> - output - the output volume
[-fix-zeros] - treat zero values as not being data
[-subvolume] - select a single subvolume to smooth
<subvol> - the subvolume number or name
The volume is smoothed within each label in the label volume using data only from
within the label. Equivalent to running volume smoothing with ROIs matching each
label separately, then adding the resulting volumes, but faster.
-volume-reduce PERFORM REDUCTION OPERATION ACROSS SUBVOLUMES
wb_command -volume-reduce
<volume-in> - the volume file to reduce <operation> - the reduction operator to use
<volume-out> - output - the output volume
[-exclude-outliers] - exclude non-numeric values and outliers by standard
deviation <sigma-below> - number of standard deviations below the mean to
include
<sigma-above> - number of standard deviations above the mean to
include
[-only-numeric] - exclude non-numeric values
For each voxel, takes the data across subvolumes as a vector, and performs the
specified reduction on it, putting the result into the single output volume at that
voxel. The reduction operators are as follows:
MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based index of the
maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all values
PRODUCT: multiply all values MEAN: the mean of the data STDEV: the standard
deviation (N denominator) SAMPSTDEV: the sample standard deviation (N-1
denominator) VARIANCE: the variance of the data TSNR: mean divided by sample
standard deviation (N-1 denominator) COV: sample standard deviation (N-1
denominator) divided by mean L2NORM: square root of sum of squares MEDIAN: the
median of the data MODE: the mode of the data COUNT_NONZERO: the number of nonzero
elements in the data
-volume-remove-islands REMOVE ISLANDS FROM AN ROI VOLUME
wb_command -volume-remove-islands
<volume-in> - the input ROI volume <volume-out> - output - the output ROI volume
Finds all face-connected parts of the ROI, and zeros out all but the largest one.
-volume-reorient CHANGE VOXEL ORDER OF A VOLUME FILE
wb_command -volume-reorient
<volume> - the volume to reorient <orient-string> - the desired orientation
<volume-out> - out - the reoriented volume
Changes the voxel order and the header spacing/origin information such that the
value of any spatial point is unchanged. Orientation strings look like 'LPI',
which means first index is left to right, second is posterior to anterior, and
third is inferior to superior. The valid characters are:
L left to right
R right to left
P posterior to anterior
A anterior to posterior
I inferior to superior
S superior to inferior
-volume-rois-from-extrema CREATE VOLUME ROI MAPS FROM EXTREMA MAPS
wb_command -volume-rois-from-extrema
<volume-in> - the input volume <limit> - distance limit from voxel center, in mm
<volume-out> - output - the output volume
[-gaussian] - generate a gaussian kernel instead of a flat ROI
<sigma> - the sigma for the gaussian kernel, in mm
[-roi] - select a region of interest to use
<roi-volume> - the region to use
[-overlap-logic] - how to handle overlapping ROIs, default ALLOW
<method> - the method of resolving overlaps
[-subvolume] - select a single subvolume to take the gradient of
<subvol> - the subvolume number or name
For each nonzero value in each map, make a map with an ROI around that location.
If the -gaussian option is specified, then normalized gaussian kernels are output
instead of ROIs. The <method> argument to -overlap-logic must be one of ALLOW,
CLOSEST, or EXCLUDE. ALLOW is the default, and means that ROIs are treated
independently and may overlap. CLOSEST means that ROIs may not overlap, and that
no ROI contains vertices that are closer to a different seed vertex. EXCLUDE means
that ROIs may not overlap, and that any vertex within range of more than one ROI
does not belong to any ROI.
-volume-set-space CHANGE VOLUME SPACE INFORMATION
wb_command -volume-set-space
<volume-in> - the input volume <volume-out> - output - the output volume
[-plumb] - set via axis order and spacing/offset
<axis-order> - a string like 'XYZ' that specifies which index is along
which spatial dimension
<x-spacing> - change in x-coordinate from incrementing the relevant
index
<y-spacing> - change in y-coordinate from incrementing the relevant
index
<z-spacing> - change in z-coordinate from incrementing the relevant
index
<x-offset> - the x-coordinate of the first voxel <y-offset> - the y-coordinate of
the first voxel <z-offset> - the z-coordinate of the first voxel
[-sform] - set via a nifti sform
<xi-spacing> - increase in x coordinate from incrementing the i index <xj-spacing>
- increase in x coordinate from incrementing the j index <xk-spacing> - increase in
x coordinate from incrementing the k index <x-offset> - x coordinate of first voxel
<yi-spacing> - increase in y coordinate from incrementing the i index <yj-spacing>
- increase in y coordinate from incrementing the j index <yk-spacing> - increase in
y coordinate from incrementing the k index <y-offset> - y coordinate of first voxel
<zi-spacing> - increase in z coordinate from incrementing the i index <zj-spacing>
- increase in z coordinate from incrementing the j index <zk-spacing> - increase in
z coordinate from incrementing the k index <z-offset> - z coordinate of first voxel
[-file] - copy spacing info from volume file with matching dimensions
<volume-ref> - volume file to use for reference space
[-ignore-dims] - copy the spacing info even if the dimensions don't
match
Writes a copy of the volume file, with the spacing information changed as
specified. No reordering of the voxel data occurs, see -volume-reorient to change
the volume indexing order and reorder the voxels to match. Exactly one of -plumb,
-sform, or -file must be specified.
-volume-smoothing SMOOTH A VOLUME FILE
wb_command -volume-smoothing
<volume-in> - the volume to smooth <kernel> - the gaussian smoothing kernel sigma,
in mm <volume-out> - output - the output volume
[-roi] - smooth only from data within an ROI
<roivol> - the volume to use as an ROI
[-fix-zeros] - treat zero values as not being data
[-subvolume] - select a single subvolume to smooth
<subvol> - the subvolume number or name
Gaussian smoothing for volumes.
By default, smooths all subvolumes with
no ROI, if ROI is given, only positive voxels in the ROI volume have their values
used, and all other voxels are set to zero. Smoothing a non-orthogonal volume will
be significantly slower, because the operation cannot be separated into
1-dimensional smoothings without distorting the kernel shape.
The -fix-zeros option causes the smoothing to not use an input value if it is zero,
but still write a smoothed value to the voxel. This is useful for zeros that
indicate lack of information, preventing them from pulling down the intensity of
nearby voxels, while giving the zero an extrapolated value.
-volume-stats SPATIAL STATISTICS ON A VOLUME FILE
wb_command -volume-stats
<volume-in> - the input volume
[-reduce] - use a reduction operation
<operation> - the reduction operation
[-percentile] - give the value at a percentile
<percent> - the percentile to find
[-subvolume] - only display output for one subvolume
<subvolume> - the subvolume number or name
[-roi] - only consider data inside an roi
<roi-volume> - the roi, as a volume file
[-match-maps] - each subvolume of input uses the corresponding
subvolume from the roi file
[-show-map-name] - print map index and name before each output
For each subvolume of the input, a single number is printed, resulting from the
specified reduction or percentile operation. Use -subvolume to only give output
for a single subvolume. Use -roi to consider only the data within a region.
Exactly one of -reduce or -percentile must be specified.
The argument to the -reduce option must be one of the following:
MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based index of the
maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all values
PRODUCT: multiply all values MEAN: the mean of the data STDEV: the standard
deviation (N denominator) SAMPSTDEV: the sample standard deviation (N-1
denominator) VARIANCE: the variance of the data TSNR: mean divided by sample
standard deviation (N-1 denominator) COV: sample standard deviation (N-1
denominator) divided by mean L2NORM: square root of sum of squares MEDIAN: the
median of the data MODE: the mode of the data COUNT_NONZERO: the number of nonzero
elements in the data
-volume-tfce DO TFCE ON A VOLUME FILE
wb_command -volume-tfce
<volume-in> - the volume to run TFCE on <volume-out> - output - the output volume
[-presmooth] - smooth the volume before running TFCE
<kernel> - the sigma for the gaussian smoothing kernel, in mm
[-roi] - select a region of interest to run TFCE on
<roi-volume> - the area to run TFCE on, as a volume
[-parameters] - set parameters for TFCE integral
<E> - exponent for cluster volume (default 0.5) <H> - exponent for threshold value
(default 2.0)
[-subvolume] - select a single subvolume
<subvolume> - the subvolume number or name
Threshold-free cluster enhancement is a method to increase the relative value of
regions that would form clusters in a standard thresholding test. This is
accomplished by evaluating the integral of:
e(h, p)^E * h^H * dh
at each vertex p, where h ranges from 0 to the maximum value in the data, and e(h,
p) is the extent of the cluster containing vertex p at threshold h. Negative
values are similarly enhanced by negating the data, running the same process, and
negating the result.
This method is explained in: Smith SM, Nichols TE., "Threshold-free cluster
enhancement: addressing problems of smoothing, threshold dependence and
localisation in cluster inference." Neuroimage. 2009 Jan 1;44(1):83-98. PMID:
18501637
-volume-to-surface-mapping MAP VOLUME TO SURFACE
wb_command -volume-to-surface-mapping
<volume> - the volume to map data from <surface> - the surface to map the data onto
<metric-out> - output - the output metric file
[-trilinear] - use trilinear volume interpolation
[-enclosing] - use value of the enclosing voxel
[-cubic] - use cubic splines
[-ribbon-constrained] - use ribbon constrained mapping algorithm
<inner-surf> - the inner surface of the ribbon <outer-surf> - the outer surface of
the ribbon
[-volume-roi] - use a volume roi
<roi-volume> - the volume file
[-voxel-subdiv] - voxel divisions while estimating voxel weights
<subdiv-num> - number of subdivisions, default 3
[-thin-columns] - use non-overlapping polyhedra
[-gaussian] - reduce weight to voxels that aren't near <surface>
<scale> - value to multiply the local thickness by, to get the
gaussian sigma
[-bad-vertices-out] - output an ROI of which vertices didn't intersect
any valid voxels <roi-out> - output - the output metric file of vertices that have
no data
[-output-weights] - write the voxel weights for a vertex to a volume
file <vertex> - the vertex number to get the voxel weights for, 0-based
<weights-out> - output - volume to write the weights to
[-output-weights-text] - write the voxel weights for all vertices to a
text file <text-out> - output - the output text filename
[-myelin-style] - use the method from myelin mapping
<ribbon-roi> - an roi volume of the cortical ribbon for this
hemisphere
<thickness> - a metric file of cortical thickness <sigma> - gaussian kernel in mm
for weighting voxels within range
[-legacy-bug] - emulate old v1.2.3 and earlier code that didn't follow
a cylinder cutoff
[-subvol-select] - select a single subvolume to map
<subvol> - the subvolume number or name
You must specify exactly one mapping method.
Enclosing voxel uses the
value from the voxel the vertex lies inside, while trilinear does a 3D linear
interpolation based on the voxels immediately on each side of the vertex's
position.
The ribbon mapping method constructs a polyhedron from the vertex's neighbors on
each surface, and estimates the amount of this polyhedron's volume that falls
inside any nearby voxels, to use as the weights for sampling. If -thin-columns is
specified, the polyhedron uses the edge midpoints and triangle centroids, so that
neighboring vertices do not have overlapping polyhedra. This may require
increasing -voxel-subdiv to get enough samples in each voxel to reliably land
inside these smaller polyhedra. The volume ROI is useful to exclude partial volume
effects of voxels the surfaces pass through, and will cause the mapping to ignore
voxels that don't have a positive value in the mask. The subdivision number
specifies how it approximates the amount of the volume the polyhedron intersects,
by splitting each voxel into NxNxN pieces, and checking whether the center of each
piece is inside the polyhedron. If you have very large voxels, consider increasing
this if you get zeros in your output. The -gaussian option makes it act more like
the myelin method, where the distance of a voxel from <surface> is used to
downweight the voxel.
The myelin style method uses part of the caret5 myelin mapping command to do the
mapping: for each surface vertex, take all voxels that are in a cylinder with
radius and height equal to cortical thickness, centered on the vertex and aligned
with the surface normal, and that are also within the ribbon ROI, and apply a
gaussian kernel with the specified sigma to them to get the weights to use. The
-legacy-bug flag reverts to the unintended behavior present from the initial
implementation up to and including v1.2.3, which had only the tangential cutoff and
a bounding box intended to be larger than where the cylinder cutoff should have
been.
-volume-vector-operation DO A VECTOR OPERATION ON VOLUME FILES
wb_command -volume-vector-operation
<vectors-a> - first vector input file <vectors-b> - second vector input file
<operation> - what vector operation to do <volume-out> - output - the output file
[-normalize-a] - normalize vectors of first input
[-normalize-b] - normalize vectors of second input
[-normalize-output] - normalize output vectors (not valid for dot
product)
[-magnitude] - output the magnitude of the result (not valid for dot
product)
Does a vector operation on two volume files (that must have a multiple of 3
subvolumes). Either of the inputs may have multiple vectors (more than 3
subvolumes), but not both (at least one must have exactly 3 subvolumes). The
-magnitude and -normalize-output options may not be specified together, or with the
DOT operation. The <operation> parameter must be one of the following:
DOT CROSS ADD SUBTRACT
-volume-warpfield-affine-regression REGRESS AFFINE FROM WARPFIELD
wb_command -volume-warpfield-affine-regression
<warpfield> - the input warpfield <affine-out> - output - the output affine file
[-roi] - only consider voxels within a mask (e.g., a brain mask)
<roi-vol> - the mask volume
[-fnirt] - input is a fnirt warpfield
<source-volume> - the source volume used when generating the fnirt
warpfield
[-flirt-out] - write output as a flirt matrix rather than a world
coordinate transform <source-volume> - the volume you want to apply the transform
to <target-volume> - the target space you want the transformed volume to
match
For all voxels in the warpfield, do a regression that predicts the post-warp
coordinate from the source coordinate. When -roi is specified, only consider
voxels with a value greater than 0 in <roi-vol>.
The default is to expect the warpfield to be in relative world coordinates (mm
space), and to write the output as a world affine (mm space to mm space). If you
are using FSL-created files and utilities, specify -fnirt and -flirt as needed, as
their coordinate conventions are different.
-volume-warpfield-resample RESAMPLE VOLUME USING WARPFIELD
wb_command -volume-warpfield-resample
<volume-in> - volume to resample <warpfield> - the warpfield to apply
<volume-space> - a volume file in the volume space you want for the
output
<method> - the resampling method <volume-out> - output - the output volume
[-fnirt] - MUST be used if using a fnirt warpfield
<source-volume> - the source volume used when generating the warpfield
Resample a volume file with a warpfield.
The recommended methods are
CUBIC (cubic spline) for most data, and ENCLOSING_VOXEL for label data. The
parameter <method> must be one of:
CUBIC ENCLOSING_VOXEL TRILINEAR
-volume-weighted-stats WEIGHTED SPATIAL STATISTICS ON A VOLUME FILE
wb_command -volume-weighted-stats
<volume-in> - the input volume
[-weight-volume] - use weights from a volume file
<weight-volume> - volume file containing the weights
[-match-maps] - each subvolume of input uses the corresponding
subvolume from the weights file
[-subvolume] - only display output for one subvolume
<subvolume> - the subvolume number or name
[-roi] - only consider data inside an roi
<roi-volume> - the roi, as a volume file
[-match-maps] - each subvolume of input uses the corresponding
subvolume from the roi file
[-mean] - compute weighted mean
[-stdev] - compute weighted standard deviation
[-sample] - estimate population stdev from the sample
[-percentile] - compute weighted percentile
<percent> - the percentile to find
[-sum] - compute weighted sum
[-show-map-name] - print map index and name before each output
For each subvolume of the input, a single number is printed, resulting from the
specified operation. If -weight-volume is not specified, each voxel's volume is
used. Use -subvolume to only give output for a single subvolume. Use -roi to
consider only the data within a region. Exactly one of -mean, -stdev, -percentile
or -sum must be specified.
Using -sum without -weight-volume is equivalent to integrating with respect to
volume.
-wbsparse-merge-dense MERGE WBSPARSE FILES ALONG DENSE DIMENSION
wb_command -wbsparse-merge-dense
<direction> - which dimension to merge along, ROW or COLUMN <wbsparse-out> - output
- the output wbsparse file
[-wbsparse] - repeatable - specify an input wbsparse file
<wbsparse-in> - a wbsparse file to merge
The input wbsparse files must have matching mappings along the direction not
specified, and the mapping along the specified direction must be brain models.
-zip-scene-file ZIP A SCENE FILE AND ITS DATA FILES
wb_command -zip-scene-file
<scene-file> - the scene file to make the zip file from <extract-folder> - the name
of the folder created when the zip file is
unzipped
<zip-file> - out - the zip file that will be created
[-base-dir] - specify a directory that all data files are somewhere
within, this will become the root of the zipfile's directory structure <directory>
- the directory
[-skip-missing] - any missing files will generate only warnings, and the
zip file will be created anyway
If zip-file already exists, it will be overwritten.
If -base-dir is not
specified, the base directory will be automatically set to the lowest level
directory containing all files. The scene file must contain only relative paths,
and no data files may be outside the base directory.
-zip-spec-file ZIP A SPEC FILE AND ITS DATA FILES
wb_command -zip-spec-file
<spec-file> - the specification file to add to zip file <extract-folder> - the name
of the folder created when the zip file is
unzipped
<zip-file> - out - the zip file that will be created
[-base-dir] - specify a directory that all data files are somewhere
within, this will become the root of the zipfile's directory structure <directory>
- the directory
[-skip-missing] - any missing files will generate only warnings, and the
zip file will be created anyway
If zip-file already exists, it will be overwritten.
If -base-dir is not
specified, the directory containing the spec file is used for the base directory.
The spec file must contain only relative paths, and no data files may be outside
the base directory. Scene files inside spec files are not checked for what files
they reference, ensure that all data files referenced by the scene files are also
referenced by the spec file.