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

-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, 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

[-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

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 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

[-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

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). 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 ('' will work on linux/mac) for <label-list-file>, which will be treated as if it is an empty file. It is assumed that a value of 0 in the input file means "unlabeled", unless -unlabeled-value is specified. Do not specify the "unlabeled" label in the text 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. 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-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 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

[-include-empty] - create parcels for labels that have no vertices or

voxels

[-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

Each non-empty label (other than the unlabeled key) in the cifti label file will be treated as a parcel, and all rows or columns within the parcel are averaged together to form the output row or column. If -include-empty is specified, empty labels will be treated as parcels with no elements, and filled with a constant value. 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 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, SUM, STDEV, SAMPSTDEV, VARIANCE, MEDIAN, or MODE.

-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 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 2)

[-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 2)

[-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

[-exponent] - specify exponent in weighting function

<exponent> - exponent 'n' to use in (1 / (distance ^ n)) as the

weighting function (default 2)

[-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

[-exponent] - specify exponent in weighting function

<exponent> - exponent 'n' to use in (area / (distance ^ n)) as

the weighting function (default 2)

[-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.

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 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-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, it will change the keys 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 2)

[-corrected-areas] - vertex areas to use instead of computing them from

the surface <area-metric> - the corrected vertex areas, as a metric

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 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, only vertices with a positive value in the ROI 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.

-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). 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 new gifti label file from a metric file with label-like values. You may specify the empty string ('' will work on linux/mac) for <label-list-file>, which will be treated as if it is an empty file. The label list file must have lines of the following format:

<labelname> <value> <red> <green> <blue> <alpha>

Do not specify the "unlabeled" key in the file, it is assumed that 0 means not labeled unless -unlabeled-value is specified. Label names must be on a separate line, but may contain spaces or other unusual characters (but not newline). Whitespace is trimmed from both ends of the label name, but is kept if it is in the middle of a 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 opaque, which is probably what you want). By default, it will set new label names with names of LABEL_# for any values encountered that are not mentioned in the list file, specify -discard-others to instead set these voxels 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 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 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 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) <image-height> - height of output image(s)

[-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

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 DEFORM A SPHERE ACCORDING TO A REGISTRATION

wb_command -surface-sphere-project-unproject

<sphere-in> - the 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 output space <sphere-out> - output - the output sphere

Each vertex of <sphere-in> is projected to <sphere-project-to> to obtain barycentric weights, which are then used to unproject from <sphere-unproject-from>. This results in a sphere with the topology of <sphere-in>, but coordinates shifted by the deformation between <sphere-project-to> and <sphere-unproject-from>. <sphere-project-to> and <sphere-unproject-from> must have the same topology as each other, but <sphere-in> may have different 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.

-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 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

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 2)

[-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

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.

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

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). 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 new 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 ('' will work on linux/mac) for <label-list-file>, which will be treated as if it is an empty file. The label list file must have pairs of lines of the following format:

<labelname> <value> <red> <green> <blue> <alpha>

Do not specify the "unlabeled" key in the file, it is assumed that 0 means not labeled unless -unlabeled-value is specified. Label names must be on a separate line, but may contain spaces or other unusual characters (but not newline). Whitespace is trimmed from both ends of the label name, but is kept if it is in the middle of a 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 opaque, which is probably what you want). By default, it will set new label names with names of LABEL_# for any values encountered that are not mentioned in the list file, specify -discard-others to instead set these voxels to the "unlabeled" key.

-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 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 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 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

[-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

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

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.