.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH WB_COMMAND "1" "October 2014" "wb_command 1.0" "User Commands"
.SH NAME
wb_command \- command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data
.SH SYNOPSIS
.B <class-name>

.SH DESCRIPTION
\fB\-add\-to\-spec\-file\fR
ADD A FILE TO A SPECIFICATION FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-add\-to\-spec\-file\fR
.IP
<specfile>
<structure>
<filename>
.TP
The resulting spec file overwrites the existing spec file.
If the spec
.TP
file doesn't exist, it is created with default metadata.
The structure
.IP
argument must be one of the following:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<specfile> \- the specification file to add to
<structure> \- the structure of the data file
<filename> \- the path to the file
.PP
\fB\-backend\-average\-dense\-roi\fR
CONNECTOME DB BACKEND COMMAND FOR CIFTI AVERAGE DENSE ROI
.IP
debian/tmp/usr/bin/wb_command \fB\-backend\-average\-dense\-roi\fR
.IP
<index\-list>
<out\-file>
.IP
This command is probably not the one you are looking for, try
\fB\-cifti\-average\-dense\-roi\fR.  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.
.IP
Descriptions of parameters and options:
.IP
<index\-list> \- comma separated list of cifti indexes to average
<out\-file> \- file to write the average row to
.PP
\fB\-backend\-average\-roi\-correlation\fR
CONNECTOME DB BACKEND COMMAND FOR CIFTI AVERAGE ROI CORRELATION
.IP
debian/tmp/usr/bin/wb_command \fB\-backend\-average\-roi\-correlation\fR
.IP
<index\-list>
<out\-file>
.IP
This command is probably not the one you are looking for, try
\fB\-cifti\-average\-roi\-correlation\fR.  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.
.IP
Descriptions of parameters and options:
.IP
<index\-list> \- comma separated list of cifti indexes to average and then
.IP
correlate
.IP
<out\-file> \- file to write the average row to
.PP
\fB\-border\-export\-color\-table\fR
WRITE BORDER NAMES AND COLORS AS TEXT
.IP
debian/tmp/usr/bin/wb_command \fB\-border\-export\-color\-table\fR
.IP
<border\-file>
<table\-out>
[\-class\-colors]
.IP
Takes the names and colors of each border, and writes it to the same
format as \fB\-metric\-label\-import\fR expects.  By default, the borders are
colored by border name, specify \fB\-class\-colors\fR to color them by class
instead.  The key values start at 1 and follow the order of the borders
in the file.
.IP
Descriptions of parameters and options:
.IP
<border\-file> \- the input border file
<table\-out> \- output \- the output text file
.IP
[\-class\-colors] \- use class colors instead of the name colors
.PP
\fB\-border\-file\-export\-to\-caret5\fR
EXPORT BORDER FILE TO CARET5 FILE FORMAT
.IP
debian/tmp/usr/bin/wb_command \fB\-border\-file\-export\-to\-caret5\fR
.IP
<border\-file>
<output\-file\-prefix>
[\-surface] (repeatable)
.IP
<surface\-in>
.IP
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.
.IP
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.
.IP
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.
.IP
One Caret5 border color file will also be produced by this command.
.IP
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.
.IP
When writing new files, this command will overwrite a file with the same
name.
.IP
Descriptions of parameters and options:
.IP
<border\-file> \- workbench border file
<output\-file\-prefix> \- prefix for name of output caret5
.IP
border/borderproj/bordercolor files
.IP
[\-surface] \- repeatable \- specify an input surface
.IP
<surface\-in> \- a surface file for unprojection of borders
.PP
\fB\-border\-merge\fR
MERGE BORDER FILES INTO A NEW FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-border\-merge\fR
.IP
<border\-file\-out>
[\-border] (repeatable)
.IP
<border\-file\-in>
[\-select] (repeatable)
.IP
<border>
[\-up\-to]
.IP
<last\-border>
[\-reverse]
.IP
Takes one or more border files and makes a new border file from the
borders in them.
.IP
Example: wb_command \fB\-border\-merge\fR out.border \fB\-border\fR first.border \fB\-select\fR
1 \fB\-border\fR second.border
.IP
This example would take the first border from first.border, followed by
all borders from second.border, and write these to out.border.
.IP
Descriptions of parameters and options:
.IP
<border\-file\-out> \- output \- the output border file
.IP
[\-border] \- repeatable \- specify an input border file
.IP
<border\-file\-in> \- a border file to use borders from
.IP
[\-select] \- repeatable \- select a single border to use
.IP
<border> \- the border number or name
.IP
[\-up\-to] \- use an inclusive range of borders
.IP
<last\-border> \- the number or name of the last column to include
.IP
[\-reverse] \- use the range in reverse order
.PP
\fB\-border\-resample\fR
RESAMPLE A BORDER FILE TO A DIFFERENT MESH
.IP
debian/tmp/usr/bin/wb_command \fB\-border\-resample\fR
.IP
<border\-in>
<current\-sphere>
<new\-sphere>
<border\-out>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<border\-in> \- the border file to resample
<current\-sphere> \- a sphere surface with the mesh that the metric is
.IP
currently on
.IP
<new\-sphere> \- a sphere surface that is in register with <current\-sphere>
.IP
and has the desired output mesh
.IP
<border\-out> \- output \- the output border file
.PP
\fB\-border\-to\-rois\fR
MAKE METRIC ROIS FROM BORDERS
.IP
debian/tmp/usr/bin/wb_command \fB\-border\-to\-rois\fR
.IP
<surface>
<border\-file>
<metric\-out>
[\-border]
.IP
<name>
.IP
[\-inverse]
.IP
By default, draws ROIs inside all borders in the border file, as separate
metric columns.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface the borders are drawn on
<border\-file> \- the border file
<metric\-out> \- output \- the output metric file
.IP
[\-border] \- create ROI for only one border
.IP
<name> \- the name of the border
.IP
[\-inverse] \- use inverse selection (outside border)
.PP
\fB\-border\-to\-vertices\fR
DRAW BORDERS AS VERTICES IN A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-border\-to\-vertices\fR
.IP
<surface>
<border\-file>
<metric\-out>
[\-border]
.IP
<name>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface the borders are drawn on
<border\-file> \- the border file
<metric\-out> \- output \- the output metric file
.IP
[\-border] \- create ROI for only one border
.IP
<name> \- the name of the border
.PP
\fB\-cifti\-all\-labels\-to\-rois\fR
MAKE ROIS FROM ALL LABELS IN A CIFTI LABEL MAP
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-all\-labels\-to\-rois\fR
.IP
<label\-in>
<map>
<cifti\-out>
.IP
The output cifti file has a column for each label in the specified input
map, other than the ??? label, each of which contains an ROI of all
brainordinates that are set to the corresponding label.
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-cifti\-average\fR
AVERAGE CIFTI FILES
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-average\fR
.IP
<cifti\-out>
[\-exclude\-outliers]
.IP
<sigma\-below>
<sigma\-above>
.IP
[\-cifti] (repeatable)
.IP
<cifti\-in>
[\-weight]
.IP
<weight>
.TP
Averages cifti files together.
Files without \fB\-weight\fR specified are given
.TP
a weight of 1.
If \fB\-exclude\-outliers\fR is specified, at each element, the
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<cifti\-out> \- output \- output cifti file
.IP
[\-exclude\-outliers] \- exclude outliers by standard deviation of each
.IP
element across files
<sigma\-below> \- number of standard deviations below the mean to
.IP
include
.IP
<sigma\-above> \- number of standard deviations above the mean to
.IP
include
.IP
[\-cifti] \- repeatable \- specify an input file
.IP
<cifti\-in> \- the input cifti file
.IP
[\-weight] \- give a weight for this file
.IP
<weight> \- the weight to use
.PP
\fB\-cifti\-average\-dense\-roi\fR
AVERAGE CIFTI ROWS ACROSS SUBJECTS BY ROI
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-average\-dense\-roi\fR
.IP
<cifti\-out>
[\-cifti\-roi]
.IP
<roi\-cifti>
[\-in\-memory]
.IP
[\-left\-roi]
.IP
<roi\-metric>
.IP
[\-right\-roi]
.IP
<roi\-metric>
.IP
[\-cerebellum\-roi]
.IP
<roi\-metric>
.IP
[\-vol\-roi]
.IP
<roi\-vol>
.IP
[\-left\-area\-surf]
.IP
<left\-surf>
.IP
[\-right\-area\-surf]
.IP
<right\-surf>
.IP
[\-cerebellum\-area\-surf]
.IP
<cerebellum\-surf>
.IP
[\-cifti] (repeatable)
.IP
<cifti\-in>
.TP
Averages rows for each map of the ROI(s), across all files.
ROIs are
.TP
always treated as weighting functions, including negative values.
For
.IP
efficiency, ensure that everything that is not intended to be used is
zero in the ROI map.  If \fB\-cifti\-roi\fR is specified, \fB\-left\-roi\fR, \fB\-right\-roi\fR,
\fB\-cerebellum\-roi\fR, and \fB\-vol\-roi\fR must not be specified.  If multiple
non\-cifti ROI files are specified, they must have the same number of
columns.
.IP
Descriptions of parameters and options:
.IP
<cifti\-out> \- output \- output cifti dscalar file
.IP
[\-cifti\-roi] \- cifti file containing combined weights
.IP
<roi\-cifti> \- the roi cifti file
.IP
[\-in\-memory] \- cache the roi in memory so that it isn't re\-read for
.IP
each input cifti
.IP
[\-left\-roi] \- weights to use for left hempsphere
.IP
<roi\-metric> \- the left roi as a metric file
.IP
[\-right\-roi] \- weights to use for right hempsphere
.IP
<roi\-metric> \- the right roi as a metric file
.IP
[\-cerebellum\-roi] \- weights to use for cerebellum surface
.IP
<roi\-metric> \- the cerebellum roi as a metric file
.IP
[\-vol\-roi] \- voxel weights to use
.IP
<roi\-vol> \- the roi volume file
.IP
[\-left\-area\-surf] \- specify the left surface for vertex area correction
.IP
<left\-surf> \- the left surface file
.IP
[\-right\-area\-surf] \- specify the right surface for vertex area correction
.IP
<right\-surf> \- the right surface file
.IP
[\-cerebellum\-area\-surf] \- specify the cerebellum surface for vertex area
.IP
correction
<cerebellum\-surf> \- the cerebellum surface file
.IP
[\-cifti] \- repeatable \- specify an input cifti file
.IP
<cifti\-in> \- a cifti file to average across
.PP
\fB\-cifti\-average\-roi\-correlation\fR
CORRELATE ROI AVERAGE WITH ALL ROWS THEN AVERAGE ACROSS SUBJECTS
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-average\-roi\-correlation\fR
.IP
<cifti\-out>
[\-cifti\-roi]
.IP
<roi\-cifti>
[\-in\-memory]
.IP
[\-left\-roi]
.IP
<roi\-metric>
.IP
[\-right\-roi]
.IP
<roi\-metric>
.IP
[\-cerebellum\-roi]
.IP
<roi\-metric>
.IP
[\-vol\-roi]
.IP
<roi\-vol>
.IP
[\-left\-area\-surf]
.IP
<left\-surf>
.IP
[\-right\-area\-surf]
.IP
<right\-surf>
.IP
[\-cerebellum\-area\-surf]
.IP
<cerebellum\-surf>
.IP
[\-cifti] (repeatable)
.IP
<cifti\-in>
.IP
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
\fB\-cifti\-roi\fR is specified, \fB\-left\-roi\fR, \fB\-right\-roi\fR, \fB\-cerebellum\-roi\fR, and
\fB\-vol\-roi\fR must not be specified.  If multiple non\-cifti ROI files are
specified, they must have the same number of columns.
.IP
Descriptions of parameters and options:
.IP
<cifti\-out> \- output \- output cifti file
.IP
[\-cifti\-roi] \- cifti file containing combined weights
.IP
<roi\-cifti> \- the roi cifti file
.IP
[\-in\-memory] \- cache the roi in memory so that it isn't re\-read for
.IP
each input cifti
.IP
[\-left\-roi] \- weights to use for left hempsphere
.IP
<roi\-metric> \- the left roi as a metric file
.IP
[\-right\-roi] \- weights to use for right hempsphere
.IP
<roi\-metric> \- the right roi as a metric file
.IP
[\-cerebellum\-roi] \- weights to use for cerebellum surface
.IP
<roi\-metric> \- the cerebellum roi as a metric file
.IP
[\-vol\-roi] \- voxel weights to use
.IP
<roi\-vol> \- the roi volume file
.IP
[\-left\-area\-surf] \- specify the left surface for vertex area correction
.IP
<left\-surf> \- the left surface file
.IP
[\-right\-area\-surf] \- specify the right surface for vertex area correction
.IP
<right\-surf> \- the right surface file
.IP
[\-cerebellum\-area\-surf] \- specify the cerebellum surface for vertex area
.IP
correction
<cerebellum\-surf> \- the cerebellum surface file
.IP
[\-cifti] \- repeatable \- specify an input cifti file
.IP
<cifti\-in> \- a cifti file to average across
.PP
\fB\-cifti\-change\-timestep\fR
CHANGE THE TIMESTEP OF A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-change\-timestep\fR
.IP
<cifti>
[\-row\-timestep]
.IP
<seconds>
.IP
[\-column\-timestep]
.IP
<seconds>
.IP
Warns if a dimension specified is not timepoints, otherwise modifies the
timestep, and finally writes the result to the same filename if any
dimensions were modified.
NOTE: you probably want \fB\-row\-timestep\fR, as that matches the .dtseries.nii
specification.  The other option is available just for completeness.
.IP
Descriptions of parameters and options:
.IP
<cifti> \- the cifti file to modify
.IP
[\-row\-timestep] \- set the timestep along rows
.IP
<seconds> \- seconds per timestep
.IP
[\-column\-timestep] \- set the timestep along columns
.IP
<seconds> \- seconds per timestep
.PP
\fB\-cifti\-convert\fR
DUMP CIFTI MATRIX INTO OTHER FORMATS
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-convert\fR
.IP
[\-to\-gifti\-ext]
.IP
<cifti\-in>
<gifti\-out>
.IP
[\-from\-gifti\-ext]
.IP
<gifti\-in>
<cifti\-out>
[\-reset\-timepoints]
.IP
<timestep>
<timestart>
.IP
[\-reset\-scalars]
[\-replace\-binary]
.IP
<binary\-in>
[\-flip\-endian]
[\-transpose]
.IP
[\-to\-nifti]
.IP
<cifti\-in>
<nifti\-out>
.IP
[\-from\-nifti]
.IP
<nifti\-in>
<cifti\-template>
<cifti\-out>
[\-reset\-timepoints]
.IP
<timestep>
<timestart>
.IP
[\-reset\-scalars]
.IP
This command is used to convert a full CIFTI matrix to/from formats that
can be used by programs that don't understand CIFTI.  If you want to
write an existing CIFTI file with a different CIFTI version, see
\fB\-file\-convert\fR, and its \fB\-cifti\-version\-convert\fR option.  If you want part
of the CIFTI file as a metric, label, or volume file, see
\fB\-cifti\-separate\fR.  If you want to create a CIFTI file from metric and/or
volume files, see the \fB\-cifti\-create\-\fR* commands.  You must specify exactly
one of \fB\-to\-gifti\-ext\fR, \fB\-from\-gifti\-ext\fR, \fB\-to\-nifti\fR, or \fB\-from\-nifti\fR.  The
\fB\-transpose\fR option to \fB\-from\-gifti\-ext\fR is needed if the binary file is in
column\-major order.
.IP
Descriptions of parameters and options:
.IP
[\-to\-gifti\-ext] \- convert to GIFTI external binary
.IP
<cifti\-in> \- the input cifti file
<gifti\-out> \- output \- the output gifti file
.IP
[\-from\-gifti\-ext] \- convert a GIFTI made with this command back into a
.IP
CIFTI
<gifti\-in> \- the input gifti file
<cifti\-out> \- output \- the output cifti file
.IP
[\-reset\-timepoints] \- reset the mapping along rows to timepoints,
.IP
taking length from the gifti file
<timestep> \- the desired time between frames
<timestart> \- the desired time offset of the initial frame
.IP
[\-reset\-scalars] \- reset mapping along rows to scalars
.IP
[\-replace\-binary] \- replace data with a binary file
.IP
<binary\-in> \- the binary file that contains replacement data
.IP
[\-flip\-endian] \- byteswap the binary file
.IP
[\-transpose] \- transpose the binary file
.IP
[\-to\-nifti] \- convert to NIFTI1
.IP
<cifti\-in> \- the input cifti file
<nifti\-out> \- output \- the output nifti file
.IP
[\-from\-nifti] \- convert a NIFTI (1 or 2) file made with this command back
.IP
into CIFTI
<nifti\-in> \- the input nifti file
<cifti\-template> \- a cifti file with the dimension(s) and mapping(s)
.IP
that should be used
.IP
<cifti\-out> \- output \- the output cifti file
.IP
[\-reset\-timepoints] \- reset the mapping along rows to timepoints,
.IP
taking length from the nifti file
<timestep> \- the desired time between frames
<timestart> \- the desired time offset of the initial frame
.IP
[\-reset\-scalars] \- reset mapping along rows to scalars
.PP
\fB\-cifti\-convert\-to\-scalar\fR
CHANGE A CIFTI DIMENSION TO NAMED SCALAR MAPS
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-convert\-to\-scalar\fR
.IP
<cifti\-in>
<direction>
<cifti\-out>
[\-name\-file]
.IP
<file>
.IP
Creates a new cifti file with the same data as the input, but with one of
the dimensions set to contain strings identifying each map.  Specifying
ROW means each row will contain one value from each scalar map.  This is
the timepoints direction in dtseries.
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- input cifti file
<direction> \- which mapping to change to scalar maps, ROW or COLUMN
<cifti\-out> \- output \- output cifti file, must not be the same as input
.IP
[\-name\-file] \- specify names for the maps
.IP
<file> \- text file containing map names, one per line
.PP
\fB\-cifti\-correlation\fR
GENERATE CORRELATION OF ROWS IN A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-correlation\fR
.IP
<cifti>
<cifti\-out>
[\-roi\-override]
.IP
[\-left\-roi]
.IP
<roi\-metric>
.IP
[\-right\-roi]
.IP
<roi\-metric>
.IP
[\-cerebellum\-roi]
.IP
<roi\-metric>
.IP
[\-vol\-roi]
.IP
<roi\-vol>
.IP
[\-cifti\-roi]
.IP
<roi\-cifti>
.IP
[\-weights]
.IP
<weight\-file>
.IP
[\-fisher\-z]
[\-mem\-limit]
.IP
<limit\-GB>
.IP
For each row (or each row inside an roi if \fB\-roi\-override\fR is specified),
correlate to all other rows.  The \fB\-cifti\-roi\fR suboption to \fB\-roi\-override\fR
may not be specified with any other \-*\-roi suboption, but you may specify
the other \-*\-roi suboptions together.
.IP
When using the \fB\-fisher\-z\fR option, the output is NOT a Z\-score, it is
artanh(r), to do further math on this output, consider using \fB\-cifti\-math\fR.
.IP
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).
.IP
Descriptions of parameters and options:
.IP
<cifti> \- input cifti file
<cifti\-out> \- output \- output cifti file
.IP
[\-roi\-override] \- perform correlation from a subset of rows to all rows
.IP
[\-left\-roi] \- use an roi for left hempsphere
.IP
<roi\-metric> \- the left roi as a metric file
.IP
[\-right\-roi] \- use an roi for right hempsphere
.IP
<roi\-metric> \- the right roi as a metric file
.IP
[\-cerebellum\-roi] \- use an roi for cerebellum
.IP
<roi\-metric> \- the cerebellum roi as a metric file
.IP
[\-vol\-roi] \- use an roi for volume
.IP
<roi\-vol> \- the volume roi file
.IP
[\-cifti\-roi] \- use a cifti file for combined rois
.IP
<roi\-cifti> \- the cifti roi file
.IP
[\-weights] \- specify column weights
.IP
<weight\-file> \- text file containing one weight per column
.IP
[\-fisher\-z] \- apply fisher small z transform (ie, artanh) to correlation
.IP
[\-mem\-limit] \- restrict memory usage
.IP
<limit\-GB> \- memory limit in gigabytes
.PP
\fB\-cifti\-correlation\-gradient\fR
CORRELATE CIFTI ROWS AND TAKE GRADIENT
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-correlation\-gradient\fR
.IP
<cifti>
<cifti\-out>
[\-left\-surface]
.IP
<surface>
[\-left\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-right\-surface]
.IP
<surface>
[\-right\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-cerebellum\-surface]
.IP
<surface>
[\-cerebellum\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-surface\-presmooth]
.IP
<surface\-kernel>
.IP
[\-volume\-presmooth]
.IP
<volume\-kernel>
.IP
[\-undo\-fisher\-z]
[\-fisher\-z]
[\-surface\-exclude]
.IP
<distance>
.IP
[\-volume\-exclude]
.IP
<distance>
.IP
[\-mem\-limit]
.IP
<limit\-GB>
.IP
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).
.IP
Descriptions of parameters and options:
.IP
<cifti> \- the input cifti
<cifti\-out> \- output \- the output cifti
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-left\-corrected\-areas] \- vertex areas to use instead of computing
.IP
them from the left surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-right\-corrected\-areas] \- vertex areas to use instead of computing
.IP
them from the right surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.IP
[\-cerebellum\-corrected\-areas] \- vertex areas to use instead of
.IP
computing them from the cerebellum surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-surface\-presmooth] \- smooth on the surface before computing the
.IP
gradient
<surface\-kernel> \- the sigma for the gaussian surface smoothing
.IP
kernel, in mm
.IP
[\-volume\-presmooth] \- smooth the volume before computing the gradient
.IP
<volume\-kernel> \- the sigma for the gaussian volume smoothing kernel,
.IP
in mm
.IP
[\-undo\-fisher\-z] \- apply the inverse fisher small z transform to the
.IP
input
.IP
[\-fisher\-z] \- apply the fisher small z transform to the correlations
.IP
before taking the gradient
.IP
[\-surface\-exclude] \- exclude vertices near each seed vertex from
.IP
computation
<distance> \- geodesic distance from seed vertex for the exclusion
.IP
zone, in mm
.IP
[\-volume\-exclude] \- exclude voxels near each seed voxel from computation
.IP
<distance> \- distance from seed voxel for the exclusion zone, in mm
.IP
[\-mem\-limit] \- restrict memory usage
.IP
<limit\-GB> \- memory limit in gigabytes
.PP
\fB\-cifti\-create\-dense\-scalar\fR
CREATE A CIFTI DENSE SCALAR FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-create\-dense\-scalar\fR
.IP
<cifti\-out>
[\-volume]
.IP
<volume\-data>
<label\-volume>
.IP
[\-left\-metric]
.IP
<metric>
[\-roi\-left]
.IP
<roi\-metric>
.IP
[\-right\-metric]
.IP
<metric>
[\-roi\-right]
.IP
<roi\-metric>
.IP
[\-cerebellum\-metric]
.IP
<metric>
[\-roi\-cerebellum]
.IP
<roi\-metric>
.TP
All input files must have the same number of columns/subvolumes.
Only
.TP
the specified components will be in the output cifti.
Map names will be
.TP
taken from one of the input files.
At least one component must be
.TP
specified.
The label volume should have some of the label names from
.IP
this list, all other label names will be ignored:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<cifti\-out> \- output \- the output cifti file
.IP
[\-volume] \- volume component
.IP
<volume\-data> \- volume file containing all voxel data for all volume
.IP
structures
.IP
<label\-volume> \- label volume file containing labels for cifti
.IP
structures
.IP
[\-left\-metric] \- metric for left surface
.IP
<metric> \- the metric file
.IP
[\-roi\-left] \- roi of vertices to use from left surface
.IP
<roi\-metric> \- the ROI as a metric file
.IP
[\-right\-metric] \- metric for left surface
.IP
<metric> \- the metric file
.IP
[\-roi\-right] \- roi of vertices to use from right surface
.IP
<roi\-metric> \- the ROI as a metric file
.IP
[\-cerebellum\-metric] \- metric for the cerebellum
.IP
<metric> \- the metric file
.IP
[\-roi\-cerebellum] \- roi of vertices to use from right surface
.IP
<roi\-metric> \- the ROI as a metric file
.PP
\fB\-cifti\-create\-dense\-timeseries\fR
CREATE A CIFTI DENSE TIMESERIES
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-create\-dense\-timeseries\fR
.IP
<cifti\-out>
[\-volume]
.IP
<volume\-data>
<label\-volume>
.IP
[\-left\-metric]
.IP
<metric>
[\-roi\-left]
.IP
<roi\-metric>
.IP
[\-right\-metric]
.IP
<metric>
[\-roi\-right]
.IP
<roi\-metric>
.IP
[\-cerebellum\-metric]
.IP
<metric>
[\-roi\-cerebellum]
.IP
<roi\-metric>
.IP
[\-timestep]
.IP
<interval>
.IP
[\-timestart]
.IP
<start>
.TP
All input files must have the same number of columns/subvolumes.
Only
.TP
the specified components will be in the output cifti.
At least one
.TP
component must be specified.
The label volume should have some of the
.IP
label names from this list, all other label names will be ignored:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<cifti\-out> \- output \- the output cifti file
.IP
[\-volume] \- volume component
.IP
<volume\-data> \- volume file containing all voxel data for all volume
.IP
structures
.IP
<label\-volume> \- label volume file containing labels for cifti
.IP
structures
.IP
[\-left\-metric] \- metric for left surface
.IP
<metric> \- the metric file
.IP
[\-roi\-left] \- roi of vertices to use from left surface
.IP
<roi\-metric> \- the ROI as a metric file
.IP
[\-right\-metric] \- metric for left surface
.IP
<metric> \- the metric file
.IP
[\-roi\-right] \- roi of vertices to use from right surface
.IP
<roi\-metric> \- the ROI as a metric file
.IP
[\-cerebellum\-metric] \- metric for the cerebellum
.IP
<metric> \- the metric file
.IP
[\-roi\-cerebellum] \- roi of vertices to use from right surface
.IP
<roi\-metric> \- the ROI as a metric file
.IP
[\-timestep] \- set the timestep
.IP
<interval> \- the timestep, in seconds (default 1.0)
.IP
[\-timestart] \- set the start time
.IP
<start> \- the time at the first frame, in seconds (default 0.0)
.PP
\fB\-cifti\-create\-label\fR
CREATE A CIFTI LABEL FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-create\-label\fR
.IP
<cifti\-out>
[\-volume]
.IP
<label\-volume>
<parcel\-volume>
.IP
[\-left\-label]
.IP
<label>
[\-roi\-left]
.IP
<roi\-metric>
.IP
[\-right\-label]
.IP
<label>
[\-roi\-right]
.IP
<roi\-metric>
.IP
[\-cerebellum\-label]
.IP
<label>
[\-roi\-cerebellum]
.IP
<roi\-metric>
.TP
All input files must have the same number of columns/subvolumes.
Only
.TP
the specified components will be in the output cifti.
At least one
.IP
component must be specified.
.IP
The \fB\-volume\fR option of \fB\-cifti\-create\-label\fR requires two volume arguments,
the label\-volume argument contains all labels you want to display (e.g.
nuclei of the thalamus), whereas the parcel\-volume argument includes all
CIFTI structures you want to include data within (e.g. THALAMUS_LEFT,
THALAMUS_RIGHT).  If you just want the labels in voxels to be the
structure names, you may use the same file for both arguments.  The
parcel\-volume must use some of the label names from this list, all other
label names in the parcel\-volume will be ignored:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<cifti\-out> \- output \- the output cifti file
.IP
[\-volume] \- volume component
.IP
<label\-volume> \- volume file containing the label data
<parcel\-volume> \- label volume file with cifti structure names to
.IP
define the volume parcels
.IP
[\-left\-label] \- label file for left surface
.IP
<label> \- the label file
.IP
[\-roi\-left] \- roi of vertices to use from left surface
.IP
<roi\-metric> \- the ROI as a metric file
.IP
[\-right\-label] \- label for left surface
.IP
<label> \- the label file
.IP
[\-roi\-right] \- roi of vertices to use from right surface
.IP
<roi\-metric> \- the ROI as a metric file
.IP
[\-cerebellum\-label] \- label for the cerebellum
.IP
<label> \- the label file
.IP
[\-roi\-cerebellum] \- roi of vertices to use from right surface
.IP
<roi\-metric> \- the ROI as a metric file
.PP
\fB\-cifti\-cross\-correlation\fR
CORRELATE A CIFTI FILE WITH ANOTHER CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-cross\-correlation\fR
.IP
<cifti\-a>
<cifti\-b>
<cifti\-out>
[\-weights]
.IP
<weight\-file>
.IP
[\-fisher\-z]
[\-mem\-limit]
.IP
<limit\-GB>
.TP
Correlates every rown in <cifti\-a> with every row in <cifti\-b>.
The
.IP
mapping along columns in <cifti\-b> becomes the mapping along rows in the
output.
.IP
When using the \fB\-fisher\-z\fR option, the output is NOT a Z\-score, it is
artanh(r), to do further math on this output, consider using \fB\-cifti\-math\fR.
.IP
Restricting the memory usage will make it calculate the output in chunks,
by reading through <cifti\-b> multiple times.
.IP
Descriptions of parameters and options:
.IP
<cifti\-a> \- first input cifti file
<cifti\-b> \- second input cifti file
<cifti\-out> \- output \- output cifti file
.IP
[\-weights] \- specify column weights
.IP
<weight\-file> \- text file containing one weight per column
.IP
[\-fisher\-z] \- apply fisher small z transform (ie, artanh) to correlation
.IP
[\-mem\-limit] \- restrict memory usage
.IP
<limit\-GB> \- memory limit in gigabytes
.PP
\fB\-cifti\-dilate\fR
DILATE A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-dilate\fR
.IP
<cifti\-in>
<direction>
<surface\-distance>
<volume\-distance>
<cifti\-out>
[\-left\-surface]
.IP
<surface>
.IP
[\-right\-surface]
.IP
<surface>
.IP
[\-cerebellum\-surface]
.IP
<surface>
.IP
[\-bad\-brainordinate\-roi]
.IP
<roi\-cifti>
.IP
[\-nearest]
[\-merged\-volume]
.IP
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 \fB\-nearest\fR is specified, it
will use the value from the closest good value within range instead of a
weighted average.
.IP
\&.If \fB\-bad\-brainordinate\-roi\fR 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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.IP
[\-bad\-brainordinate\-roi] \- specify an roi of brainordinates to overwrite,
.IP
rather than zeros
<roi\-cifti> \- cifti dscalar or dtseries file, positive values denote
.IP
brainordinates to have their values replaced
.IP
[\-nearest] \- use nearest value when dilating non\-label data
.IP
[\-merged\-volume] \- treat volume components as if they were a single
.IP
component
.PP
\fB\-cifti\-estimate\-fwhm\fR
ESTIMATE FWHM SMOOTHNESS OF A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-estimate\-fwhm\fR
.IP
<cifti>
[\-merged\-volume]
[\-column]
.IP
<column>
.IP
[\-surface] (repeatable)
.IP
<structure>
<surface>
.IP
Estimate the smoothness of the components of the cifti file, printing the
estimates to standard output.  If \fB\-merged\-volume\fR is used, all voxels are
used as a single component, rather than separated by structure.
.IP
<structure> must be one of the following:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<cifti> \- the input cifti file
.IP
[\-merged\-volume] \- treat volume components as if they were a single
.IP
component
.IP
[\-column] \- only output estimates for one column
.IP
<column> \- the column number
.IP
[\-surface] \- repeatable \- specify an input surface
.IP
<structure> \- what structure to use this surface for
<surface> \- the surface file
.PP
\fB\-cifti\-export\-dense\-mapping\fR
WRITE INDEX TO ELEMENT MAPPING AS TEXT
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-export\-dense\-mapping\fR
.IP
<cifti>
<direction>
[\-volume\-all]
.IP
<text\-out>
[\-no\-cifti\-index]
[\-structure]
.IP
[\-surface] (repeatable)
.IP
<structure>
<text\-out>
[\-no\-cifti\-index]
.IP
[\-volume] (repeatable)
.IP
<structure>
<text\-out>
[\-no\-cifti\-index]
.IP
This command produces text files that describe the mapping from cifti
indices to surface vertices or voxels.  The default format for \fB\-surface\fR
is lines of the form:
.IP
<cifti\-index> <vertex>
.IP
The default format for \fB\-volume\fR and \fB\-volume\-all\fR is lines of the form:
.IP
<cifti\-index> <i> <j> <k>
.IP
Descriptions of parameters and options:
.IP
<cifti> \- the cifti file
<direction> \- which direction to export the mapping from, ROW or COLUMN
.IP
[\-volume\-all] \- export the the mapping of all voxels
.IP
<text\-out> \- output \- the output text file
.IP
[\-no\-cifti\-index] \- don't write the cifti index in the output file
.IP
[\-structure] \- write the structure each voxel belongs to in the output
.IP
file
.IP
[\-surface] \- repeatable \- export the the mapping of one surface structure
.IP
<structure> \- the structure to output
<text\-out> \- output \- the output text file
.IP
[\-no\-cifti\-index] \- don't write the cifti index in the output file
.IP
[\-volume] \- repeatable \- export the the mapping of one volume structure
.IP
<structure> \- the structure to output
<text\-out> \- output \- the output text file
.IP
[\-no\-cifti\-index] \- don't write the cifti index in the output file
.PP
\fB\-cifti\-extrema\fR
FIND EXTREMA IN A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-extrema\fR
.IP
<cifti>
<surface\-distance>
<volume\-distance>
<direction>
<cifti\-out>
[\-left\-surface]
.IP
<surface>
.IP
[\-right\-surface]
.IP
<surface>
.IP
[\-cerebellum\-surface]
.IP
<surface>
.IP
[\-surface\-presmooth]
.IP
<surface\-kernel>
.IP
[\-volume\-presmooth]
.IP
<volume\-kernel>
.IP
[\-threshold]
.IP
<low>
<high>
.IP
[\-merged\-volume]
[\-sum\-maps]
[\-consolidate\-mode]
[\-only\-maxima]
[\-only\-minima]
.IP
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, you probably want ROW.
.IP
Descriptions of parameters and options:
.IP
<cifti> \- the input cifti
<surface\-distance> \- the minimum distance between extrema of the same
.IP
type, for surface components
.IP
<volume\-distance> \- the minimum distance between extrema of the same
.IP
type, for volume components
.IP
<direction> \- which dimension to find extrema along, ROW or COLUMN
<cifti\-out> \- output \- the output cifti
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.IP
[\-surface\-presmooth] \- smooth on the surface before finding extrema
.IP
<surface\-kernel> \- the sigma for the gaussian surface smoothing
.IP
kernel, in mm
.IP
[\-volume\-presmooth] \- smooth volume components before finding extrema
.IP
<volume\-kernel> \- the sigma for the gaussian volume smoothing kernel,
.IP
in mm
.IP
[\-threshold] \- ignore small extrema
.IP
<low> \- the largest value to consider for being a minimum
<high> \- the smallest value to consider for being a maximum
.IP
[\-merged\-volume] \- treat volume components as if they were a single
.IP
component
.IP
[\-sum\-maps] \- output the sum of the extrema maps instead of each map
.IP
separately
.IP
[\-consolidate\-mode] \- use consolidation of local minima instead of a
.IP
large neighborhood
.IP
[\-only\-maxima] \- only find the maxima
.IP
[\-only\-minima] \- only find the minima
.PP
\fB\-cifti\-false\-correlation\fR
COMPARE CORRELATION LOCALLY AND ACROSS/THROUGH SULCI/GYRI
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-false\-correlation\fR
.IP
<cifti\-in>
<3D\-dist>
<geo\-outer>
<geo\-inner>
<cifti\-out>
[\-left\-surface]
.IP
<surface>
[\-dump\-text]
.IP
<text\-out>
.IP
[\-right\-surface]
.IP
<surface>
[\-dump\-text]
.IP
<text\-out>
.IP
[\-cerebellum\-surface]
.IP
<surface>
[\-dump\-text]
.IP
<text\-out>
.TP
This is where you set the help text.
DO NOT add the info about what the
.IP
command line format is, and do not give the command switch, short
description, or the short descriptions of parameters.  Do not indent, add
newlines, or format the text in any way other than to separate paragraphs
within the help text prose.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
correlation
.IP
<geo\-inner> \- minimum geodesic distance to use for neighboring
.IP
correlation
.IP
<cifti\-out> \- output \- the output cifti dscalar file
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-dump\-text] \- dump the raw measures used to a text file
.IP
<text\-out> \- the output text file
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-dump\-text] \- dump the raw measures used to a text file
.IP
<text\-out> \- the output text file
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.IP
[\-dump\-text] \- dump the raw measures used to a text file
.IP
<text\-out> \- the output text file
.PP
\fB\-cifti\-find\-clusters\fR
FILTER CLUSTERS BY AREA/VOLUME
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-find\-clusters\fR
.IP
<cifti>
<surface\-value\-threshold>
<surface\-minimum\-area>
<volume\-value\-threshold>
<volume\-minimum\-size>
<direction>
<cifti\-out>
[\-less\-than]
[\-left\-surface]
.IP
<surface>
[\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-right\-surface]
.IP
<surface>
[\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-cerebellum\-surface]
.IP
<surface>
[\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-cifti\-roi]
.IP
<roi\-cifti>
.IP
[\-merged\-volume]
[\-start]
.IP
<startval>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
COLUMN
.IP
<cifti\-out> \- output \- the output cifti
.IP
[\-less\-than] \- find values less than <value\-threshold>, rather than
.IP
greater
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-corrected\-areas] \- vertex areas to use instead of computing them
.IP
from the surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-corrected\-areas] \- vertex areas to use instead of computing them
.IP
from the surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.IP
[\-corrected\-areas] \- vertex areas to use instead of computing them
.IP
from the surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-cifti\-roi] \- search only within regions of interest
.IP
<roi\-cifti> \- the regions to search within, as a cifti file
.IP
[\-merged\-volume] \- treat volume components as if they were a single
.IP
component
.IP
[\-start] \- start labeling clusters from a value other than 1
.IP
<startval> \- the value to give the first cluster found
.PP
\fB\-cifti\-gradient\fR
TAKE GRADIENT OF A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-gradient\fR
.IP
<cifti>
<direction>
<cifti\-out>
[\-left\-surface]
.IP
<surface>
.IP
[\-right\-surface]
.IP
<surface>
.IP
[\-cerebellum\-surface]
.IP
<surface>
.IP
[\-surface\-presmooth]
.IP
<surface\-kernel>
.IP
[\-volume\-presmooth]
.IP
<volume\-kernel>
.IP
[\-average\-output]
.IP
Performs gradient calculation on each component of the cifti file, and
optionally averages the resulting gradients.  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 \fB\-average\-output\fR.
.IP
Descriptions of parameters and options:
.IP
<cifti> \- the input cifti
<direction> \- which dimension to take the gradient along, ROW or COLUMN
<cifti\-out> \- output \- the output cifti
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.IP
[\-surface\-presmooth] \- smooth on the surface before computing the
.IP
gradient
<surface\-kernel> \- the sigma for the gaussian surface smoothing
.IP
kernel, in mm
.IP
[\-volume\-presmooth] \- smooth on the surface before computing the gradient
.IP
<volume\-kernel> \- the sigma for the gaussian volume smoothing kernel,
.IP
in mm
.IP
[\-average\-output] \- output the average of the gradient magnitude maps
.IP
instead of each gradient map separately
.PP
\fB\-cifti\-label\-adjacency\fR
MAKE ADJACENCY MATRIX OF A CIFTI LABEL FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-label\-adjacency\fR
.IP
<label\-in>
<adjacency\-out>
[\-left\-surface]
.IP
<surface>
.IP
[\-right\-surface]
.IP
<surface>
.IP
[\-cerebellum\-surface]
.IP
<surface>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<label\-in> \- the input cifti label file
<adjacency\-out> \- output \- the output cifti pconn adjacency matrix
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.PP
\fB\-cifti\-label\-export\-table\fR
EXPORT LABEL TABLE FROM CIFTI AS TEXT
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-label\-export\-table\fR
.IP
<label\-in>
<map>
<table\-out>
.IP
Takes the label table from the cifti label map, and writes it to a text
format matching what is expected by \fB\-cifti\-label\-import\fR.
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-cifti\-label\-import\fR
MAKE A CIFTI LABEL FILE FROM A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-label\-import\fR
.IP
<input>
<label\-list\-file>
<output>
[\-discard\-others]
[\-unlabeled\-value]
.IP
<value>
.IP
[\-drop\-unused\-labels]
.TP
Creates a cifti label file from a cifti file with label\-like values.
You
.IP
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:
.IP
<labelname>
<value> <red> <green> <blue> <alpha>
.IP
Do not specify the "unlabeled" key in the file, it is assumed that 0
means not labeled unless \fB\-unlabeled\-value\fR 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 \fB\-discard\-others\fR to instead set these to the
"unlabeled" key.
.IP
Descriptions of parameters and options:
.IP
<input> \- the input cifti file
<label\-list\-file> \- text file containing the values and names for labels
<output> \- output \- the output cifti label file
.IP
[\-discard\-others] \- set any values not mentioned in the label list to the
.IP
??? label
.IP
[\-unlabeled\-value] \- set the value that will be interpreted as unlabeled
.IP
<value> \- the numeric value for unlabeled (default 0)
.IP
[\-drop\-unused\-labels] \- remove any unused label values from the label
.IP
table
.PP
\fB\-cifti\-label\-to\-roi\fR
MAKE A CIFTI LABEL INTO AN ROI
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-label\-to\-roi\fR
.IP
<label\-in>
<scalar\-out>
[\-name]
.IP
<label\-name>
.IP
[\-key]
.IP
<label\-key>
.IP
[\-map]
.IP
<map>
.IP
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
\fB\-name\fR and \fB\-key\fR must be specified.  Specify \fB\-map\fR to use only one map from
<label\-in>.
.IP
Descriptions of parameters and options:
.IP
<label\-in> \- the input cifti label file
<scalar\-out> \- output \- the output cifti scalar file
.IP
[\-name] \- select label by name
.IP
<label\-name> \- the label name that you want an roi of
.IP
[\-key] \- select label by key
.IP
<label\-key> \- the label key that you want an roi of
.IP
[\-map] \- select a single label map to use
.IP
<map> \- the map number or name
.PP
\fB\-cifti\-math\fR
EVALUATE EXPRESSION ON CIFTI FILES
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-math\fR
.IP
<expression>
<cifti\-out>
[\-fixnan]
.IP
<replace>
.IP
[\-override\-mapping\-check]
[\-var] (repeatable)
.IP
<name>
<cifti>
[\-select] (repeatable)
.IP
<dim>
<index>
[\-repeat]
.IP
This command evaluates <expression> at each (row, column) location
independently.  There must be at least one \fB\-var\fR option (to get the output
layout from), even if the <name> specified in it isn't used in
<expression>.
.IP
To select a single column from a 2D file (most cifti files are 2D), use
\fB\-select\fR 1 <index>, where <index> is 1\-based.  To select a single row from
a 2D file, use \fB\-select\fR 2 <index>.  Where \fB\-select\fR 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
\fB\-override\-mapping\-check\fR to skip this checking.
.IP
Filenames are not valid in <expression>, use a variable name and a \fB\-var\fR
option with matching <name> to specify an input file.  The format of
<expression> is as follows:
.IP
Expressions consist of constants, variables, operators, parentheses, and
functions, in infix notation, such as 'exp(\fB\-x\fR + 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 the rest.  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.
.IP
Comparison operators return 0 or 1, you can do masking with expressions
like 'x * (mask > 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 '(x > 0) * (x < 5)' to
get the desired behavior.
.IP
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, use '2 *
x'.  Parentheses are (), do not use [] or {}.  Functions require
parentheses, the expression 'sin x' is an error.
.IP
The following functions are supported:
.IP
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
.IP
(y/x), in radians, determining quadrant by the sign of both arguments
.IP
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 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
.IP
zero
.IP
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)
.IP
Descriptions of parameters and options:
.IP
<expression> \- the expression to evaluate, in quotes
<cifti\-out> \- output \- the output cifti file
.IP
[\-fixnan] \- replace NaN results with a value
.IP
<replace> \- value to replace NaN with
.IP
[\-override\-mapping\-check] \- don't check the mappings for compatibility,
.IP
only check length
.IP
[\-var] \- repeatable \- a cifti file to use as a variable
.IP
<name> \- the name of the variable, as used in the expression
<cifti> \- the cifti file to use as this variable
.IP
[\-select] \- repeatable \- select a single index from a dimension
.IP
<dim> \- the dimension to select from (1\-based)
<index> \- the index to use (1\-based)
.IP
[\-repeat] \- repeat the selected values for each index of output in
.IP
this dimension
.PP
\fB\-cifti\-merge\fR
MERGE CIFTI TIMESERIES, SCALAR, OR LABEL FILES
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-merge\fR
.IP
<cifti\-out>
[\-cifti] (repeatable)
.IP
<cifti\-in>
[\-column] (repeatable)
.IP
<column>
[\-up\-to]
.IP
<last\-column>
[\-reverse]
.IP
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).
.IP
Example: wb_command \fB\-cifti\-merge\fR out.dtseries.nii \fB\-cifti\fR
first.dtseries.nii \fB\-column\fR 1 \fB\-cifti\fR second.dtseries.nii
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<cifti\-out> \- output \- output cifti file
.IP
[\-cifti] \- repeatable \- specify an input cifti file
.IP
<cifti\-in> \- a cifti file to use columns from
.IP
[\-column] \- repeatable \- select a single column to use
.IP
<column> \- the column index (starting from 1)
.IP
[\-up\-to] \- use an inclusive range of columns
.IP
<last\-column> \- the index of the last column to include
.IP
[\-reverse] \- use the range in reverse order
.PP
\fB\-cifti\-merge\-dense\fR
MERGE CIFTI FILES ALONG DENSE DIMENSION
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-merge\-dense\fR
.IP
<direction>
<cifti\-out>
[\-cifti] (repeatable)
.IP
<cifti\-in>
.IP
The input cifti files must have matching mappings along the direction not
specified, and the mapping along the specified direction must be brain
models.
.IP
Descriptions of parameters and options:
.IP
<direction> \- which dimension to merge along, ROW or COLUMN
<cifti\-out> \- output \- the output cifti file
.IP
[\-cifti] \- repeatable \- specify an input cifti file
.IP
<cifti\-in> \- a cifti file to merge
.PP
\fB\-cifti\-pairwise\-correlation\fR
CORRELATE PAIRED ROWS BETWEEN TWO CIFTI FILES
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-pairwise\-correlation\fR
.IP
<cifti\-a>
<cifti\-b>
<cifti\-out>
[\-fisher\-z]
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<cifti\-a> \- first input cifti file
<cifti\-b> \- second input cifti file
<cifti\-out> \- output \- output cifti file
.IP
[\-fisher\-z] \- apply fisher small z transform (ie, artanh) to correlation
.PP
\fB\-cifti\-palette\fR
SET PALETTE ON A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-palette\fR
.IP
<cifti\-in>
<mode>
<cifti\-out>
[\-column]
.IP
<column>
.IP
[\-pos\-percent]
.IP
<pos\-min\-%>
<pos\-max\-%>
.IP
[\-neg\-percent]
.IP
<neg\-min\-%>
<neg\-max\-%>
.IP
[\-pos\-user]
.IP
<pos\-min\-user>
<pos\-max\-user>
.IP
[\-neg\-user]
.IP
<neg\-min\-user>
<neg\-max\-user>
.IP
[\-interpolate]
.IP
<interpolate>
.IP
[\-disp\-pos]
.IP
<display>
.IP
[\-disp\-neg]
.IP
<display>
.IP
[\-disp\-zero]
.IP
<display>
.IP
[\-palette\-name]
.IP
<name>
.IP
[\-thresholding]
.IP
<type>
<test>
<min>
<max>
.IP
NOTE: The output file must be a different file than the input file.
.IP
For scalar maps, by default the palette is changed for every map, specify
\fB\-column\fR 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:
.IP
MODE_AUTO_SCALE
MODE_AUTO_SCALE_PERCENTAGE
MODE_USER_SCALE
.IP
The <name> argument to \fB\-palette\-name\fR must be one of the following:
.IP
PSYCH
PSYCH\-NO\-NONE
ROY\-BIG
ROY\-BIG\-BL
Orange\-Yellow
Gray_Interp_Positive
Gray_Interp
clear_brain
videen_style
fidl
raich4_clrmid
raich6_clrmid
HSB8_clrmid
RBGYR20
RBGYR20P
POS_NEG
red\-yellow
blue\-lightblue
FSL
power_surf
fsl_red
fsl_green
fsl_blue
fsl_yellow
JET256
.IP
The <type> argument to \fB\-thresholding\fR must be one of the following:
.IP
THRESHOLD_TYPE_OFF
THRESHOLD_TYPE_NORMAL
.IP
The <test> argument to \fB\-thresholding\fR must be one of the following:
.IP
THRESHOLD_TEST_SHOW_OUTSIDE
THRESHOLD_TEST_SHOW_INSIDE
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- the cifti input
<mode> \- the mapping mode
<cifti\-out> \- output \- the output cifti file
.IP
[\-column] \- select a single column for scalar maps
.IP
<column> \- the column number or name
.IP
[\-pos\-percent] \- percentage min/max for positive data coloring
.IP
<pos\-min\-%> \- the percentile for the least positive data
<pos\-max\-%> \- the percentile for the most positive data
.IP
[\-neg\-percent] \- percentage min/max for negative data coloring
.IP
<neg\-min\-%> \- the percentile for the least negative data
<neg\-max\-%> \- the percentile for the most negative data
.IP
[\-pos\-user] \- user min/max values for positive data coloring
.IP
<pos\-min\-user> \- the value for the least positive data
<pos\-max\-user> \- the value for the most positive data
.IP
[\-neg\-user] \- user min/max values for negative data coloring
.IP
<neg\-min\-user> \- the value for the least negative data
<neg\-max\-user> \- the value for the most negative data
.IP
[\-interpolate] \- interpolate colors
.IP
<interpolate> \- boolean, whether to interpolate
.IP
[\-disp\-pos] \- display positive data
.IP
<display> \- boolean, whether to display
.IP
[\-disp\-neg] \- display positive data
.IP
<display> \- boolean, whether to display
.IP
[\-disp\-zero] \- display data closer to zero than the min cutoff
.IP
<display> \- boolean, whether to display
.IP
[\-palette\-name] \- set the palette used
.IP
<name> \- the name of the palette
.IP
[\-thresholding] \- set the thresholding
.IP
<type> \- thresholding setting
<test> \- show values inside or outside thresholds
<min> \- lower threshold
<max> \- upper threshold
.PP
\fB\-cifti\-parcellate\fR
PARCELLATE A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-parcellate\fR
.IP
<cifti\-in>
<cifti\-label>
<direction>
<cifti\-out>
.IP
Each label 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 ROW is specified, then the input mapping along
rows must be brainordinates, and the output mapping along rows will be
parcels, meaning columns will be averaged together.  For dtseries or
dscalar, use COLUMN.
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- the cifti file to parcellate
<cifti\-label> \- a cifti label file to use for the parcellation
<direction> \- which mapping to parcellate, ROW or COLUMN
<cifti\-out> \- output \- output cifti file
.PP
\fB\-cifti\-reduce\fR
PERFORM REDUCTION OPERATION ALONG CIFTI ROWS
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-reduce\fR
.IP
<cifti\-in>
<operation>
<cifti\-out>
[\-exclude\-outliers]
.IP
<sigma\-below>
<sigma\-above>
.IP
For each cifti row, takes the data along a row as a vector, and performs
the specified reduction on it, putting the result into the single output
column in that row.  The reduction operators are as follows:
.IP
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
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
MEDIAN: the median of the data
MODE: the mode of the data
COUNT_NONZERO: the number of nonzero elements in the data
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- the cifti file to reduce
<operation> \- the reduction operator to use
<cifti\-out> \- output \- the output cifti file
.IP
[\-exclude\-outliers] \- exclude outliers from each row by standard
.IP
deviation
<sigma\-below> \- number of standard deviations below the mean to
.IP
include
.IP
<sigma\-above> \- number of standard deviations above the mean to
.IP
include
.PP
\fB\-cifti\-reorder\fR
REORDER THE PARCELS OR SCALAR/LABEL MAPS IN A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-reorder\fR
.IP
<cifti\-in>
<direction>
<reorder\-list>
<cifti\-out>
.IP
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'.
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- input parcellated 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
.PP
\fB\-cifti\-replace\-structure\fR
REPLACE DATA IN A STRUCTURE IN A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-replace\-structure\fR
.IP
<cifti>
<direction>
[\-volume\-all]
.IP
<volume>
[\-from\-cropped]
.IP
[\-label] (repeatable)
.IP
<structure>
<label>
.IP
[\-metric] (repeatable)
.IP
<structure>
<metric>
.IP
[\-volume] (repeatable)
.IP
<structure>
<volume>
[\-from\-cropped]
.IP
You must specify at least one of \fB\-metric\fR, \fB\-label\fR, \fB\-volume\fR, or \fB\-volume\-all\fR
for this command to do anything.  Input volumes must line up with the
output of \fB\-cifti\-separate\fR.  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:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<cifti> \- the cifti to modify
<direction> \- which dimension to interpret as a single map, ROW or COLUMN
.IP
[\-volume\-all] \- replace the data in all volume components
.IP
<volume> \- the input volume
.IP
[\-from\-cropped] \- the input is cropped to the size of the data
.IP
[\-label] \- repeatable \- replace the data in a surface label component
.IP
<structure> \- the structure to replace the data of
<label> \- the input label file
.IP
[\-metric] \- repeatable \- replace the data in a surface component
.IP
<structure> \- the structure to replace the data of
<metric> \- the input metric
.IP
[\-volume] \- repeatable \- replace the data in a volume component
.IP
<structure> \- the structure to replace the data of
<volume> \- the input volume
.IP
[\-from\-cropped] \- the input is cropped to the size of the component
.PP
\fB\-cifti\-resample\fR
RESAMPLE A CIFTI FILE TO A NEW CIFTI SPACE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-resample\fR
.IP
<cifti\-in>
<direction>
<cifti\-template>
<template\-direction>
<surface\-method>
<volume\-method>
<cifti\-out>
[\-surface\-largest]
[\-volume\-predilate]
.IP
<dilate\-mm>
.IP
[\-surface\-postdilate]
.IP
<dilate\-mm>
.IP
[\-affine]
.IP
<affine\-file>
[\-flirt]
.IP
<source\-volume>
<target\-volume>
.IP
[\-warpfield]
.IP
<warpfield>
[\-fnirt]
.IP
<source\-volume>
.IP
[\-left\-spheres]
.IP
<current\-sphere>
<new\-sphere>
[\-left\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-left\-area\-metrics]
.IP
<current\-area>
<new\-area>
.IP
[\-right\-spheres]
.IP
<current\-sphere>
<new\-sphere>
[\-right\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-right\-area\-metrics]
.IP
<current\-area>
<new\-area>
.IP
[\-cerebellum\-spheres]
.IP
<current\-sphere>
<new\-sphere>
[\-cerebellum\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-cerebellum\-area\-metrics]
.IP
<current\-area>
<new\-area>
.TP
Resample cifti data to a different brainordinate space.
Use COLUMN for
.TP
the direction to resample dscalar, dlabel, or dtseries.
Resampling both
.IP
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
\fB\-cifti\-resample\-dconn\-memory\fR to avoid writing and rereading an
intermediate file.  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.
.IP
The <volume\-method> argument must be one of the following:
.IP
CUBIC
ENCLOSING_VOXEL
TRILINEAR
.IP
The <surface\-method> argument must be one of the following:
.IP
ADAP_BARY_AREA
BARYCENTRIC
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- the cifti file to resample
<direction> \- the direction of the input that should be resampled
<cifti\-template> \- a cifti file containing the cifti space to resample to
<template\-direction> \- the direction of the template to use as the
.IP
resampling space
.IP
<surface\-method> \- specify a surface resampling method
<volume\-method> \- specify a volume interpolation method
<cifti\-out> \- output \- the output cifti file
.IP
[\-surface\-largest] \- use largest weight instead of weighted average when
.IP
doing surface resampling
.IP
[\-volume\-predilate] \- dilate the volume components before resampling
.IP
<dilate\-mm> \- distance, in mm, to dilate
.IP
[\-surface\-postdilate] \- dilate the surface components after resampling
.IP
<dilate\-mm> \- distance, in mm, to dilate
.IP
[\-affine] \- use an affine transformation on the volume components
.IP
<affine\-file> \- the affine file to use
.IP
[\-flirt] \- MUST be used if affine is a flirt affine
.IP
<source\-volume> \- the source volume used when generating the affine
<target\-volume> \- the target volume used when generating the affine
.IP
[\-warpfield] \- use a warpfield on the volume components
.IP
<warpfield> \- the warpfield to use
.IP
[\-fnirt] \- MUST be used if using a fnirt warpfield
.IP
<source\-volume> \- the source volume used when generating the
.IP
warpfield
.IP
[\-left\-spheres] \- specify spheres for left surface resampling
.IP
<current\-sphere> \- a sphere with the same mesh as the current left
.IP
surface
.IP
<new\-sphere> \- a sphere with the new left mesh that is in register
.IP
with the current sphere
.IP
[\-left\-area\-surfs] \- specify left surfaces to do vertex area
.IP
correction based on
<current\-area> \- a relevant left anatomical surface with current
.IP
mesh
.IP
<new\-area> \- a relevant left anatomical surface with new mesh
.IP
[\-left\-area\-metrics] \- specify left vertex area metrics to do area
.IP
correction based on
<current\-area> \- a metric file with vertex areas for the current
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for the new mesh
.IP
[\-right\-spheres] \- specify spheres for right surface resampling
.IP
<current\-sphere> \- a sphere with the same mesh as the current right
.IP
surface
.IP
<new\-sphere> \- a sphere with the new right mesh that is in register
.IP
with the current sphere
.IP
[\-right\-area\-surfs] \- specify right surfaces to do vertex area
.IP
correction based on
<current\-area> \- a relevant right anatomical surface with current
.IP
mesh
.IP
<new\-area> \- a relevant right anatomical surface with new mesh
.IP
[\-right\-area\-metrics] \- specify right vertex area metrics to do area
.IP
correction based on
<current\-area> \- a metric file with vertex areas for the current
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for the new mesh
.IP
[\-cerebellum\-spheres] \- specify spheres for cerebellum surface resampling
.IP
<current\-sphere> \- a sphere with the same mesh as the current
.IP
cerebellum surface
.IP
<new\-sphere> \- a sphere with the new cerebellum mesh that is in
.IP
register with the current sphere
.IP
[\-cerebellum\-area\-surfs] \- specify cerebellum surfaces to do vertex
.IP
area correction based on
<current\-area> \- a relevant cerebellum anatomical surface with
.IP
current mesh
.IP
<new\-area> \- a relevant cerebellum anatomical surface with new mesh
.IP
[\-cerebellum\-area\-metrics] \- specify cerebellum vertex area metrics to
.IP
do area correction based on
<current\-area> \- a metric file with vertex areas for the current
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for the new mesh
.PP
\fB\-cifti\-resample\-dconn\-memory\fR
USE LOTS OF MEMORY TO RESAMPLE DCONN
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-resample\-dconn\-memory\fR
.IP
<cifti\-in>
<cifti\-template>
<template\-direction>
<surface\-method>
<volume\-method>
<cifti\-out>
[\-surface\-largest]
[\-volume\-predilate]
.IP
<dilate\-mm>
.IP
[\-surface\-postdilate]
.IP
<dilate\-mm>
.IP
[\-affine]
.IP
<affine\-file>
[\-flirt]
.IP
<source\-volume>
<target\-volume>
.IP
[\-warpfield]
.IP
<warpfield>
[\-fnirt]
.IP
<source\-volume>
.IP
[\-left\-spheres]
.IP
<current\-sphere>
<new\-sphere>
[\-left\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-left\-area\-metrics]
.IP
<current\-area>
<new\-area>
.IP
[\-right\-spheres]
.IP
<current\-sphere>
<new\-sphere>
[\-right\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-right\-area\-metrics]
.IP
<current\-area>
<new\-area>
.IP
[\-cerebellum\-spheres]
.IP
<current\-sphere>
<new\-sphere>
[\-cerebellum\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-cerebellum\-area\-metrics]
.IP
<current\-area>
<new\-area>
.IP
This command does the same thing as running \fB\-cifti\-resample\fR 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.  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.
.IP
The <volume\-method> argument must be one of the following:
.IP
CUBIC
ENCLOSING_VOXEL
TRILINEAR
.IP
The <surface\-method> argument must be one of the following:
.IP
ADAP_BARY_AREA
BARYCENTRIC
.IP
Descriptions of parameters and options:
.IP
<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
.IP
resampling space
.IP
<surface\-method> \- specify a surface resampling method
<volume\-method> \- specify a volume interpolation method
<cifti\-out> \- output \- the output cifti file
.IP
[\-surface\-largest] \- use largest weight instead of weighted average when
.IP
doing surface resampling
.IP
[\-volume\-predilate] \- dilate the volume components before resampling
.IP
<dilate\-mm> \- distance, in mm, to dilate
.IP
[\-surface\-postdilate] \- dilate the surface components after resampling
.IP
<dilate\-mm> \- distance, in mm, to dilate
.IP
[\-affine] \- use an affine transformation on the volume components
.IP
<affine\-file> \- the affine file to use
.IP
[\-flirt] \- MUST be used if affine is a flirt affine
.IP
<source\-volume> \- the source volume used when generating the affine
<target\-volume> \- the target volume used when generating the affine
.IP
[\-warpfield] \- use a warpfield on the volume components
.IP
<warpfield> \- the warpfield to use
.IP
[\-fnirt] \- MUST be used if using a fnirt warpfield
.IP
<source\-volume> \- the source volume used when generating the
.IP
warpfield
.IP
[\-left\-spheres] \- specify spheres for left surface resampling
.IP
<current\-sphere> \- a sphere with the same mesh as the current left
.IP
surface
.IP
<new\-sphere> \- a sphere with the new left mesh that is in register
.IP
with the current sphere
.IP
[\-left\-area\-surfs] \- specify left surfaces to do vertex area
.IP
correction based on
<current\-area> \- a relevant left anatomical surface with current
.IP
mesh
.IP
<new\-area> \- a relevant left anatomical surface with new mesh
.IP
[\-left\-area\-metrics] \- specify left vertex area metrics to do area
.IP
correction based on
<current\-area> \- a metric file with vertex areas for the current
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for the new mesh
.IP
[\-right\-spheres] \- specify spheres for right surface resampling
.IP
<current\-sphere> \- a sphere with the same mesh as the current right
.IP
surface
.IP
<new\-sphere> \- a sphere with the new right mesh that is in register
.IP
with the current sphere
.IP
[\-right\-area\-surfs] \- specify right surfaces to do vertex area
.IP
correction based on
<current\-area> \- a relevant right anatomical surface with current
.IP
mesh
.IP
<new\-area> \- a relevant right anatomical surface with new mesh
.IP
[\-right\-area\-metrics] \- specify right vertex area metrics to do area
.IP
correction based on
<current\-area> \- a metric file with vertex areas for the current
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for the new mesh
.IP
[\-cerebellum\-spheres] \- specify spheres for cerebellum surface resampling
.IP
<current\-sphere> \- a sphere with the same mesh as the current
.IP
cerebellum surface
.IP
<new\-sphere> \- a sphere with the new cerebellum mesh that is in
.IP
register with the current sphere
.IP
[\-cerebellum\-area\-surfs] \- specify cerebellum surfaces to do vertex
.IP
area correction based on
<current\-area> \- a relevant cerebellum anatomical surface with
.IP
current mesh
.IP
<new\-area> \- a relevant cerebellum anatomical surface with new mesh
.IP
[\-cerebellum\-area\-metrics] \- specify cerebellum vertex area metrics to
.IP
do area correction based on
<current\-area> \- a metric file with vertex areas for the current
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for the new mesh
.PP
\fB\-cifti\-roi\-average\fR
AVERAGE ROWS IN A SINGLE CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-roi\-average\fR
.IP
<cifti\-in>
<text\-out>
[\-cifti\-roi]
.IP
<roi\-cifti>
.IP
[\-left\-roi]
.IP
<roi\-metric>
.IP
[\-right\-roi]
.IP
<roi\-metric>
.IP
[\-cerebellum\-roi]
.IP
<roi\-metric>
.IP
[\-vol\-roi]
.IP
<roi\-vol>
.IP
Average the rows that are within the specified ROIs, and write the
resulting average row to a text file, seperated by newlines.  If
\fB\-cifti\-roi\fR is specified, \fB\-left\-roi\fR, \fB\-right\-roi\fR, \fB\-cerebellum\-roi\fR, and
\fB\-vol\-roi\fR must not be specified.
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- the cifti file to average rows from
<text\-out> \- output text file of the average values
.IP
[\-cifti\-roi] \- cifti file containing combined rois
.IP
<roi\-cifti> \- the rois as a cifti file
.IP
[\-left\-roi] \- vertices to use from left hemisphere
.IP
<roi\-metric> \- the left roi as a metric file
.IP
[\-right\-roi] \- vertices to use from right hemisphere
.IP
<roi\-metric> \- the right roi as a metric file
.IP
[\-cerebellum\-roi] \- vertices to use from cerebellum
.IP
<roi\-metric> \- the cerebellum roi as a metric file
.IP
[\-vol\-roi] \- voxels to use
.IP
<roi\-vol> \- the roi volume file
.PP
\fB\-cifti\-rois\-from\-extrema\fR
CREATE CIFTI ROI MAPS FROM EXTREMA MAPS
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-rois\-from\-extrema\fR
.IP
<cifti>
<surf\-limit>
<vol\-limit>
<direction>
<cifti\-out>
[\-left\-surface]
.IP
<surface>
.IP
[\-right\-surface]
.IP
<surface>
.IP
[\-cerebellum\-surface]
.IP
<surface>
.IP
[\-gaussian]
.IP
<surf\-sigma>
<vol\-sigma>
.IP
[\-overlap\-logic]
.IP
<method>
.IP
[\-merged\-volume]
.IP
For each nonzero value in each map, make a map with an ROI around that
location.  If the \fB\-gaussian\fR option is specified, then normalized gaussian
kernels are output instead of ROIs.  The <method> argument to
\fB\-overlap\-logic\fR 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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.IP
[\-gaussian] \- generate gaussian kernels instead of flat ROIs
.IP
<surf\-sigma> \- the sigma for the surface gaussian kernel, in mm
<vol\-sigma> \- the sigma for the volume gaussian kernel, in mm
.IP
[\-overlap\-logic] \- how to handle overlapping ROIs, default ALLOW
.IP
<method> \- the method of resolving overlaps
.IP
[\-merged\-volume] \- treat volume components as if they were a single
.IP
component
.PP
\fB\-cifti\-separate\fR
WRITE A CIFTI MODEL AS METRIC, LABEL OR VOLUME
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-separate\fR
.IP
<cifti\-in>
<direction>
[\-volume\-all]
.IP
<volume\-out>
[\-roi]
.IP
<roi\-out>
.IP
[\-crop]
.IP
[\-label] (repeatable)
.IP
<structure>
<label\-out>
[\-roi]
.IP
<roi\-out>
.IP
[\-metric] (repeatable)
.IP
<structure>
<metric\-out>
[\-roi]
.IP
<roi\-out>
.IP
[\-volume] (repeatable)
.IP
<structure>
<volume\-out>
[\-roi]
.IP
<roi\-out>
.IP
[\-crop]
.IP
You must specify \fB\-metric\fR, \fB\-volume\-all\fR, \fB\-volume\fR, or \fB\-label\fR for this
command to do anything.  Output volumes will spatially line up with their
original positions, whether or not they are cropped.  For dtseries,
dscalar, and dlabel, use COLUMN, and if your matrix is fully symmetric,
COLUMN is more efficient.  The structure argument must be one of the
following:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- the cifti to separate a component of
<direction> \- which direction to separate into components, ROW or COLUMN
.IP
[\-volume\-all] \- separate all volume models into a volume file
.IP
<volume\-out> \- output \- the output volume
.IP
[\-roi] \- also output the roi of which voxels have data
.IP
<roi\-out> \- output \- the roi output volume
.IP
[\-crop] \- crop volume to the size of the data rather than using the
.IP
original volume size
.IP
[\-label] \- repeatable \- separate a surface model into a surface label
.IP
file
<structure> \- the structure to output
<label\-out> \- output \- the output label file
.IP
[\-roi] \- also output the roi of which vertices have data
.IP
<roi\-out> \- output \- the roi output metric
.IP
[\-metric] \- repeatable \- separate a surface model into a metric file
.IP
<structure> \- the structure to output
<metric\-out> \- output \- the output metric
.IP
[\-roi] \- also output the roi of which vertices have data
.IP
<roi\-out> \- output \- the roi output metric
.IP
[\-volume] \- repeatable \- separate a volume model into a volume file
.IP
<structure> \- the structure to output
<volume\-out> \- output \- the output volume
.IP
[\-roi] \- also output the roi of which voxels have data
.IP
<roi\-out> \- output \- the roi output volume
.IP
[\-crop] \- crop volume to the size of the component rather than using
.IP
the original volume size
.PP
\fB\-cifti\-separate\-all\fR
DEPRECATED: use \fB\-cifti\-separate\fR
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-separate\-all\fR
.IP
<cifti\-in>
[\-left]
.IP
<left\-metric>
[\-left\-roi]
.IP
<left\-roi\-metric>
.IP
[\-right]
.IP
<right\-metric>
[\-right\-roi]
.IP
<right\-roi\-metric>
.IP
[\-cerebellum]
.IP
<cerebellum\-metric>
[\-cerebellum\-roi]
.IP
<cerebellum\-roi\-metric>
.IP
[\-volume]
.IP
<volume\-out>
[\-volume\-roi]
.IP
<volume\-roi\-out>
.IP
[\-direction]
.IP
<direction>
.IP
DEPRECATED: this command will be removed in a future release, use
\fB\-cifti\-separate\fR.
.IP
All volume components are put together into one volume, the boundaries
between volume components are not output by this command.  The COLUMN
direction (default) is usually what you want, ROW will only work for
dconn.  Using this command with \fB\-volume\fR will usually take (much) more
memory than the cifti file, since it must create the whole volume, rather
than just the included voxels.
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- the cifti to split
.IP
[\-left] \- output the left surface data
.IP
<left\-metric> \- output \- the output metric for the left surface
.IP
[\-left\-roi] \- output the ROI for the left surface data
.IP
<left\-roi\-metric> \- output \- output metric for the left ROI
.IP
[\-right] \- output the right surface data
.IP
<right\-metric> \- output \- the output metric for the right surface
.IP
[\-right\-roi] \- output the ROI for the right surface data
.IP
<right\-roi\-metric> \- output \- output metric for the right ROI
.IP
[\-cerebellum] \- output the cerebellum surface data
.IP
<cerebellum\-metric> \- output \- the output metric for the cerebellum
.IP
surface
.IP
[\-cerebellum\-roi] \- output the ROI for the cerebellum surface data
.IP
<cerebellum\-roi\-metric> \- output \- output metric for the cerebellum
.IP
ROI
.IP
[\-volume] \- output the voxel data
.IP
<volume\-out> \- output \- output volume file
.IP
[\-volume\-roi] \- output the combined ROI for the volume data
.IP
<volume\-roi\-out> \- output \- output volume for ROI
.IP
[\-direction] \- choose the direction to separate (default COLUMN)
.IP
<direction> \- which direction to separate into components, ROW or
.IP
COLUMN
.PP
\fB\-cifti\-smoothing\fR
SMOOTH A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-smoothing\fR
.IP
<cifti>
<surface\-kernel>
<volume\-kernel>
<direction>
<cifti\-out>
[\-left\-surface]
.IP
<surface>
[\-left\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-right\-surface]
.IP
<surface>
[\-right\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-cerebellum\-surface]
.IP
<surface>
[\-cerebellum\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-cifti\-roi]
.IP
<roi\-cifti>
.IP
[\-fix\-zeros\-volume]
[\-fix\-zeros\-surface]
.IP
The input cifti file must have a brain models mapping on the chosen
dimension, columns for .dtseries, and either for .dconn.  Data in
different structures is smoothed independently (i.e., "parcel
constrained" smoothing), so volume structures that touch do not smooth
across this boundary.  Surface smoothing uses the GEO_GAUSS_AREA
smoothing method.
.IP
The \-*\-corrected\-areas options are 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.
.IP
The \fB\-fix\-zeros\-\fR* 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.
.IP
Descriptions of parameters and options:
.IP
<cifti> \- the input cifti
<surface\-kernel> \- the sigma for the gaussian surface smoothing kernel,
.IP
in mm
.IP
<volume\-kernel> \- the sigma for the gaussian volume smoothing kernel, in
.IP
mm
.IP
<direction> \- which dimension to smooth along, ROW or COLUMN
<cifti\-out> \- output \- the output cifti
.IP
[\-left\-surface] \- specify the left surface to use
.IP
<surface> \- the left surface file
.IP
[\-left\-corrected\-areas] \- vertex areas to use instead of computing
.IP
them from the left surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-right\-surface] \- specify the right surface to use
.IP
<surface> \- the right surface file
.IP
[\-right\-corrected\-areas] \- vertex areas to use instead of computing
.IP
them from the right surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-cerebellum\-surface] \- specify the cerebellum surface to use
.IP
<surface> \- the cerebellum surface file
.IP
[\-cerebellum\-corrected\-areas] \- vertex areas to use instead of
.IP
computing them from the cerebellum surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-cifti\-roi] \- smooth only within regions of interest
.IP
<roi\-cifti> \- the regions to smooth within, as a cifti file
.IP
[\-fix\-zeros\-volume] \- treat values of zero in the volume as missing data
.IP
[\-fix\-zeros\-surface] \- treat values of zero on the surface as missing
.IP
data
.PP
\fB\-cifti\-transpose\fR
TRANSPOSE A CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-cifti\-transpose\fR
.IP
<cifti\-in>
<cifti\-out>
[\-mem\-limit]
.IP
<limit\-GB>
.TP
The input must be a 2\-dimensional cifti file.
The output is a cifti file
.IP
where every row in the input is a column in the output.
.IP
Descriptions of parameters and options:
.IP
<cifti\-in> \- the input cifti file
<cifti\-out> \- output \- the output cifti file
.IP
[\-mem\-limit] \- restrict memory usage
.IP
<limit\-GB> \- memory limit in gigabytes
.PP
\fB\-class\-add\-member\fR
.PP
Add members to class header (.h) and implementation (.cxx) files.
.IP
[\-add\-to\-files]
[\-m <member\-name> <data\-type> <description>]...
.IP
If the \fB\-add\-to\-files\fR is not specified, the code for the
header and implementation files is printed to the
terminal.
.IP
If the \fB\-add\-to\-files\fR 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:
.IP
// ADD_NEW_MEMBERS_HERE
.IP
The implementation file must contain this text in
its public section:
.IP
// ADD_NEW_METHODS_HERE
.IP
If either of these text string are missing, the code
that would have been added to the file(s) is printed
to the terminal.
.IP
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 ("").
.IP
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.
.PP
\fB\-class\-create\fR
.PP
Create class header (.h) and implementation (.cxx) files.
.PP
Usage:  <class\-name>
.IP
[\-copy]
[\-event\-class <event\-type\-enum>]
[\-event\-listener]
[\-no\-parent]
[\-parent <parent\-class\-name>]
.SH OPTIONS
.HP
\fB\-copy\fR
.IP
Adds copy constructor and assignment operator
.HP
\fB\-event\-class\fR <event\-type\-enum>
.IP
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.
.IP
For the <event\-type\-enum> there is no need
to prepend it with "EventTypeEnum::".
.HP
\fB\-event\-listener\fR
.IP
Implement the EventListenerInterface so
that the class may listen for events.
.HP
\fB\-no\-parent\fR
.IP
Created class is not derived from any other
class.  By default, the parent class is
CaretObject.
.HP
\fB\-parent\fR <parent\-class\-name>
.IP
Specify the parent (derived from) class.
By default, the parent class is CaretObject.
.HP
\fB\-scene\fR
.IP
Implement the SceneableInterface so that
instances of the class can be restored from
and saved to scenes.
.HP
\fB\-scene\-sub\-class\fR
.IP
Adds methods that can be called by the superclass so that this sub\-class can save and
restore data to and from scenes.
.IP
This option should only be used when creating
a class whose super class implements the
SceneableInterface
.PP
\fB\-class\-create\-algorithm\fR
.PP
Create Algorithm Class header (.h) and implementation (.cxx) files.
.PP
Usage:  <algorithm\-class\-name>
.IP
<command\-line\-switch>
<short\-description>
.IP
algorithm\-class\-name
.IP
Required name of the algorithm class that MUST start with "Algorithm"
.IP
command\-line\-switch
.IP
Required command line switch for algorithm.
.IP
short\-description
.IP
Required short description within double quotes.
.PP
\fB\-class\-create\-enum\fR
.PP
Create enumerated type header (.h) and implementation (.cxx) files.
.PP
Usage:  <enum\-class\-name>
.IP
<number\-of\-values>
<auto\-number>
.IP
enum\-class\-name
.TP
Name of the enumerated type.
Must end in "Enum"
.IP
number\-of\-values
.IP
Number of values in the enumerated type.
.IP
auto\-number
.IP
Automatically generated integer codes corresponding
to the enumerated values.  Value for this parameter
are "true" and "false".
.IP
[enum\-name\-1] [enum\-name\-2]...[enum\-name\-N]
.IP
Optional names for the enumerated values.
.IP
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.
.PP
\fB\-class\-create\-operation\fR
.PP
Create Operation Class header (.h) and implementation (.cxx) files.
.PP
Usage:  <operation\-class\-name>
.IP
<command\-line\-switch>
<short\-description>
[\-no\-parameters]
.IP
operation\-class\-name
.IP
Required name of the operation class that MUST start with "Operation"
.IP
command\-line\-switch
.IP
Required command line switch for operation.
.IP
short\-description
.IP
Required short description within double quotes.
.HP
\fB\-no\-parameters\fR
.IP
Optional parameter if the operation does not use parameters.
.PP
\fB\-convert\-affine\fR
CONVERT AN AFFINE FILE BETWEEN CONVENTIONS
.IP
debian/tmp/usr/bin/wb_command \fB\-convert\-affine\fR
.IP
[\-from\-world]
.IP
<input>
.IP
[\-from\-flirt]
.IP
<input>
<source\-volume>
<target\-volume>
.IP
[\-to\-world]
.IP
<output>
.IP
[\-to\-flirt] (repeatable)
.IP
<output>
<source\-volume>
<target\-volume>
.IP
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.
.IP
You must specify exactly one \fB\-from\fR option, but you may specify multiple
\fB\-to\fR options, and any \fB\-to\fR option that takes volumes may be specified more
than once.
.IP
Descriptions of parameters and options:
.IP
[\-from\-world] \- input is a NIFTI 'world' affine
.IP
<input> \- the input affine
.IP
[\-from\-flirt] \- input is a flirt matrix
.IP
<input> \- the input affine
<source\-volume> \- the source volume used when generating the input
.IP
affine
.IP
<target\-volume> \- the target volume used when generating the input
.IP
affine
.IP
[\-to\-world] \- write output as a NIFTI 'world' affine
.IP
<output> \- output \- the output affine
.IP
[\-to\-flirt] \- repeatable \- write output as a flirt matrix
.IP
<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
.IP
match
.PP
\fB\-convert\-fiber\-orientations\fR
CONVERT BINGHAM PARAMETER VOLUMES TO FIBER ORIENTATION FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-convert\-fiber\-orientations\fR
.IP
<label\-volume>
<fiber\-out>
[\-fiber] (repeatable)
.IP
<mean\-f>
<stdev\-f>
<theta>
<phi>
<psi>
<ka>
<kb>
.IP
Takes precomputed bingham parameters from volume files and converts them
to the format workbench uses for display.
.IP
Descriptions of parameters and options:
.IP
<label\-volume> \- volume of cifti structure labels
<fiber\-out> \- output \- the output fiber orientation file
.IP
[\-fiber] \- repeatable \- specify the parameter volumes for a fiber
.IP
<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
.PP
\fB\-convert\-matrix4\-to\-matrix2\fR
GENERATES A MATRIX2 CIFTI FROM MATRIX4 WBSPARSE
.IP
debian/tmp/usr/bin/wb_command \fB\-convert\-matrix4\-to\-matrix2\fR
.IP
<matrix4\-wbsparse>
<counts\-out>
[\-distances]
.IP
<distance\-out>
.IP
This command makes a cifti file from the fiber counts in a matrix4
wbsparse file, and optionally a second cifti file from the distances.
.IP
Descriptions of parameters and options:
.IP
<matrix4\-wbsparse> \- a wbsparse matrix4 file
<counts\-out> \- output \- the total fiber counts, as a cifti file
.IP
[\-distances] \- output average trajectory distance
.IP
<distance\-out> \- output \- the distances, as a cifti file
.PP
\fB\-convert\-matrix4\-to\-workbench\-sparse\fR
CONVERT A 3\-FILE MATRIX4 TO A WORKBENCH SPARSE FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-convert\-matrix4\-to\-workbench\-sparse\fR
.IP
<matrix4_1>
<matrix4_2>
<matrix4_3>
<orientation\-file>
<voxel\-list>
<wb\-sparse\-out>
[\-surface\-seeds]
.IP
<seed\-roi>
.IP
[\-volume\-seeds]
.IP
<cifti\-template>
<direction>
.IP
Converts the matrix 4 output of probtrackx to workbench sparse file
format.  Exactly one of \fB\-surface\-seeds\fR and \fB\-volume\-seeds\fR must be
specified.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
to
.IP
<voxel\-list> \- list of white matter voxel index triplets as used in the
.IP
trajectory matrix
.IP
<wb\-sparse\-out> \- output \- the output workbench sparse file
.IP
[\-surface\-seeds] \- specify the surface seed space
.IP
<seed\-roi> \- metric roi file of all nodes used in the seed space
.IP
[\-volume\-seeds] \- specify the volume seed space
.IP
<cifti\-template> \- cifti file to use the volume mappings from
<direction> \- dimension along the cifti file to take the mapping from,
.IP
ROW or COLUMN
.PP
\fB\-convert\-warpfield\fR
CONVERT A WARPFIELD BETWEEN CONVENTIONS
.IP
debian/tmp/usr/bin/wb_command \fB\-convert\-warpfield\fR
.IP
[\-from\-world]
.IP
<input>
.IP
[\-from\-fnirt]
.IP
<input>
<source\-volume>
.IP
[\-to\-world]
.IP
<output>
.IP
[\-to\-fnirt] (repeatable)
.IP
<output>
<source\-volume>
.IP
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.
.IP
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.
.IP
You must specify exactly one \fB\-from\fR option, but you may specify multiple
\fB\-to\fR options, and any \fB\-to\fR option that takes volumes may be specified more
than once.
.IP
Descriptions of parameters and options:
.IP
[\-from\-world] \- input is a NIFTI 'world' warpfield
.IP
<input> \- the input warpfield
.IP
[\-from\-fnirt] \- input is a fnirt warpfield
.IP
<input> \- the input warpfield
<source\-volume> \- the source volume used when generating the input
.IP
warpfield
.IP
[\-to\-world] \- write output as a NIFTI 'world' warpfield
.IP
<output> \- output \- the output warpfield
.IP
[\-to\-fnirt] \- repeatable \- write output as a flirt warpfield
.IP
<output> \- output \- the output warpfield
<source\-volume> \- the volume you want to apply the warpfield to
.PP
\fB\-create\-signed\-distance\-volume\fR
CREATE SIGNED DISTANCE VOLUME FROM SURFACE
.IP
debian/tmp/usr/bin/wb_command \fB\-create\-signed\-distance\-volume\fR
.IP
<surface>
<refspace>
<outvol>
[\-roi\-out]
.IP
<roi\-vol>
.IP
[\-fill\-value]
.IP
<value>
.IP
[\-exact\-limit]
.IP
<dist>
.IP
[\-approx\-limit]
.IP
<dist>
.IP
[\-approx\-neighborhood]
.IP
<num>
.IP
[\-winding]
.IP
<method>
.TP
Computes the signed distance function of the surface.
Exact distance is
.IP
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:
.IP
EVEN_ODD (default)
NEGATIVE
NONZERO
NORMALS
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the input surface
<refspace> \- a volume in the desired output space (dims, spacing, origin)
<outvol> \- output \- the output volume
.IP
[\-roi\-out] \- output an roi volume of where the output has a computed
.IP
value
<roi\-vol> \- output \- the output roi volume
.IP
[\-fill\-value] \- specify a value to put in all voxels that don't get
.IP
assigned a distance
<value> \- value to fill with (default 0)
.IP
[\-exact\-limit] \- specify distance for exact output
.IP
<dist> \- distance in mm (default 5)
.IP
[\-approx\-limit] \- specify distance for approximate output
.IP
<dist> \- distance in mm (default 20)
.IP
[\-approx\-neighborhood] \- voxel neighborhood for approximate calculation
.IP
<num> \- size of neighborhood cube measured from center to face, in
.IP
voxels (default 2 = 5x5x5)
.IP
[\-winding] \- winding method for point inside surface test
.IP
<method> \- name of the method (default EVEN_ODD)
.PP
\fB\-estimate\-fiber\-binghams\fR
ESTIMATE FIBER ORIENTATION DISTRIBUTIONS FROM BEDPOSTX SAMPLES
.IP
debian/tmp/usr/bin/wb_command \fB\-estimate\-fiber\-binghams\fR
.IP
<merged_f1samples>
<merged_th1samples>
<merged_ph1samples>
<merged_f2samples>
<merged_th2samples>
<merged_ph2samples>
<merged_f3samples>
<merged_th3samples>
<merged_ph3samples>
<label\-volume>
<cifti\-out>
.IP
This command does an estimation of a bingham distribution for each fiber
orientation in each voxel which is labeled with a name equal to a CIFTI
structure identifier.  These identifiers must be one of the following for
it to be used:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-fiber\-dot\-products\fR
COMPUTE DOT PRODUCTS OF FIBER ORIENTATIONS WITH SURFACE NORMALS
.IP
debian/tmp/usr/bin/wb_command \fB\-fiber\-dot\-products\fR
.IP
<white\-surf>
<fiber\-file>
<max\-dist>
<direction>
<dot\-metric>
<f\-metric>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<white\-surf> \- the white/gray boundary surface
<fiber\-file> \- the fiber orientation file
<max\-dist> \- the maximum distance from any surface node a fiber
.IP
population may be, in mm
.IP
<direction> \- test against surface for whether a fiber population should
.IP
be used
.IP
<dot\-metric> \- output \- the metric of dot products
<f\-metric> \- output \- a metric of the f values of the fiber distributions
.PP
\fB\-file\-convert\fR
CHANGE VERSION OF FILE FORMAT
.IP
debian/tmp/usr/bin/wb_command \fB\-file\-convert\fR
.IP
[\-border\-version\-convert]
.IP
<border\-in>
<out\-version>
<border\-out>
[\-surface]
.IP
<surface>
.IP
[\-nifti\-version\-convert]
.IP
<input>
<version>
<output>
.IP
[\-cifti\-version\-convert]
.IP
<cifti\-in>
<version>
<cifti\-out>
.IP
You may only specify one top\-level option.
.IP
Descriptions of parameters and options:
.IP
[\-border\-version\-convert] \- write a border file with a different version
.IP
<border\-in> \- the input border file
<out\-version> \- the format version to write as, 1 or 3 (2 doesn't
.IP
exist)
.IP
<border\-out> \- output \- the output border file
.IP
[\-surface] \- must be specified if the input is version 1
.IP
<surface> \- use this surface file for structure and number of
.IP
vertices, ignore borders on other structures
.IP
[\-nifti\-version\-convert] \- write a nifti file with a different version
.IP
<input> \- the input nifti file
<version> \- the nifti version to write as
<output> \- output \- the output nifti file
.IP
[\-cifti\-version\-convert] \- write a cifti file with a different version
.IP
<cifti\-in> \- the input cifti file
<version> \- the cifti version to write as
<cifti\-out> \- output \- the output cifti file
.PP
\fB\-file\-information\fR
LIST INFORMATION ABOUT A FILE'S CONTENT
.IP
debian/tmp/usr/bin/wb_command \fB\-file\-information\fR
.IP
<data\-file>
[\-no\-map\-info]
[\-only\-step\-interval]
[\-only\-number\-of\-maps]
.TP
List information about the content of a data file.
Only one \fB\-only\fR option
.TP
may be specified.
The information listed when no \fB\-only\fR option is present
.IP
is dependent upon the type of data file.
.IP
Descriptions of parameters and options:
.IP
<data\-file> \- data file
.IP
[\-no\-map\-info] \- do not show map information for files that support maps
.IP
[\-only\-step\-interval] \- suppress normal output, print the interval
.IP
between maps
.IP
[\-only\-number\-of\-maps] \- suppress normal output, print the number of maps
.PP
\fB\-foci\-get\-projection\-vertex\fR
GET PROJECTION VERTEX FOR FOCI
.IP
debian/tmp/usr/bin/wb_command \fB\-foci\-get\-projection\-vertex\fR
.IP
<foci>
<surface>
<metric\-out>
[\-name]
.IP
<name>
.IP
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 \fB\-name\fR is used, only one focus will
be used.
.IP
Descriptions of parameters and options:
.IP
<foci> \- the foci file
<surface> \- the surface related to the foci file
<metric\-out> \- output \- the output metric file
.IP
[\-name] \- select a focus by name
.IP
<name> \- the name of the focus
.PP
\fB\-foci\-list\-coords\fR
OUTPUT FOCI COORDINATES IN A TEXT FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-foci\-list\-coords\fR
.IP
<foci\-file>
<coord\-file\-out>
[\-names\-out]
.IP
<names\-file\-out>
.IP
Output the coordinates for every focus in the foci file, and optionally
the focus names in a second text file.
.IP
Descriptions of parameters and options:
.IP
<foci\-file> \- input foci file
<coord\-file\-out> \- output \- the output coordinate text file
.IP
[\-names\-out] \- output the foci names
.IP
<names\-file\-out> \- output \- text file to put foci names in
.PP
\fB\-gifti\-all\-labels\-to\-rois\fR
MAKE ROIS FROM ALL LABELS IN A GIFTI COLUMN
.IP
debian/tmp/usr/bin/wb_command \fB\-gifti\-all\-labels\-to\-rois\fR
.IP
<label\-in>
<map>
<metric\-out>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-gifti\-convert\fR
Convert GIFTI file to different encoding
.PP
Usage:  <gifti\-encoding>
.IP
<input\-gifti\-file>
<output\-gifti\-file>
.IP
gifti\-encoding
.IP
Required GIFTI encoding.
.IP
input\-gifti\-file
.IP
Required input GIFTI file name.
.IP
output\-gifti\-file
.IP
Required output GIFTI file name.
.IP
Valid GIFTI Encodings:
.IP
ASCII
BASE64_BINARY
GZIP_BASE64_BINARY
EXTERNAL_FILE_BINARY
.PP
\fB\-gifti\-label\-add\-prefix\fR
ADD PREFIX TO ALL LABEL NAMES IN A GIFTI LABEL FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-gifti\-label\-add\-prefix\fR
.IP
<label\-in>
<prefix>
<label\-out>
.IP
For each label other than '???', prepend <prefix> to the label name.
.IP
Descriptions of parameters and options:
.IP
<label\-in> \- the input label file
<prefix> \- the prefix string to add
<label\-out> \- output \- the output label file
.PP
\fB\-gifti\-label\-to\-roi\fR
MAKE A GIFTI LABEL INTO AN ROI METRIC
.IP
debian/tmp/usr/bin/wb_command \fB\-gifti\-label\-to\-roi\fR
.IP
<label\-in>
<metric\-out>
[\-name]
.IP
<label\-name>
.IP
[\-key]
.IP
<label\-key>
.IP
[\-map]
.IP
<map>
.IP
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
\fB\-name\fR and \fB\-key\fR must be specified.  Specify \fB\-map\fR to use only one map from
<label\-in>.
.IP
Descriptions of parameters and options:
.IP
<label\-in> \- the input gifti label file
<metric\-out> \- output \- the output metric file
.IP
[\-name] \- select label by name
.IP
<label\-name> \- the label name that you want an roi of
.IP
[\-key] \- select label by key
.IP
<label\-key> \- the label key that you want an roi of
.IP
[\-map] \- select a single label map to use
.IP
<map> \- the map number or name
.PP
\fB\-label\-dilate\fR
DILATE A LABEL FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-label\-dilate\fR
.IP
<label>
<surface>
<dilate\-dist>
<label\-out>
[\-bad\-vertex\-roi]
.IP
<roi\-metric>
.IP
[\-column]
.IP
<column>
.IP
Fills in label information for all vertices designated as bad, up to the
specified distance away from other labels.  If \fB\-bad\-vertex\-roi\fR 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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-bad\-vertex\-roi] \- specify an roi of vertices to overwrite, rather than
.IP
vertices with the unlabeled key
<roi\-metric> \- metric file, positive values denote vertices to have
.IP
their values replaced
.IP
[\-column] \- select a single column to dilate
.IP
<column> \- the column number or name
.PP
\fB\-label\-export\-table\fR
EXPORT LABEL TABLE FROM GIFTI AS TEXT
.IP
debian/tmp/usr/bin/wb_command \fB\-label\-export\-table\fR
.IP
<label\-in>
<table\-out>
.IP
Takes the label table from the gifti label file, and writes it to a text
format matching what is expected by \fB\-metric\-label\-import\fR.
.IP
Descriptions of parameters and options:
.IP
<label\-in> \- the input label file
<table\-out> \- output \- the output text file
.PP
\fB\-label\-mask\fR
MASK A LABEL FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-label\-mask\fR
.IP
<label>
<mask>
<label\-out>
[\-column]
.IP
<column>
.IP
By default, the output label is a copy of the input label, but with the
\&'unused' label wherever the mask metric is not positive.  if \fB\-column\fR is
specified, the output contains only one column, the masked version of the
specified input column.
.IP
Descriptions of parameters and options:
.IP
<label> \- the label file to mask
<mask> \- the mask metric
<label\-out> \- output \- the output label file
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.PP
\fB\-label\-merge\fR
MERGE LABEL FILES INTO A NEW FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-label\-merge\fR
.IP
<label\-out>
[\-label] (repeatable)
.IP
<label\-in>
[\-column] (repeatable)
.IP
<column>
[\-up\-to]
.IP
<last\-column>
[\-reverse]
.IP
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.
.IP
Example: wb_command \fB\-label\-merge\fR out.label.gii \fB\-label\fR first.label.gii
\fB\-column\fR 1 \fB\-label\fR second.label.gii
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<label\-out> \- output \- the output label
.IP
[\-label] \- repeatable \- specify an input label
.IP
<label\-in> \- a label file to use columns from
.IP
[\-column] \- repeatable \- select a single column to use
.IP
<column> \- the column number or name
.IP
[\-up\-to] \- use an inclusive range of columns
.IP
<last\-column> \- the number or name of the last column to include
.IP
[\-reverse] \- use the range in reverse order
.PP
\fB\-label\-modify\-keys\fR
CHANGE KEY VALUES IN A LABEL FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-label\-modify\-keys\fR
.IP
<label\-in>
<remap\-file>
<label\-out>
[\-column]
.IP
<column>
.IP
<remap\-file> should have lines of the form 'oldkey newkey', like so:
.IP
3 5
5 8
8 2
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<label\-in> \- the input label file
<remap\-file> \- text file with old and new key values
<label\-out> \- output \- output label file
.IP
[\-column] \- select a single column to use
.IP
<column> \- the column number or name
.PP
\fB\-label\-resample\fR
RESAMPLE A LABEL FILE TO A DIFFERENT MESH
.IP
debian/tmp/usr/bin/wb_command \fB\-label\-resample\fR
.IP
<label\-in>
<current\-sphere>
<new\-sphere>
<method>
<label\-out>
[\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-area\-metrics]
.IP
<current\-area>
<new\-area>
.IP
[\-current\-roi]
.IP
<roi\-metric>
.IP
[\-valid\-roi\-out]
.IP
<roi\-out>
.IP
[\-largest]
.IP
Resamples a label file, given two spherical surfaces that are in
register.  If the method does area correction, exactly one of \fB\-area\-surfs\fR
or \fB\-area\-metrics\fR must be specified.
.IP
The \fB\-largest\fR option results in nearest vertex behavior when used with
BARYCENTRIC, it uses the value of the source vertex that has the largest
weight.  When \fB\-largest\fR is not specified, the vertex weights are summed
according to which label they correspond to, and the label with the
largest sum is used.
.IP
The <method> argument must be one of the following:
.IP
ADAP_BARY_AREA
BARYCENTRIC
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<label\-in> \- the label file to resample
<current\-sphere> \- a sphere surface with the mesh that the label file is
.IP
currently on
.IP
<new\-sphere> \- a sphere surface that is in register with <current\-sphere>
.IP
and has the desired output mesh
.IP
<method> \- the method name
<label\-out> \- output \- the output label file
.IP
[\-area\-surfs] \- specify surfaces to do vertex area correction based on
.IP
<current\-area> \- a relevant anatomical surface with <current\-sphere>
.IP
mesh
.IP
<new\-area> \- a relevant anatomical surface with <new\-sphere> mesh
.IP
[\-area\-metrics] \- specify vertex area metrics to do area correction based
.IP
on
<current\-area> \- a metric file with vertex areas for <current\-sphere>
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for <new\-sphere> mesh
.IP
[\-current\-roi] \- use an input roi on the current mesh to exclude non\-data
.IP
vertices
<roi\-metric> \- the roi, as a metric file
.IP
[\-valid\-roi\-out] \- output the ROI of vertices that got data from valid
.IP
source vertices
<roi\-out> \- output \- the output roi as a metric
.IP
[\-largest] \- use only the label of the vertex with the largest weight
.PP
\fB\-label\-to\-border\fR
DRAW BORDERS AROUND LABELS
.IP
debian/tmp/usr/bin/wb_command \fB\-label\-to\-border\fR
.IP
<surface>
<label\-in>
<border\-out>
[\-placement]
.IP
<fraction>
.IP
[\-column]
.IP
<column>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to use for neighbor information
<label\-in> \- the input label file
<border\-out> \- output \- the output border file
.IP
[\-placement] \- set how far along the edge border points are drawn
.IP
<fraction> \- fraction along edge from inside node (default 0.33)
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.PP
\fB\-metadata\-remove\-provenance\fR
REMOVE PROVENANCE INFORMATION FROM FILE METADATA
.IP
debian/tmp/usr/bin/wb_command \fB\-metadata\-remove\-provenance\fR
.IP
<input\-file>
<output\-file>
.IP
Removes the provenance metadata fields added by workbench during
processing.
.IP
Descriptions of parameters and options:
.IP
<input\-file> \- the file to remove provenance information from
<output\-file> \- output \- the name to save the modified file as
.PP
\fB\-metadata\-string\-replace\fR
REPLACE A STRING IN ALL METADATA OF A FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metadata\-string\-replace\fR
.IP
<input\-file>
<find\-string>
<replace\-string>
<output\-file>
[\-case\-insensitive]
.IP
Replaces all occurrences of <find\-string> in the metadata and map names
of <input\-file> with <replace\-string>.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-case\-insensitive] \- match with case variation also
.PP
\fB\-metric\-convert\fR
CONVERT METRIC FILE TO FAKE NIFTI
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-convert\fR
.IP
[\-to\-nifti]
.IP
<metric\-in>
<nifti\-out>
.IP
[\-from\-nifti]
.IP
<nifti\-in>
<surface\-in>
<metric\-out>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
[\-to\-nifti] \- convert metric to nifti
.IP
<metric\-in> \- the metric to convert
<nifti\-out> \- output \- the output nifti file
.IP
[\-from\-nifti] \- convert nifti to metric
.IP
<nifti\-in> \- the nifti file to convert
<surface\-in> \- surface file to use number of nodes and structure from
<metric\-out> \- output \- the output metric file
.PP
\fB\-metric\-dilate\fR
DILATE A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-dilate\fR
.IP
<metric>
<surface>
<distance>
<metric\-out>
[\-bad\-vertex\-roi]
.IP
<roi\-metric>
.IP
[\-data\-roi]
.IP
<roi\-metric>
.IP
[\-column]
.IP
<column>
.IP
[\-nearest]
[\-linear]
[\-exponent]
.IP
<exponent>
.IP
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 \fB\-nearest\fR is specified, it will use the
value from the closest non\-bad vertex with data within range instead of a
weighted average.
.IP
If \fB\-bad\-vertex\-roi\fR 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 \fB\-data\-roi\fR is not specified, all
vertices are assumed to have data.
.IP
Descriptions of parameters and options:
.IP
<metric> \- the metric to dilate
<surface> \- the surface to compute on
<distance> \- distance in mm to dilate
<metric\-out> \- output \- the output metric
.IP
[\-bad\-vertex\-roi] \- specify an roi of vertices to overwrite, rather than
.IP
vertices with value zero
<roi\-metric> \- metric file, positive values denote vertices to have
.IP
their values replaced
.IP
[\-data\-roi] \- specify an roi of where there is data
.IP
<roi\-metric> \- metric file, positive values denote vertices that have
.IP
data
.IP
[\-column] \- select a single column to dilate
.IP
<column> \- the column number or name
.IP
[\-nearest] \- use the nearest good value instead of a weighted average
.IP
[\-linear] \- fill in values with linear interpolation along strongest
.IP
gradient
.IP
[\-exponent] \- use a different exponent in the weighting function
.IP
<exponent> \- exponent 'n' to use in (area / (distance ^ n)) as the
.IP
weighting function (default 2)
.PP
\fB\-metric\-estimate\-fwhm\fR
ESTIMATE FWHM SMOOTHNESS OF A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-estimate\-fwhm\fR
.IP
<surface>
<metric\-in>
[\-roi]
.IP
<roi\-metric>
.IP
[\-column]
.IP
<column>
.IP
Estimates the smoothness of the metric columns, printing the estimates to
standard output.  These estimates ignore variation in vertex spacing.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to use for distance and neighbor information
<metric\-in> \- the input metric
.IP
[\-roi] \- use only data within an ROI
.IP
<roi\-metric> \- the metric file to use as an ROI
.IP
[\-column] \- select a single column to estimate smoothness of
.IP
<column> \- the column number or name
.PP
\fB\-metric\-extrema\fR
FIND EXTREMA IN A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-extrema\fR
.IP
<surface>
<metric\-in>
<distance>
<metric\-out>
[\-presmooth]
.IP
<kernel>
.IP
[\-roi]
.IP
<roi\-metric>
.IP
[\-threshold]
.IP
<low>
<high>
.IP
[\-sum\-columns]
[\-consolidate\-mode]
[\-only\-maxima]
[\-only\-minima]
[\-column]
.IP
<column>
.IP
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 \fB\-1\fR for
minima, 1 for maxima, 0 otherwise.  If \fB\-only\-maxima\fR or \fB\-only\-minima\fR is
specified, then it will ignore extrema not of the specified type.  These
options are mutually exclusive.
.IP
If \fB\-roi\fR 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.
.IP
If \fB\-sum\-columns\fR is specified, these extrema columns are summed, and the
output has a single column with this result.
.IP
By default, a datapoint is an extrema only if it is more extreme than
every other datapoint that is within <distance> from it.  If
\fB\-consolidate\-mode\fR 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.
.IP
By default, all input columns are used with no smoothing, use \fB\-column\fR to
specify a single column to use, and \fB\-presmooth\fR to smooth the input before
finding the extrema.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
type
.IP
<metric\-out> \- output \- the output extrema metric
.IP
[\-presmooth] \- smooth the metric before finding extrema
.IP
<kernel> \- the sigma for the gaussian smoothing kernel, in mm
.IP
[\-roi] \- ignore values outside the selected area
.IP
<roi\-metric> \- the area to find extrema in, as a metric
.IP
[\-threshold] \- ignore small extrema
.IP
<low> \- the largest value to consider for being a minimum
<high> \- the smallest value to consider for being a maximum
.IP
[\-sum\-columns] \- output the sum of the extrema columns instead of each
.IP
column separately
.IP
[\-consolidate\-mode] \- use consolidation of local minima instead of a
.IP
large neighborhood
.IP
[\-only\-maxima] \- only find the maxima
.IP
[\-only\-minima] \- only find the minima
.IP
[\-column] \- select a single column to find extrema in
.IP
<column> \- the column number or name
.PP
\fB\-metric\-false\-correlation\fR
COMPARE CORRELATION LOCALLY AND ACROSS/THROUGH SULCI/GYRI
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-false\-correlation\fR
.IP
<surface>
<metric\-in>
<3D\-dist>
<geo\-outer>
<geo\-inner>
<metric\-out>
[\-roi]
.IP
<roi\-metric>
.IP
[\-dump\-text]
.IP
<text\-out>
.TP
This is where you set the help text.
DO NOT add the info about what the
.IP
command line format is, and do not give the command switch, short
description, or the short descriptions of parameters.  Do not indent, add
newlines, or format the text in any way other than to separate paragraphs
within the help text prose.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
correlation
.IP
<geo\-inner> \- minimum geodesic distance to use for neighboring
.IP
correlation
.IP
<metric\-out> \- output \- the output metric
.IP
[\-roi] \- select a region of interest that has data
.IP
<roi\-metric> \- the region, as a metric file
.IP
[\-dump\-text] \- dump the raw measures used to a text file
.IP
<text\-out> \- the output text file
.PP
\fB\-metric\-fill\-holes\fR
FILL HOLES IN AN ROI METRIC
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-fill\-holes\fR
.IP
<surface>
<metric\-in>
<metric\-out>
.IP
Finds all connected areas that are not included in the ROI, and fills all
but the largest one with ones.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to use for neighbor information
<metric\-in> \- the input ROI metric
<metric\-out> \- output \- the output ROI metric
.PP
\fB\-metric\-find\-clusters\fR
FILTER CLUSTERS BY SURFACE AREA
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-find\-clusters\fR
.IP
<surface>
<metric\-in>
<value\-threshold>
<minimum\-area>
<metric\-out>
[\-less\-than]
[\-roi]
.IP
<roi\-metric>
.IP
[\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-column]
.IP
<column>
.IP
[\-start]
.IP
<startval>
.IP
Outputs a metric with cluster labels for all vertices within a large
enough cluster, and zeros elsewhere.  By default, values greater than
<value\-threshold> are considered to be in a cluster, use \fB\-less\-than\fR to
test for values less than the threshold.  To apply this as a mask to the
data, or to do more complicated thresholding, see \fB\-metric\-math\fR.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-less\-than] \- find values less than <value\-threshold>, rather than
.IP
greater
.IP
[\-roi] \- select a region of interest
.IP
<roi\-metric> \- the roi, as a metric
.IP
[\-corrected\-areas] \- vertex areas to use instead of computing them from
.IP
the surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.IP
[\-start] \- start labeling clusters from a value other than 1
.IP
<startval> \- the value to give the first cluster found
.PP
\fB\-metric\-gradient\fR
SURFACE GRADIENT OF A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-gradient\fR
.IP
<surface>
<metric\-in>
<metric\-out>
[\-presmooth]
.IP
<kernel>
.IP
[\-roi]
.IP
<roi\-metric>
[\-match\-columns]
.IP
[\-vectors]
.IP
<vector\-metric\-out>
.IP
[\-column]
.IP
<column>
.IP
[\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-average\-normals]
.IP
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.
.IP
When using \fB\-corrected\-areas\fR, 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.
.IP
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.
.IP
By default, the first column of the roi metric is used for all input
columns.  When \fB\-match\-columns\fR is specified to the \fB\-roi\fR 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
\fB\-match\-columns\fR option to \fB\-roi\fR is used while the \fB\-column\fR 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.
.IP
The vector output metric is organized such that the X, Y, and Z
components from a single input column are consecutive columns.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-presmooth] \- smooth the metric before computing the gradient
.IP
<kernel> \- the sigma for the gaussian smoothing kernel, in mm
.IP
[\-roi] \- select a region of interest to take the gradient of
.IP
<roi\-metric> \- the area to take the gradient within, as a metric
.IP
[\-match\-columns] \- for each input column, use the corresponding column
.IP
from the roi
.IP
[\-vectors] \- output vectors
.IP
<vector\-metric\-out> \- output \- the vectors as a metric file
.IP
[\-column] \- select a single column to compute the gradient of
.IP
<column> \- the column number or name
.IP
[\-corrected\-areas] \- vertex areas to use instead of computing them from
.IP
the surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-average\-normals] \- average the normals of each vertex with its
.IP
neighbors before using them to compute the gradient
.PP
\fB\-metric\-label\-import\fR
IMPORT A GIFTI LABEL FILE FROM A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-label\-import\fR
.IP
<input>
<label\-list\-file>
<output>
[\-discard\-others]
[\-unlabeled\-value]
.IP
<value>
.IP
[\-column]
.IP
<column>
.IP
[\-drop\-unused\-labels]
.IP
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:
.IP
<labelname>
<value> <red> <green> <blue> <alpha>
.IP
Do not specify the "unlabeled" key in the file, it is assumed that 0
means not labeled unless \fB\-unlabeled\-value\fR 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 \fB\-discard\-others\fR to instead set these voxels to the
"unlabeled" key.
.IP
Descriptions of parameters and options:
.IP
<input> \- the input metric file
<label\-list\-file> \- text file containing the values and names for labels
<output> \- output \- the output gifti label file
.IP
[\-discard\-others] \- set any values not mentioned in the label list to the
.IP
??? label
.IP
[\-unlabeled\-value] \- set the value that will be interpreted as unlabeled
.IP
<value> \- the numeric value for unlabeled (default 0)
.IP
[\-column] \- select a single column to import
.IP
<column> \- the column number or name
.IP
[\-drop\-unused\-labels] \- remove any unused label values from the label
.IP
table
.PP
\fB\-metric\-mask\fR
MASK A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-mask\fR
.IP
<metric>
<mask>
<metric\-out>
[\-column]
.IP
<column>
.IP
By default, the output metric is a copy of the input metric, but with
zeros wherever the mask metric is not positive.  if \fB\-column\fR is specified,
the output contains only one column, the masked version of the specified
input column.
.IP
Descriptions of parameters and options:
.IP
<metric> \- the input metric
<mask> \- the mask metric
<metric\-out> \- output \- the output metric
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.PP
\fB\-metric\-math\fR
EVALUATE EXPRESSION ON METRIC FILES
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-math\fR
.IP
<expression>
<metric\-out>
[\-fixnan]
.IP
<replace>
.IP
[\-var] (repeatable)
.IP
<name>
<metric>
[\-column]
.IP
<column>
.IP
[\-repeat]
.IP
This command evaluates <expression> at each surface vertex independently.
There must be at least one \fB\-var\fR 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 \fB\-var\fR option with matching <name> to specify an input file.  If the
\fB\-column\fR option is given to any \fB\-var\fR option, only one column is used from
that file.  If \fB\-repeat\fR is specified, the file must either have only one
column, or have the \fB\-column\fR option specified.  All files that don't use
\fB\-repeat\fR must have the same number of columns requested to be used.  The
format of <expression> is as follows:
.IP
Expressions consist of constants, variables, operators, parentheses, and
functions, in infix notation, such as 'exp(\fB\-x\fR + 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 the rest.  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.
.IP
Comparison operators return 0 or 1, you can do masking with expressions
like 'x * (mask > 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 '(x > 0) * (x < 5)' to
get the desired behavior.
.IP
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, use '2 *
x'.  Parentheses are (), do not use [] or {}.  Functions require
parentheses, the expression 'sin x' is an error.
.IP
The following functions are supported:
.IP
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
.IP
(y/x), in radians, determining quadrant by the sign of both arguments
.IP
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 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
.IP
zero
.IP
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)
.IP
Descriptions of parameters and options:
.IP
<expression> \- the expression to evaluate, in quotes
<metric\-out> \- output \- the output metric
.IP
[\-fixnan] \- replace NaN results with a value
.IP
<replace> \- value to replace NaN with
.IP
[\-var] \- repeatable \- a metric to use as a variable
.IP
<name> \- the name of the variable, as used in the expression
<metric> \- the metric file to use as this variable
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.IP
[\-repeat] \- reuse a single column for each column of calculation
.PP
\fB\-metric\-merge\fR
MERGE METRIC FILES INTO A NEW FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-merge\fR
.IP
<metric\-out>
[\-metric] (repeatable)
.IP
<metric\-in>
[\-column] (repeatable)
.IP
<column>
[\-up\-to]
.IP
<last\-column>
[\-reverse]
.IP
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.
.IP
Example: wb_command \fB\-metric\-merge\fR out.func.gii \fB\-metric\fR first.func.gii
\fB\-column\fR 1 \fB\-metric\fR second.func.gii
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<metric\-out> \- output \- the output metric
.IP
[\-metric] \- repeatable \- specify an input metric
.IP
<metric\-in> \- a metric file to use columns from
.IP
[\-column] \- repeatable \- select a single column to use
.IP
<column> \- the column number or name
.IP
[\-up\-to] \- use an inclusive range of columns
.IP
<last\-column> \- the number or name of the last column to include
.IP
[\-reverse] \- use the range in reverse order
.PP
\fB\-metric\-palette\fR
SET THE PALETTE OF A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-palette\fR
.IP
<metric>
<mode>
[\-column]
.IP
<column>
.IP
[\-pos\-percent]
.IP
<pos\-min\-%>
<pos\-max\-%>
.IP
[\-neg\-percent]
.IP
<neg\-min\-%>
<neg\-max\-%>
.IP
[\-pos\-user]
.IP
<pos\-min\-user>
<pos\-max\-user>
.IP
[\-neg\-user]
.IP
<neg\-min\-user>
<neg\-max\-user>
.IP
[\-interpolate]
.IP
<interpolate>
.IP
[\-disp\-pos]
.IP
<display>
.IP
[\-disp\-neg]
.IP
<display>
.IP
[\-disp\-zero]
.IP
<display>
.IP
[\-palette\-name]
.IP
<name>
.IP
[\-thresholding]
.IP
<type>
<test>
<min>
<max>
.TP
The original metric file is overwritten with the modified version.
By
.IP
default, all columns of the metric file are adjusted to the new settings,
use the \fB\-column\fR 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:
.IP
MODE_AUTO_SCALE
MODE_AUTO_SCALE_PERCENTAGE
MODE_USER_SCALE
.IP
The <name> argument to \fB\-palette\-name\fR must be one of the following:
.IP
PSYCH
PSYCH\-NO\-NONE
ROY\-BIG
ROY\-BIG\-BL
Orange\-Yellow
Gray_Interp_Positive
Gray_Interp
clear_brain
videen_style
fidl
raich4_clrmid
raich6_clrmid
HSB8_clrmid
RBGYR20
RBGYR20P
POS_NEG
red\-yellow
blue\-lightblue
FSL
power_surf
fsl_red
fsl_green
fsl_blue
fsl_yellow
JET256
.IP
The <type> argument to \fB\-thresholding\fR must be one of the following:
.IP
THRESHOLD_TYPE_OFF
THRESHOLD_TYPE_NORMAL
.IP
The <test> argument to \fB\-thresholding\fR must be one of the following:
.IP
THRESHOLD_TEST_SHOW_OUTSIDE
THRESHOLD_TEST_SHOW_INSIDE
.IP
Descriptions of parameters and options:
.IP
<metric> \- the metric to modify
<mode> \- the mapping mode
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.IP
[\-pos\-percent] \- percentage min/max for positive data coloring
.IP
<pos\-min\-%> \- the percentile for the least positive data
<pos\-max\-%> \- the percentile for the most positive data
.IP
[\-neg\-percent] \- percentage min/max for negative data coloring
.IP
<neg\-min\-%> \- the percentile for the least negative data
<neg\-max\-%> \- the percentile for the most negative data
.IP
[\-pos\-user] \- user min/max values for positive data coloring
.IP
<pos\-min\-user> \- the value for the least positive data
<pos\-max\-user> \- the value for the most positive data
.IP
[\-neg\-user] \- user min/max values for negative data coloring
.IP
<neg\-min\-user> \- the value for the least negative data
<neg\-max\-user> \- the value for the most negative data
.IP
[\-interpolate] \- interpolate colors
.IP
<interpolate> \- boolean, whether to interpolate
.IP
[\-disp\-pos] \- display positive data
.IP
<display> \- boolean, whether to display
.IP
[\-disp\-neg] \- display positive data
.IP
<display> \- boolean, whether to display
.IP
[\-disp\-zero] \- display data closer to zero than the min cutoff
.IP
<display> \- boolean, whether to display
.IP
[\-palette\-name] \- set the palette used
.IP
<name> \- the name of the palette
.IP
[\-thresholding] \- set the thresholding
.IP
<type> \- thresholding setting
<test> \- show values inside or outside thresholds
<min> \- lower threshold
<max> \- upper threshold
.PP
\fB\-metric\-reduce\fR
PERFORM REDUCTION OPERATION ACROSS METRIC COLUMNS
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-reduce\fR
.IP
<metric\-in>
<operation>
<metric\-out>
[\-exclude\-outliers]
.IP
<sigma\-below>
<sigma\-above>
.IP
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:
.IP
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
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
MEDIAN: the median of the data
MODE: the mode of the data
COUNT_NONZERO: the number of nonzero elements in the data
.IP
Descriptions of parameters and options:
.IP
<metric\-in> \- the metric to reduce
<operation> \- the reduction operator to use
<metric\-out> \- output \- the output metric
.IP
[\-exclude\-outliers] \- exclude outliers from each vector by standard
.IP
deviation
<sigma\-below> \- number of standard deviations below the mean to
.IP
include
.IP
<sigma\-above> \- number of standard deviations above the mean to
.IP
include
.PP
\fB\-metric\-regression\fR
REGRESS METRICS OUT OF A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-regression\fR
.IP
<metric\-in>
<metric\-out>
[\-roi]
.IP
<roi\-metric>
.IP
[\-column]
.IP
<column>
.IP
[\-remove] (repeatable)
.IP
<metric>
[\-remove\-column]
.IP
<column>
.IP
[\-keep] (repeatable)
.IP
<metric>
[\-keep\-column]
.IP
<column>
.IP
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
\fB\-remove\fR are multiplied with their respective regressor maps, and these
are subtracted from the input map.
.IP
Descriptions of parameters and options:
.IP
<metric\-in> \- the metric to regress from
<metric\-out> \- output \- the output metric
.IP
[\-roi] \- only regress inside an roi
.IP
<roi\-metric> \- the area to use for regression, as a metric
.IP
[\-column] \- select a single column to regress from
.IP
<column> \- the column number or name
.IP
[\-remove] \- repeatable \- specify a metric to regress out
.IP
<metric> \- the metric file to use
.IP
[\-remove\-column] \- select a column to use, rather than all
.IP
<column> \- the column number or name
.IP
[\-keep] \- repeatable \- specify a metric to include in regression, but not
.IP
remove
<metric> \- the metric file to use
.IP
[\-keep\-column] \- select a column to use, rather than all
.IP
<column> \- the column number or name
.PP
\fB\-metric\-remove\-islands\fR
REMOVE ISLANDS FROM AN ROI METRIC
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-remove\-islands\fR
.IP
<surface>
<metric\-in>
<metric\-out>
.IP
Finds all connected areas in the ROI, and zeros out all but the largest
one.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to use for neighbor information
<metric\-in> \- the input ROI metric
<metric\-out> \- output \- the output ROI metric
.PP
\fB\-metric\-resample\fR
RESAMPLE A METRIC FILE TO A DIFFERENT MESH
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-resample\fR
.IP
<metric\-in>
<current\-sphere>
<new\-sphere>
<method>
<metric\-out>
[\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-area\-metrics]
.IP
<current\-area>
<new\-area>
.IP
[\-current\-roi]
.IP
<roi\-metric>
.IP
[\-valid\-roi\-out]
.IP
<roi\-out>
.IP
[\-largest]
.IP
Resamples a metric file, given two spherical surfaces that are in
register.  If the method does area correction, exactly one of \fB\-area\-surfs\fR
or \fB\-area\-metrics\fR must be specified.
.IP
The \fB\-current\-roi\fR option only masks the input, the output may be slightly
dilated in comparison, consider using \fB\-metric\-mask\fR on the output when
using \fB\-current\-roi\fR.
.IP
The \fB\-largest\fR option results in nearest vertex behavior when used with
BARYCENTRIC, instead of doing a weighted average, it uses the value of
the source vertex that has the largest weight for each target vertex.
This is mainly intended for resampling ROI metrics.
.IP
The <method> argument must be one of the following:
.IP
ADAP_BARY_AREA
BARYCENTRIC
.IP
The ADAP_BARY_AREA method is recommended for ordinary metric data,
because it should use all data while downsampling, unlike BARYCENTRIC.
.IP
Descriptions of parameters and options:
.IP
<metric\-in> \- the metric file to resample
<current\-sphere> \- a sphere surface with the mesh that the metric is
.IP
currently on
.IP
<new\-sphere> \- a sphere surface that is in register with <current\-sphere>
.IP
and has the desired output mesh
.IP
<method> \- the method name
<metric\-out> \- output \- the output metric
.IP
[\-area\-surfs] \- specify surfaces to do vertex area correction based on
.IP
<current\-area> \- a relevant anatomical surface with <current\-sphere>
.IP
mesh
.IP
<new\-area> \- a relevant anatomical surface with <new\-sphere> mesh
.IP
[\-area\-metrics] \- specify vertex area metrics to do area correction based
.IP
on
<current\-area> \- a metric file with vertex areas for <current\-sphere>
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for <new\-sphere> mesh
.IP
[\-current\-roi] \- use an input roi on the current mesh to exclude non\-data
.IP
vertices
<roi\-metric> \- the roi, as a metric file
.IP
[\-valid\-roi\-out] \- output the ROI of vertices that got data from valid
.IP
source vertices
<roi\-out> \- output \- the output roi as a metric
.IP
[\-largest] \- use only the value of the vertex with the largest weight
.PP
\fB\-metric\-rois\-from\-extrema\fR
CREATE METRIC ROI MAPS FROM EXTREMA MAPS
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-rois\-from\-extrema\fR
.IP
<surface>
<metric>
<limit>
<metric\-out>
[\-gaussian]
.IP
<sigma>
.IP
[\-roi]
.IP
<roi\-metric>
.IP
[\-overlap\-logic]
.IP
<method>
.IP
[\-column]
.IP
<column>
.IP
For each nonzero value in each map, make a map with an ROI around that
location.  If the \fB\-gaussian\fR option is specified, then normalized gaussian
kernels are output instead of ROIs.  The <method> argument to
\fB\-overlap\-logic\fR 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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-gaussian] \- generate a gaussian kernel instead of a flat ROI
.IP
<sigma> \- the sigma for the gaussian kernel, in mm
.IP
[\-roi] \- select a region of interest to use
.IP
<roi\-metric> \- the area to use, as a metric
.IP
[\-overlap\-logic] \- how to handle overlapping ROIs, default ALLOW
.IP
<method> \- the method of resolving overlaps
.IP
[\-column] \- select a single input column to use
.IP
<column> \- the column number or name
.PP
\fB\-metric\-rois\-to\-border\fR
DRAW BORDERS AROUND METRIC ROIS
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-rois\-to\-border\fR
.IP
<surface>
<metric>
<class\-name>
<border\-out>
[\-placement]
.IP
<fraction>
.IP
[\-column]
.IP
<column>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-placement] \- set how far along the edge border points are drawn
.IP
<fraction> \- fraction along edge from inside node (default 0.33)
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.PP
\fB\-metric\-smoothing\fR
SMOOTH A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-smoothing\fR
.IP
<surface>
<metric\-in>
<smoothing\-kernel>
<metric\-out>
[\-roi]
.IP
<roi\-metric>
[\-match\-columns]
.IP
[\-fix\-zeros]
[\-column]
.IP
<column>
.IP
[\-corrected\-areas]
.IP
<area\-metric>
.IP
[\-method]
.IP
<method>
.TP
Smooth a metric file on a surface.
By default, smooths all input columns
.IP
on the entire surface, specify \fB\-column\fR to use only one input column, and
\fB\-roi\fR to smooth only where the roi metric is greater than 0, outputting
zeros elsewhere.
.IP
When using \fB\-roi\fR, 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 \fB\-match\-columns\fR is specified to the \fB\-roi\fR
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 \fB\-match\-columns\fR option to \fB\-roi\fR is used while the
\fB\-column\fR 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.
.IP
The \fB\-fix\-zeros\fR 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.
.IP
The \fB\-corrected\-areas\fR 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.
.IP
Valid values for <method> are:
.IP
GEO_GAUSS_AREA \- uses a geodesic gaussian kernel, and normalizes based on
vertex area in order to work more reliably on irregular surfaces
.IP
GEO_GAUSS_EQUAL \- uses a geodesic gaussian kernel, and normalizes
assuming each vertex has equal importance
.IP
GEO_GAUSS \- matches geodesic gaussian smoothing from caret5, but does not
check kernels for having unequal importance
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-roi] \- select a region of interest to smooth
.IP
<roi\-metric> \- the roi to smooth within, as a metric
.IP
[\-match\-columns] \- for each input column, use the corresponding column
.IP
from the roi
.IP
[\-fix\-zeros] \- treat zero values as not being data
.IP
[\-column] \- select a single column to smooth
.IP
<column> \- the column number or name
.IP
[\-corrected\-areas] \- vertex areas to use instead of computing them from
.IP
the surface
<area\-metric> \- the corrected vertex areas, as a metric
.IP
[\-method] \- select smoothing method, default GEO_GAUSS_AREA
.IP
<method> \- the name of the smoothing method
.PP
\fB\-metric\-tfce\fR
DO TFCE ON A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-tfce\fR
.IP
<surface>
<metric\-in>
<metric\-out>
[\-presmooth]
.IP
<kernel>
.IP
[\-roi]
.IP
<roi\-metric>
.IP
[\-parameters]
.IP
<E>
<H>
.IP
[\-column]
.IP
<column>
.IP
[\-corrected\-areas]
.IP
<area\-metric>
.IP
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:
.IP
e(h, p)^E * h^H * dh
.IP
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.
.IP
When using \fB\-presmooth\fR with \fB\-corrected\-areas\fR, 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.
.IP
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
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to compute on
<metric\-in> \- the metric to run TFCE on
<metric\-out> \- output \- the output metric
.IP
[\-presmooth] \- smooth the metric before running TFCE
.IP
<kernel> \- the sigma for the gaussian smoothing kernel, in mm
.IP
[\-roi] \- select a region of interest to run TFCE on
.IP
<roi\-metric> \- the area to run TFCE on, as a metric
.IP
[\-parameters] \- set parameters for TFCE integral
.IP
<E> \- exponent for cluster area (default 1.0)
<H> \- exponent for threshold value (default 2.0)
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.IP
[\-corrected\-areas] \- vertex areas to use instead of computing them from
.IP
the surface
<area\-metric> \- the corrected vertex areas, as a metric
.PP
\fB\-metric\-vertex\-sum\fR
SUM VALUES ACROSS VERTICES IN A METRIC FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-metric\-vertex\-sum\fR
.IP
<metric\-in>
[\-integrate]
.IP
<surface>
.IP
[\-integrate\-metric]
.IP
<area\-metric>
.IP
[\-roi]
.IP
<roi\-metric>
.IP
[\-column]
.IP
<column>
.IP
For each column in <metric\-in>, sum the values across all vertices, then
print the sum on standard output.  \fB\-integrate\fR and \fB\-integrate\-metric\fR
multiply each vertex value by the vertex area before doing the sum.  Only
one of \fB\-integrate\fR and \fB\-integrate\-metric\fR may be specified.  Use \fB\-roi\fR to
only sum within a specific area.  Use \fB\-column\fR to only report for one
column.
.IP
Descriptions of parameters and options:
.IP
<metric\-in> \- the metric to sum
.IP
[\-integrate] \- integrate across a surface, rather than summing
.IP
<surface> \- the surface to integrate on
.IP
[\-integrate\-metric] \- integrate using vertex areas from a metric file
.IP
<area\-metric> \- metric file containing vertex areas
.IP
[\-roi] \- only use data inside an roi
.IP
<roi\-metric> \- the roi, as a metric file
.IP
[\-column] \- select a single column
.IP
<column> \- the column number or name
.PP
\fB\-nifti\-information\fR
DISPLAY INFORMATION ABOUT A NIFTI/CIFTI FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-nifti\-information\fR
.IP
<nifti\-file>
[\-print\-header]
[\-print\-matrix]
[\-print\-xml]
.IP
You must specify at least one \fB\-print\-\fR* option.
.IP
Descriptions of parameters and options:
.IP
<nifti\-file> \- the nifti/cifti file to examine
.IP
[\-print\-header] \- display the header contents
.IP
[\-print\-matrix] \- output the values in the matrix (cifti only)
.IP
[\-print\-xml] \- print the cifti XML (cifti only)
.PP
\fB\-probtrackx\-dot\-convert\fR
CONVERT A .DOT FILE FROM PROBTRACKX TO CIFTI
.IP
debian/tmp/usr/bin/wb_command \fB\-probtrackx\-dot\-convert\fR
.IP
<dot\-file>
<cifti\-out>
[\-row\-voxels]
.IP
<voxel\-list\-file>
<label\-vol>
.IP
[\-row\-surface]
.IP
<roi\-metric>
.IP
[\-row\-cifti]
.IP
<cifti>
<direction>
.IP
[\-col\-voxels]
.IP
<voxel\-list\-file>
<label\-vol>
.IP
[\-col\-surface]
.IP
<roi\-metric>
.IP
[\-col\-cifti]
.IP
<cifti>
<direction>
.IP
[\-transpose]
[\-make\-symmetric]
.IP
NOTE: exactly one \fB\-row\fR option and one \fB\-col\fR option must be used.
.IP
If the input file does not have its indexes sorted in the correct
ordering, this command may take longer than expected.  Specifying
\fB\-transpose\fR 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 \fB\-row\fR option is specified: if \fB\-row\-voxels\fR 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:
.IP
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
.IP
Descriptions of parameters and options:
.IP
<dot\-file> \- input .dot file
<cifti\-out> \- output \- output cifti file
.IP
[\-row\-voxels] \- the output mapping along a row will be voxels
.IP
<voxel\-list\-file> \- a text file containing IJK indices for the voxels
.IP
used
.IP
<label\-vol> \- a label volume with the dimensions and sform used, with
.IP
structure labels
.IP
[\-row\-surface] \- the output mapping along a row will be surface vertices
.IP
<roi\-metric> \- a metric file with positive values on all nodes used
.IP
[\-row\-cifti] \- take the mapping along a row from a cifti file
.IP
<cifti> \- the cifti file to take the mapping from
<direction> \- which dimension to take the mapping along, ROW or COLUMN
.IP
[\-col\-voxels] \- the output mapping along a column will be voxels
.IP
<voxel\-list\-file> \- a text file containing IJK indices for the voxels
.IP
used
.IP
<label\-vol> \- a label volume with the dimensions and sform used, with
.IP
structure labels
.IP
[\-col\-surface] \- the output mapping along a column will be surface
.IP
vertices
<roi\-metric> \- a metric file with positive values on all nodes used
.IP
[\-col\-cifti] \- take the mapping along a column from a cifti file
.IP
<cifti> \- the cifti file to take the mapping from
<direction> \- which dimension to take the mapping along, ROW or COLUMN
.IP
[\-transpose] \- transpose the input matrix
.IP
[\-make\-symmetric] \- transform half\-square input into full matrix output
.PP
\fB\-set\-map\-name\fR
DEPRECATED: use \fB\-set\-map\-names\fR
.IP
debian/tmp/usr/bin/wb_command \fB\-set\-map\-name\fR
.IP
<data\-file>
<index>
<name>
.IP
DEPRECATED: this command will be removed in a future release, use
\fB\-set\-map\-names\fR.
.IP
Sets the name of a map for metric, shape, label, volume, cifti scalar or
cifti label files.
.IP
Descriptions of parameters and options:
.IP
<data\-file> \- the file to set a map name of
<index> \- the map index to set the name of
<name> \- the name to set for the map
.PP
\fB\-set\-map\-names\fR
SET THE NAME OF ONE OR MORE MAPS IN A FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-set\-map\-names\fR
.IP
<data\-file>
[\-map] (repeatable)
.IP
<index>
<new\-name>
.IP
Sets the name of one or more maps for metric, shape, label, volume, cifti
scalar or cifti label files.  The \fB\-map\fR option must be specified at least
once.
.IP
Descriptions of parameters and options:
.IP
<data\-file> \- the file to set the map names of
.IP
[\-map] \- repeatable \- specify a map to set the name of
.IP
<index> \- the map index to change the name of
<new\-name> \- the name to set for the map
.PP
\fB\-set\-structure\fR
SET STRUCTURE OF A DATA FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-set\-structure\fR
.IP
<data\-file>
<structure>
[\-surface\-type]
.IP
<type>
.IP
[\-surface\-secondary\-type]
.IP
<secondary type>
.TP
The existing file is modified and rewritten to the same filename.
Valid
.IP
values for the structure name are:
.IP
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
.IP
Valid names for the surface type are:
.IP
UNKNOWN
RECONSTRUCTION
ANATOMICAL
INFLATED
VERY_INFLATED
SPHERICAL
SEMI_SPHERICAL
ELLIPSOID
FLAT
HULL
.IP
Valid names for the surface secondary type are:
.IP
INVALID
GRAY_WHITE
MIDTHICKNESS
PIAL
.IP
Descriptions of parameters and options:
.IP
<data\-file> \- the file to set the structure of
<structure> \- the structure to set the file to
.IP
[\-surface\-type] \- set the type of a surface (only used if file is a
.IP
surface file)
<type> \- name of surface type
.IP
[\-surface\-secondary\-type] \- set the secondary type of a surface (only
.IP
used if file is a surface file)
<secondary type> \- name of surface secondary type
.PP
\fB\-show\-scene\fR
OFFSCREEN RENDERING OF SCENE TO AN IMAGE FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-show\-scene\fR
.IP
<scene\-file>
<scene\-name\-or\-number>
<image\-file\-name>
<image\-width>
<image\-height>
.IP
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.
.IP
The image format is determined by the image file extension.
Image formats available on this sytem are:
.IP
bmp
ico
jpeg
jpg
png
ppm
tif
tiff
xbm
xpm
.IP
Note: Available image formats may vary by operating system.
.IP
Descriptions of parameters and options:
.IP
<scene\-file> \- scene file
<scene\-name\-or\-number> \- name or number (starting at one) of the scene in
.IP
the scene file
.IP
<image\-file\-name> \- output image file name
<image\-width> \- width of output image(s)
<image\-height> \- height of output image(s)
.PP
\fB\-signed\-distance\-to\-surface\fR
COMPUTE SIGNED DISTANCE FROM ONE SURFACE TO ANOTHER
.IP
debian/tmp/usr/bin/wb_command \fB\-signed\-distance\-to\-surface\fR
.IP
<surface\-comp>
<surface\-ref>
<metric>
[\-winding]
.IP
<method>
.IP
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:
.IP
EVEN_ODD (default)
NEGATIVE
NONZERO
NORMALS
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<surface\-comp> \- the comparison surface to measure the signed distance on
<surface\-ref> \- the reference surface that defines the signed distance
.IP
function
.IP
<metric> \- output \- the output metric
.IP
[\-winding] \- winding method for point inside surface test
.IP
<method> \- name of the method (default EVEN_ODD)
.PP
\fB\-spec\-file\-merge\fR
MERGE TWO SPEC FILES INTO ONE
.IP
debian/tmp/usr/bin/wb_command \fB\-spec\-file\-merge\fR
.IP
<spec\-1>
<spec\-2>
<out\-spec>
.IP
The output spec file contains every file that is in either of the input
spec files.
.IP
Descriptions of parameters and options:
.IP
<spec\-1> \- first spec file to merge
<spec\-2> \- second spec file to merge
<out\-spec> \- output \- output spec file
.PP
\fB\-surface\-affine\-regression\fR
REGRESS THE AFFINE TRANSFORM BETWEEN SURFACES ON THE SAME MESH
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-affine\-regression\fR
.IP
<source>
<target>
<affine\-out>
.IP
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 \fB\-convert\-affine\fR to convert it for use in other software.
.IP
Descriptions of parameters and options:
.IP
<source> \- the surface to warp
<target> \- the surface to match the coordinates of
<affine\-out> \- output \- the output affine file
.PP
\fB\-surface\-apply\-affine\fR
APPLY AFFINE TRANSFORM TO SURFACE FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-apply\-affine\fR
.IP
<in\-surf>
<affine>
<out\-surf>
[\-flirt]
.IP
<source\-volume>
<target\-volume>
.IP
For flirt matrices, you must use the \fB\-flirt\fR option, because flirt
matrices are not a complete description of the coordinate transform they
represent.  If the \fB\-flirt\fR option is not present, the affine must be a
nifti 'world' affine, which can be obtained with the \fB\-convert\-affine\fR
command, or aff_conv from the 4dfp suite.
.IP
Descriptions of parameters and options:
.IP
<in\-surf> \- the surface to transform
<affine> \- the affine file
<out\-surf> \- output \- the output transformed surface
.IP
[\-flirt] \- MUST be used if affine is a flirt affine
.IP
<source\-volume> \- the source volume used when generating the affine
<target\-volume> \- the target volume used when generating the affine
.PP
\fB\-surface\-apply\-warpfield\fR
APPLY WARPFIELD TO SURFACE FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-apply\-warpfield\fR
.IP
<in\-surf>
<warpfield>
<out\-surf>
[\-fnirt]
.IP
<forward\-warp>
.IP
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 \fB\-fnirt\fR option in order to correctly interpret the
displacements in the fnirt warpfield.
.IP
If the \fB\-fnirt\fR option is not present, the warpfield must be a nifti
\&'world' warpfield, which can be obtained with the \fB\-convert\-warpfield\fR
command.
.IP
Descriptions of parameters and options:
.IP
<in\-surf> \- the surface to transform
<warpfield> \- the INVERSE warpfield
<out\-surf> \- output \- the output transformed surface
.IP
[\-fnirt] \- MUST be used if using a fnirt warpfield
.IP
<forward\-warp> \- the forward warpfield
.PP
\fB\-surface\-average\fR
AVERAGE SURFACE FILES TOGETHER
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-average\fR
.IP
<surface\-out>
[\-stddev]
.IP
<stddev\-metric\-out>
.IP
[\-uncertainty]
.IP
<uncert\-metric\-out>
.IP
[\-surf] (repeatable)
.IP
<surface>
.IP
The 3D sample standard deviation is computed as
\&'sqrt(sum(squaredlength(xyz \- mean(xyz)))/(n \- 1))'.
.IP
Uncertainty is a legacy measure used in caret5, and is computed as
\&'sum(length(xyz \- mean(xyz)))/n'.
.IP
Descriptions of parameters and options:
.IP
<surface\-out> \- output \- the output averaged surface
.IP
[\-stddev] \- compute 3D sample standard deviation
.IP
<stddev\-metric\-out> \- output \- the output metric for 3D sample
.IP
standard deviation
.IP
[\-uncertainty] \- compute caret5 'uncertainty'
.IP
<uncert\-metric\-out> \- output \- the output metric for uncertainty
.IP
[\-surf] \- repeatable \- specify a surface to include in the average
.IP
<surface> \- a surface file to average
.PP
\fB\-surface\-closest\-vertex\fR
FIND CLOSEST SURFACE VERTEX TO COORDINATES
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-closest\-vertex\fR
.IP
<surface>
<coord\-list\-file>
<vertex\-list\-out>
.IP
For each coordinate XYZ triple, find the closest vertex in the surface,
and output its vertex number into a text file.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to use
<coord\-list\-file> \- text file with coordinates
<vertex\-list\-out> \- output \- the output text file with vertex numbers
.PP
\fB\-surface\-coordinates\-to\-metric\fR
MAKE METRIC FILE OF SURFACE COORDINATES
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-coordinates\-to\-metric\fR
.IP
<surface>
<metric\-out>
.IP
Puts the coordinates of the surface into a 3\-map metric file, as x, y, z.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to use the coordinates of
<metric\-out> \- output \- the output metric
.PP
\fB\-surface\-cortex\-layer\fR
CREATE SURFACE APPROXIMATING A CORTICAL LAYER
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-cortex\-layer\fR
.IP
<white\-surface>
<pial\-surface>
<location>
<out\-surface>
[\-placement\-out]
.IP
<placement\-metric>
.IP
[\-untwist]
.TP
The input surfaces must have node correspondence.
The output surface is
.IP
generated by placing nodes 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).
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-placement\-out] \- output the placement as a distance fraction from pial
.IP
to white
<placement\-metric> \- output \- output metric
.IP
[\-untwist] \- temporary option for comparing methods, specify to use old
.IP
method
.PP
\fB\-surface\-create\-sphere\fR
GENERATE A SPHERE WITH CONSISTENT VERTEX AREAS
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-create\-sphere\fR
.IP
<num\-vertices>
<sphere\-out>
.IP
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 \fB\-surface\-flip\-lr\fR to generate the other sphere, then
\fB\-set\-structure\fR on each.  For example:
.IP
\f(CW$ wb_command -surface-create-sphere 6000 Sphere.6k.R.surf.gii\fR
.br
\f(CW$ wb_command -surface-flip-lr Sphere.6k.R.surf.gii Sphere.6k.L.surf.gii\fR
.br
\f(CW$ wb_command -set-structure Sphere.6k.R.surf.gii CORTEX_RIGHT\fR
.br
\f(CW$ wb_command -set-structure Sphere.6k.L.surf.gii CORTEX_LEFT\fR
.IP
Descriptions of parameters and options:
.IP
<num\-vertices> \- desired number of vertices
<sphere\-out> \- output \- the output sphere
.PP
\fB\-surface\-cut\-resample\fR
RESAMPLE A CUT SURFACE
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-cut\-resample\fR
.IP
<surface\-in>
<current\-sphere>
<new\-sphere>
<surface\-out>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<surface\-in> \- the surface file to resample
<current\-sphere> \- a sphere surface with the mesh that the input surface
.IP
is currently on
.IP
<new\-sphere> \- a sphere surface that is in register with <current\-sphere>
.IP
and has the desired output mesh
.IP
<surface\-out> \- output \- the output surface file
.PP
\fB\-surface\-distortion\fR
MEASURE DISTORTION BETWEEN SURFACES
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-distortion\fR
.IP
<surface\-reference>
<surface\-distorted>
<metric\-out>
[\-smooth]
.IP
<sigma>
.IP
[\-caret5\-method]
.IP
This command, when not using \fB\-caret5\-method\fR, is equivalent to using
\fB\-surface\-vertex\-areas\fR on each surface, smoothing both output metrics with
the GEO_GAUSS_EQUAL method on the surface they came from if \fB\-smooth\fR is
specified, and then using the formula 'ln(distorted/reference)/ln(2)' on
the smoothed results.
.IP
When using \fB\-caret5\-method\fR, 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.
.IP
Descriptions of parameters and options:
.IP
<surface\-reference> \- the reference surface
<surface\-distorted> \- the distorted surface
<metric\-out> \- output \- the output distortion metric
.IP
[\-smooth] \- smooth the area data
.IP
<sigma> \- the smoothing kernel sigma in mm
.IP
[\-caret5\-method] \- use the surface distortion method from caret5
.PP
\fB\-surface\-flip\-lr\fR
MIRROR A SURFACE THROUGH THE YZ PLANE
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-flip\-lr\fR
.IP
<surface>
<surface\-out>
.IP
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 node 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.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to flip
<surface\-out> \- output \- the output flipped surface
.PP
\fB\-surface\-flip\-normals\fR
FLIP ALL TILES ON A SURFACE
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-flip\-normals\fR
.IP
<surface>
<surface\-out>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to flip the normals of
<surface\-out> \- output \- the output surface
.PP
\fB\-surface\-generate\-inflated\fR
SURFACE GENERATE INFLATED
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-generate\-inflated\fR
.IP
<anatomical\-surface\-in>
<inflated\-surface\-out>
<very\-inflated\-surface\-out>
[\-iterations\-scale]
.IP
<iterations\-scale\-value>
.IP
Generate inflated and very inflated surfaces. The output surfaces are
\&'matched' (have same XYZ range) to the anatomcal surface. In most cases,
an iterations\-scale of 1.0 (default) is sufficient.  However, if the
surface contains a large number of nodes (150,000), try an
iterations\-scale of 2.5.
.IP
Descriptions of parameters and options:
.IP
<anatomical\-surface\-in> \- the anatomical surface
<inflated\-surface\-out> \- output \- the output inflated surface
<very\-inflated\-surface\-out> \- output \- the output very inflated surface
.IP
[\-iterations\-scale] \- optional iterations scaling
.IP
<iterations\-scale\-value> \- iterations\-scale value
.PP
\fB\-surface\-geodesic\-distance\fR
COMPUTE GEODESIC DISTANCE FROM ONE VERTEX TO THE ENTIRE SURFACE
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-geodesic\-distance\fR
.IP
<surface>
<vertex>
<metric\-out>
[\-naive]
[\-limit]
.IP
<limit\-mm>
.IP
Unless \fB\-limit\fR 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 \fB\-1\fR for vertices that the distance was not
computed for.  If \fB\-naive\fR is not specified, it uses not just immediate
neighbors, but also neighbors derived from crawling across pairs of
triangles that share an edge.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to compute on
<vertex> \- the vertex to compute geodesic distance from
<metric\-out> \- output \- the output metric
.IP
[\-naive] \- use only neighbors, don't crawl triangles (not recommended)
.IP
[\-limit] \- stop at a certain distance
.IP
<limit\-mm> \- distance in mm to stop at
.PP
\fB\-surface\-geodesic\-rois\fR
DRAW GEODESIC LIMITED ROIS AT VERTICES
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-geodesic\-rois\fR
.IP
<surface>
<limit>
<vertex\-list\-file>
<metric\-out>
[\-gaussian]
.IP
<sigma>
.IP
[\-overlap\-logic]
.IP
<method>
.IP
[\-names]
.IP
<name\-list\-file>
.IP
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
\fB\-gaussian\fR 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 \fB\-overlap\-logic\fR 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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
around
.IP
<metric\-out> \- output \- the output metric
.IP
[\-gaussian] \- generate a gaussian kernel instead of a flat ROI
.IP
<sigma> \- the sigma for the gaussian kernel, in mm
.IP
[\-overlap\-logic] \- how to handle overlapping ROIs, default ALLOW
.IP
<method> \- the method of resolving overlaps
.IP
[\-names] \- name the columns from text file
.IP
<name\-list\-file> \- a text file containing column names, one per line
.PP
\fB\-surface\-inflation\fR
SURFACE INFLATION
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-inflation\fR
.IP
<anatomical\-surface\-in>
<surface\-in>
<number\-of\-smoothing\-cycles>
<smoothing\-strength>
<smoothing\-iterations>
<inflation\-factor>
<surface\-out>
.IP
Inflate a surface by performing cycles that consist of smoothing
followed by inflation (to correct shrinkage caused by smoothing).
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-surface\-information\fR
DISPLAY INFORMATION ABOUT A SURFACE
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-information\fR
.IP
<Surface File>
.IP
Information about surface is displayed including vertices,
triangles, bounding box, and spacing.
.IP
Descriptions of parameters and options:
.IP
<Surface File> \- Surface for which information is displayed
.PP
\fB\-surface\-match\fR
SURFACE MATCH
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-match\fR
.IP
<Match Surface File>
<Input Surface File>
<Output Surface Name>
.IP
The Input Surface File will be transformed so that its coordinate ranges
(bounding box) match that of the Match Surface File
.IP
Descriptions of parameters and options:
.IP
<Match Surface File> \- Match (Reference) Surface
<Input Surface File> \- File containing surface that will be transformed
<Output Surface Name> \- Surface File after transformation
.PP
\fB\-surface\-modify\-sphere\fR
CHANGE RADIUS AND OPTIONALLY RECENTER A SPHERE
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-modify\-sphere\fR
.IP
<sphere\-in>
<radius>
<sphere\-out>
[\-recenter]
.IP
This command may be useful if you have used \fB\-surface\-resample\fR to resample
a sphere, which can suffer from problems generally not present in
\fB\-surface\-sphere\-project\-unproject\fR.  If the sphere should already be
centered around the origin, using \fB\-recenter\fR may still shift it slightly
before changing the radius, which is likely to be undesireable.
.IP
If <sphere\-in> is not close to spherical, or not centered around the
origin and \fB\-recenter\fR is not used, a warning is printed.
.IP
Descriptions of parameters and options:
.IP
<sphere\-in> \- the sphere to modify
<radius> \- the radius the output sphere should have
<sphere\-out> \- output \- the output sphere
.IP
[\-recenter] \- recenter the sphere by means of the bounding box
.PP
\fB\-surface\-resample\fR
RESAMPLE A SURFACE TO A DIFFERENT MESH
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-resample\fR
.IP
<surface\-in>
<current\-sphere>
<new\-sphere>
<method>
<surface\-out>
[\-area\-surfs]
.IP
<current\-area>
<new\-area>
.IP
[\-area\-metrics]
.IP
<current\-area>
<new\-area>
.IP
Resamples a surface file, given two spherical surfaces that are in
register.  If the method does area correction, exactly one of \fB\-area\-surfs\fR
or \fB\-area\-metrics\fR must be specified.  This option is not used in normal
circumstances, but is provided for completeness.
.IP
The <method> argument must be one of the following:
.IP
ADAP_BARY_AREA
BARYCENTRIC
.IP
The BARYCENTRIC method is recommended for anatomical surfaces, unless
they are fairly rough, in order to minimize smoothing.
.IP
For cut surfaces (including flatmaps), use \fB\-surface\-cut\-resample\fR.
.IP
Instead of resampling a spherical surface, the
\fB\-surface\-sphere\-project\-unproject\fR command is recommended.
.IP
Descriptions of parameters and options:
.IP
<surface\-in> \- the surface file to resample
<current\-sphere> \- a sphere surface with the mesh that the input surface
.IP
is currently on
.IP
<new\-sphere> \- a sphere surface that is in register with <current\-sphere>
.IP
and has the desired output mesh
.IP
<method> \- the method name
<surface\-out> \- output \- the output surface file
.IP
[\-area\-surfs] \- specify surfaces to do vertex area correction based on
.IP
<current\-area> \- a relevant surface with <current\-sphere> mesh
<new\-area> \- a relevant surface with <new\-sphere> mesh
.IP
[\-area\-metrics] \- specify vertex area metrics to do area correction based
.IP
on
<current\-area> \- a metric file with vertex areas for <current\-sphere>
.IP
mesh
.IP
<new\-area> \- a metric file with vertex areas for <new\-sphere> mesh
.PP
\fB\-surface\-smoothing\fR
SURFACE SMOOTHING
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-smoothing\fR
.IP
<surface\-in>
<smoothing\-strength>
<smoothing\-iterations>
<surface\-out>
.IP
Smooths a surface by averaging nodes with their neighbors.
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-surface\-sphere\-project\-unproject\fR
DEFORM A SPHERE ACCORDING TO A REGISTRATION
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-sphere\-project\-unproject\fR
.IP
<sphere\-in>
<sphere\-project\-to>
<sphere\-unproject\-from>
<sphere\-out>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-surface\-to\-surface\-3d\-distance\fR
COMPUTE DISTANCE BETWEEN CORRESPONDING VERTICES
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-to\-surface\-3d\-distance\fR
.IP
<surface\-comp>
<surface\-ref>
<dists\-out>
[\-vectors]
.IP
<vectors\-out>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<surface\-comp> \- the surface to compare to the reference
<surface\-ref> \- the surface to use as the reference
<dists\-out> \- output \- the output distances
.IP
[\-vectors] \- output the displacement vectors
.IP
<vectors\-out> \- output \- the output vectors
.PP
\fB\-surface\-vertex\-areas\fR
MEASURE SURFACE AREA EACH VERTEX IS RESPONSIBLE FOR
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-vertex\-areas\fR
.IP
<surface>
<metric>
.IP
Each vertex gets one third of the area of each triangle it is a part of.
.IP
Descriptions of parameters and options:
.IP
<surface> \- the surface to measure
<metric> \- output \- the output metric
.PP
\fB\-surface\-wedge\-volume\fR
MEASURE PER\-VERTEX VOLUME BETWEEN SURFACES
.IP
debian/tmp/usr/bin/wb_command \fB\-surface\-wedge\-volume\fR
.IP
<inner\-surface>
<outer\-surface>
<metric>
.IP
Compute the volume of each vertex's area from one surface to another.
The surfaces must have node correspondence.
.IP
Descriptions of parameters and options:
.IP
<inner\-surface> \- the inner surface
<outer\-surface> \- the outer surface
<metric> \- output \- the output metric
.PP
\fB\-unit\-test\fR
.PP
\fB\-volume\-affine\-resample\fR
RESAMPLE VOLUME USING AFFINE TRANSFORM
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-affine\-resample\fR
.IP
<volume\-in>
<affine>
<volume\-space>
<method>
<volume\-out>
[\-flirt]
.IP
<source\-volume>
<target\-volume>
.TP
Resample a volume file with an affine transformation.
The parameter
.IP
<method> must be one of:
.IP
CUBIC
ENCLOSING_VOXEL
TRILINEAR
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- volume to resample
<affine> \- the affine file to apply
<volume\-space> \- a volume file in the volume space you want for the
.IP
output
.IP
<method> \- the resampling method
<volume\-out> \- output \- the output volume
.IP
[\-flirt] \- MUST be used if affine is a flirt affine
.IP
<source\-volume> \- the source volume used when generating the affine
<target\-volume> \- the target volume used when generating the affine
.PP
\fB\-volume\-all\-labels\-to\-rois\fR
MAKE ROIS FROM ALL LABELS IN A VOLUME FRAME
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-all\-labels\-to\-rois\fR
.IP
<label\-in>
<map>
<volume\-out>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-volume\-capture\-plane\fR
INTERPOLATE IMAGE FROM PLANE THROUGH VOLUME
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-capture\-plane\fR
.IP
<volume>
<subvolume>
<interp>
<h\-dim>
<v\-dim>
<scale\-min>
<scale\-max>
<bottom\-left\-x>
<bottom\-left\-y>
<bottom\-left\-z>
<bottom\-right\-x>
<bottom\-right\-y>
<bottom\-right\-z>
<top\-left\-x>
<top\-left\-y>
<top\-left\-z>
<image>
.IP
NOTE: If you want to generate an image with all of the capabilities of
the GUI rendering, see \fB\-show\-scene\fR.
.IP
Renders an image of an arbitrary plane through the volume file, with a
simple linear grayscale palette.  The parameter <interp> must be one of:
.IP
CUBIC
ENCLOSING_VOXEL
TRILINEAR
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-volume\-copy\-extensions\fR
COPY EXTENDED DATA TO ANOTHER VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-copy\-extensions\fR
.IP
<data\-volume>
<extension\-volume>
<volume\-out>
[\-drop\-unknown]
.IP
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 \fB\-drop\-unknown\fR is not specified, it
also copies similar kinds of information set by other software.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-drop\-unknown] \- don't copy extensions that workbench doesn't understand
.PP
\fB\-volume\-create\fR
CREATE A BLANK VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-create\fR
.IP
<i\-dim>
<j\-dim>
<k\-dim>
<volume\-out>
[\-plumb]
.IP
<axis\-order>
<x\-spacing>
<y\-spacing>
<z\-spacing>
<x\-offset>
<y\-offset>
<z\-offset>
.IP
[\-sform]
.IP
<xi\-spacing>
<xj\-spacing>
<xk\-spacing>
<x\-offset>
<yi\-spacing>
<yj\-spacing>
<yk\-spacing>
<y\-offset>
<zi\-spacing>
<zj\-spacing>
<zk\-spacing>
<z\-offset>
.TP
Creates a volume file full of zeros.
Exactly one of \fB\-plumb\fR or \fB\-sform\fR
.IP
must be specified.
.IP
Descriptions of parameters and options:
.IP
<i\-dim> \- length of first dimension
<j\-dim> \- length of second dimension
<k\-dim> \- length of third dimension
<volume\-out> \- output \- the output volume
.IP
[\-plumb] \- set via axis order and spacing/offset
.IP
<axis\-order> \- a string like 'XYZ' that specifies which index is along
.IP
which spatial dimension
.IP
<x\-spacing> \- change in x\-coordinate from incrementing the relevant
.IP
index
.IP
<y\-spacing> \- change in y\-coordinate from incrementing the relevant
.IP
index
.IP
<z\-spacing> \- change in z\-coordinate from incrementing the relevant
.IP
index
.IP
<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
.IP
[\-sform] \- set via a nifti sform
.IP
<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
.PP
\fB\-volume\-dilate\fR
DILATE A VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-dilate\fR
.IP
<volume>
<distance>
<method>
<volume\-out>
[\-bad\-voxel\-roi]
.IP
<roi\-volume>
.IP
[\-data\-roi]
.IP
<roi\-volume>
.IP
[\-subvolume]
.IP
<subvol>
.IP
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.
.IP
By default, voxels that have data with the value 0 are bad, specify
\fB\-bad\-voxel\-roi\fR to only count voxels as bad if they are selected by the
roi.  If \fB\-data\-roi\fR is not specified, all voxels are assumed to have data.
.IP
Valid values for <method> are:
.IP
NEAREST \- use the value from the nearest good voxel
WEIGHTED \- use a weighted average based on distance
.IP
Descriptions of parameters and options:
.IP
<volume> \- the volume to dilate
<distance> \- distance in mm to dilate
<method> \- dilation method to use
<volume\-out> \- output \- the output volume
.IP
[\-bad\-voxel\-roi] \- specify an roi of voxels to overwrite, rather than
.IP
voxels with value zero
<roi\-volume> \- volume file, positive values denote voxels to have
.IP
their values replaced
.IP
[\-data\-roi] \- specify an roi of where there is data
.IP
<roi\-volume> \- volume file, positive values denote voxels that have
.IP
data
.IP
[\-subvolume] \- select a single subvolume to dilate
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-estimate\-fwhm\fR
ESTIMATE FWHM SMOOTHNESS OF A VOLUME
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-estimate\-fwhm\fR
.IP
<volume>
[\-roi]
.IP
<roivol>
.IP
[\-subvolume]
.IP
<subvol>
.IP
Estimates the smoothness of the input volume in X, Y, and Z directions
separately, printing the estimates to standard output.  If \fB\-subvolume\fR is
not specified, each subvolume is estimated and displayed separately.
.IP
Descriptions of parameters and options:
.IP
<volume> \- the input volume
.IP
[\-roi] \- use only data within an ROI
.IP
<roivol> \- the volume to use as an ROI
.IP
[\-subvolume] \- select a single subvolume to estimate smoothness of
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-extrema\fR
FIND EXTREMA IN A VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-extrema\fR
.IP
<volume\-in>
<distance>
<volume\-out>
[\-presmooth]
.IP
<kernel>
.IP
[\-roi]
.IP
<roi\-volume>
.IP
[\-threshold]
.IP
<low>
<high>
.IP
[\-sum\-subvols]
[\-consolidate\-mode]
[\-only\-maxima]
[\-only\-minima]
[\-subvolume]
.IP
<subvolume>
.IP
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 \fB\-1\fR for
minima, 1 for maxima, 0 otherwise.  If \fB\-only\-maxima\fR or \fB\-only\-minima\fR is
specified, then it will ignore extrema not of the specified type.  These
options are mutually exclusive.
.IP
If \fB\-sum\-subvols\fR is specified, these extrema subvolumes are summed, and
the output has a single subvolume with this result.
.IP
By default, a datapoint is an extrema only if it is more extreme than
every other datapoint that is within <distance> from it.  If
\fB\-consolidate\-mode\fR 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.
.IP
By default, all input subvolumes are used with no smoothing, use
\fB\-subvolume\fR to specify a single subvolume to use, and \fB\-presmooth\fR to smooth
the input before finding the extrema.
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- volume file to find the extrema of
<distance> \- the minimum distance between identified extrema of the same
.IP
type
.IP
<volume\-out> \- output \- the output extrema volume
.IP
[\-presmooth] \- smooth the volume before finding extrema
.IP
<kernel> \- the sigma for the gaussian smoothing kernel, in mm
.IP
[\-roi] \- ignore values outside the selected area
.IP
<roi\-volume> \- the area to find extrema in
.IP
[\-threshold] \- ignore small extrema
.IP
<low> \- the largest value to consider for being a minimum
<high> \- the smallest value to consider for being a maximum
.IP
[\-sum\-subvols] \- output the sum of the extrema subvolumes instead of each
.IP
subvolume separately
.IP
[\-consolidate\-mode] \- use consolidation of local minima instead of a
.IP
large neighborhood
.IP
[\-only\-maxima] \- only find the maxima
.IP
[\-only\-minima] \- only find the minima
.IP
[\-subvolume] \- select a single subvolume to find extrema in
.IP
<subvolume> \- the subvolume number or name
.PP
\fB\-volume\-fill\-holes\fR
FILL HOLES IN AN ROI VOLUME
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-fill\-holes\fR
.IP
<volume\-in>
<volume\-out>
.IP
Finds all face\-connected parts that are not included in the ROI, and
fills all but the largest one with ones.
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- the input ROI volume
<volume\-out> \- output \- the output ROI volume
.PP
\fB\-volume\-find\-clusters\fR
FILTER CLUSTERS BY VOLUME
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-find\-clusters\fR
.IP
<volume\-in>
<value\-threshold>
<minimum\-volume>
<volume\-out>
[\-less\-than]
[\-roi]
.IP
<roi\-volume>
.IP
[\-subvolume]
.IP
<subvol>
.IP
[\-start]
.IP
<startval>
.IP
Outputs a volume with cluster labels for all voxels within a large enough
cluster, and zeros elsewhere.  By default, values greater than
<value\-threshold> are considered to be in a cluster, use \fB\-less\-than\fR to
test for values less than the threshold.  To apply this as a mask to the
data, or to do more complicated thresholding, see \fB\-volume\-math\fR.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-less\-than] \- find values less than <value\-threshold>, rather than
.IP
greater
.IP
[\-roi] \- select a region of interest
.IP
<roi\-volume> \- the roi, as a volume file
.IP
[\-subvolume] \- select a single subvolume
.IP
<subvol> \- the subvolume number or name
.IP
[\-start] \- start labeling clusters from a value other than 1
.IP
<startval> \- the value to give the first cluster found
.PP
\fB\-volume\-gradient\fR
GRADIENT OF A VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-gradient\fR
.IP
<volume\-in>
<volume\-out>
[\-presmooth]
.IP
<kernel>
.IP
[\-roi]
.IP
<roi\-volume>
.IP
[\-vectors]
.IP
<vector\-volume\-out>
.IP
[\-subvolume]
.IP
<subvol>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- the input volume
<volume\-out> \- output \- the output gradient magnitude volume
.IP
[\-presmooth] \- smooth the volume before computing the gradient
.IP
<kernel> \- sigma for gaussian weighting function, in mm
.IP
[\-roi] \- select a region of interest to take the gradient of
.IP
<roi\-volume> \- the region to take the gradient within
.IP
[\-vectors] \- output vectors
.IP
<vector\-volume\-out> \- output \- the vectors as a volume file
.IP
[\-subvolume] \- select a single subvolume to take the gradient of
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-label\-export\-table\fR
EXPORT LABEL TABLE FROM VOLUME AS TEXT
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-label\-export\-table\fR
.IP
<label\-in>
<map>
<table\-out>
.IP
Takes the label table from the volume label map, and writes it to a text
format matching what is expected by \fB\-volume\-label\-import\fR.
.IP
Descriptions of parameters and options:
.IP
<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
.PP
\fB\-volume\-label\-import\fR
IMPORT A LABEL VOLUME TO CARET FORMAT
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-label\-import\fR
.IP
<input>
<label\-list\-file>
<output>
[\-discard\-others]
[\-unlabeled\-value]
.IP
<value>
.IP
[\-subvolume]
.IP
<subvol>
.IP
[\-drop\-unused\-labels]
.IP
Creates a new volume with label information in the header in the caret
nifti extension format.  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:
.IP
<labelname>
<value> <red> <green> <blue> <alpha>
.IP
Do not specify the "unlabeled" key in the file, it is assumed that 0
means not labeled unless \fB\-unlabeled\-value\fR 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 \fB\-discard\-others\fR to instead set these voxels to the
"unlabeled" key.
.IP
Descriptions of parameters and options:
.IP
<input> \- the label volume to import
<label\-list\-file> \- text file containing the values and names for labels
<output> \- output \- the output workbench label volume
.IP
[\-discard\-others] \- set any voxels with values not mentioned in the label
.IP
list to the ??? label
.IP
[\-unlabeled\-value] \- set the value that will be interpreted as unlabeled
.IP
<value> \- the numeric value for unlabeled (default 0)
.IP
[\-subvolume] \- select a single subvolume to import
.IP
<subvol> \- the subvolume number or name
.IP
[\-drop\-unused\-labels] \- remove any unused label values from the label
.IP
table
.PP
\fB\-volume\-label\-to\-roi\fR
MAKE A VOLUME LABEL INTO AN ROI VOLUME
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-label\-to\-roi\fR
.IP
<label\-in>
<volume\-out>
[\-name]
.IP
<label\-name>
.IP
[\-key]
.IP
<label\-key>
.IP
[\-map]
.IP
<map>
.IP
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
\fB\-name\fR and \fB\-key\fR must be specified.  Specify \fB\-map\fR to use only one map from
<label\-in>.
.IP
Descriptions of parameters and options:
.IP
<label\-in> \- the input volume label file
<volume\-out> \- output \- the output volume file
.IP
[\-name] \- select label by name
.IP
<label\-name> \- the label name that you want an roi of
.IP
[\-key] \- select label by key
.IP
<label\-key> \- the label key that you want an roi of
.IP
[\-map] \- select a single label map to use
.IP
<map> \- the map number or name
.PP
\fB\-volume\-label\-to\-surface\-mapping\fR
MAP A LABEL VOLUME TO A SURFACE LABEL FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-label\-to\-surface\-mapping\fR
.IP
<volume>
<surface>
<label\-out>
[\-subvol\-select]
.IP
<subvol>
.IP
Uses the enclosing voxel mapping method to map label data to a gifti
label file.
.IP
Descriptions of parameters and options:
.IP
<volume> \- the volume to map data from
<surface> \- the surface to map the data onto
<label\-out> \- output \- the output gifti label file
.IP
[\-subvol\-select] \- select a single subvolume to map
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-math\fR
EVALUATE EXPRESSION ON VOLUME FILES
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-math\fR
.IP
<expression>
<volume\-out>
[\-fixnan]
.IP
<replace>
.IP
[\-var] (repeatable)
.IP
<name>
<volume>
[\-subvolume]
.IP
<subvol>
.IP
[\-repeat]
.TP
This command evaluates <expression> at each voxel independently.
There
.IP
must be at least one \fB\-var\fR 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 \fB\-var\fR option with matching <name> to specify an
input file.  If the \fB\-subvolume\fR option is given to any \fB\-var\fR option, only
one subvolume is used from that file.  If \fB\-repeat\fR is specified, the file
must either have only one subvolume, or have the \fB\-subvolume\fR option
specified.  All files that don't use \fB\-repeat\fR must have the same number of
subvolumes requested to be used.  The format of <expression> is as
follows:
.IP
Expressions consist of constants, variables, operators, parentheses, and
functions, in infix notation, such as 'exp(\fB\-x\fR + 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 the rest.  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.
.IP
Comparison operators return 0 or 1, you can do masking with expressions
like 'x * (mask > 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 '(x > 0) * (x < 5)' to
get the desired behavior.
.IP
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, use '2 *
x'.  Parentheses are (), do not use [] or {}.  Functions require
parentheses, the expression 'sin x' is an error.
.IP
The following functions are supported:
.IP
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
.IP
(y/x), in radians, determining quadrant by the sign of both arguments
.IP
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 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
.IP
zero
.IP
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)
.IP
Descriptions of parameters and options:
.IP
<expression> \- the expression to evaluate, in quotes
<volume\-out> \- output \- the output volume
.IP
[\-fixnan] \- replace NaN results with a value
.IP
<replace> \- value to replace NaN with
.IP
[\-var] \- repeatable \- a volume file to use as a variable
.IP
<name> \- the name of the variable, as used in the expression
<volume> \- the volume file to use as this variable
.IP
[\-subvolume] \- select a single subvolume
.IP
<subvol> \- the subvolume number or name
.IP
[\-repeat] \- reuse a single subvolume for each subvolume of calculation
.PP
\fB\-volume\-merge\fR
MERGE VOLUME FILES INTO A NEW FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-merge\fR
.IP
<volume\-out>
[\-volume] (repeatable)
.IP
<volume\-in>
[\-subvolume] (repeatable)
.IP
<subvol>
[\-up\-to]
.IP
<last\-subvol>
[\-reverse]
.IP
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.
.IP
Example: wb_command \fB\-volume\-merge\fR out.nii \fB\-volume\fR first.nii \fB\-subvolume\fR 1
\fB\-volume\fR second.nii
.IP
This example would take the first subvolume from first.nii, followed by
all subvolumes from second.nii, and write these to out.nii.
.IP
Descriptions of parameters and options:
.IP
<volume\-out> \- output \- the output volume file
.IP
[\-volume] \- repeatable \- specify an input volume file
.IP
<volume\-in> \- a volume file to use subvolumes from
.IP
[\-subvolume] \- repeatable \- select a single subvolume to use
.IP
<subvol> \- the subvolume number or name
.IP
[\-up\-to] \- use an inclusive range of subvolumes
.IP
<last\-subvol> \- the number or name of the last subvolume to
.IP
include
.IP
[\-reverse] \- use the range in reverse order
.PP
\fB\-volume\-palette\fR
SET THE PALETTE OF A VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-palette\fR
.IP
<volume>
<mode>
[\-subvolume]
.IP
<subvolume>
.IP
[\-pos\-percent]
.IP
<pos\-min\-%>
<pos\-max\-%>
.IP
[\-neg\-percent]
.IP
<neg\-min\-%>
<neg\-max\-%>
.IP
[\-pos\-user]
.IP
<pos\-min\-user>
<pos\-max\-user>
.IP
[\-neg\-user]
.IP
<neg\-min\-user>
<neg\-max\-user>
.IP
[\-interpolate]
.IP
<interpolate>
.IP
[\-disp\-pos]
.IP
<display>
.IP
[\-disp\-neg]
.IP
<display>
.IP
[\-disp\-zero]
.IP
<display>
.IP
[\-palette\-name]
.IP
<name>
.IP
[\-thresholding]
.IP
<type>
<test>
<min>
<max>
.TP
The original volume file is overwritten with the modified version.
By
.IP
default, all columns of the volume file are adjusted to the new settings,
use the \fB\-subvolume\fR 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:
.IP
MODE_AUTO_SCALE
MODE_AUTO_SCALE_PERCENTAGE
MODE_USER_SCALE
.IP
The <name> argument to \fB\-palette\-name\fR must be one of the following:
.IP
PSYCH
PSYCH\-NO\-NONE
ROY\-BIG
ROY\-BIG\-BL
Orange\-Yellow
Gray_Interp_Positive
Gray_Interp
clear_brain
videen_style
fidl
raich4_clrmid
raich6_clrmid
HSB8_clrmid
RBGYR20
RBGYR20P
POS_NEG
red\-yellow
blue\-lightblue
FSL
power_surf
fsl_red
fsl_green
fsl_blue
fsl_yellow
JET256
.IP
The <type> argument to \fB\-thresholding\fR must be one of the following:
.IP
THRESHOLD_TYPE_OFF
THRESHOLD_TYPE_NORMAL
.IP
The <test> argument to \fB\-thresholding\fR must be one of the following:
.IP
THRESHOLD_TEST_SHOW_OUTSIDE
THRESHOLD_TEST_SHOW_INSIDE
.IP
Descriptions of parameters and options:
.IP
<volume> \- the volume file to modify
<mode> \- the mapping mode
.IP
[\-subvolume] \- select a single subvolume
.IP
<subvolume> \- the subvolume number or name
.IP
[\-pos\-percent] \- percentage min/max for positive data coloring
.IP
<pos\-min\-%> \- the percentile for the least positive data
<pos\-max\-%> \- the percentile for the most positive data
.IP
[\-neg\-percent] \- percentage min/max for negative data coloring
.IP
<neg\-min\-%> \- the percentile for the least negative data
<neg\-max\-%> \- the percentile for the most negative data
.IP
[\-pos\-user] \- user min/max values for positive data coloring
.IP
<pos\-min\-user> \- the value for the least positive data
<pos\-max\-user> \- the value for the most positive data
.IP
[\-neg\-user] \- user min/max values for negative data coloring
.IP
<neg\-min\-user> \- the value for the least negative data
<neg\-max\-user> \- the value for the most negative data
.IP
[\-interpolate] \- interpolate colors
.IP
<interpolate> \- boolean, whether to interpolate
.IP
[\-disp\-pos] \- display positive data
.IP
<display> \- boolean, whether to display
.IP
[\-disp\-neg] \- display positive data
.IP
<display> \- boolean, whether to display
.IP
[\-disp\-zero] \- display data closer to zero than the min cutoff
.IP
<display> \- boolean, whether to display
.IP
[\-palette\-name] \- set the palette used
.IP
<name> \- the name of the palette
.IP
[\-thresholding] \- set the thresholding
.IP
<type> \- thresholding setting
<test> \- show values inside or outside thresholds
<min> \- lower threshold
<max> \- upper threshold
.PP
\fB\-volume\-parcel\-resampling\fR
SMOOTH AND RESAMPLE VOLUME PARCELS
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-parcel\-resampling\fR
.IP
<volume\-in>
<cur\-parcels>
<new\-parcels>
<kernel>
<volume\-out>
[\-fix\-zeros]
[\-subvolume]
.IP
<subvol>
.IP
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 \fB\-fix\-zeros\fR 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.
.TP
Note: all volumes must have the same dimensions and spacing.
To use a
.IP
different output space, see \fB\-volume\-parcel\-resampling\-generic\fR.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-fix\-zeros] \- treat zero values as not being data
.IP
[\-subvolume] \- select a single subvolume as input
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-parcel\-resampling\-generic\fR
SMOOTH AND RESAMPLE VOLUME PARCELS FROM DIFFERENT VOLUME SPACE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-parcel\-resampling\-generic\fR
.IP
<volume\-in>
<cur\-parcels>
<new\-parcels>
<kernel>
<volume\-out>
[\-fix\-zeros]
[\-subvolume]
.IP
<subvol>
.IP
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 \fB\-fix\-zeros\fR 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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-fix\-zeros] \- treat zero values as not being data
.IP
[\-subvolume] \- select a single subvolume as input
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-parcel\-smoothing\fR
SMOOTH PARCELS IN A VOLUME SEPARATELY
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-parcel\-smoothing\fR
.IP
<data\-volume>
<label\-volume>
<kernel>
<volume\-out>
[\-fix\-zeros]
[\-subvolume]
.IP
<subvol>
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<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
.IP
[\-fix\-zeros] \- treat zero values as not being data
.IP
[\-subvolume] \- select a single subvolume to smooth
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-reduce\fR
PERFORM REDUCTION OPERATION ACROSS SUBVOLUMES
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-reduce\fR
.IP
<volume\-in>
<operation>
<volume\-out>
[\-exclude\-outliers]
.IP
<sigma\-below>
<sigma\-above>
.IP
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:
.IP
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
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
MEDIAN: the median of the data
MODE: the mode of the data
COUNT_NONZERO: the number of nonzero elements in the data
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- the volume file to reduce
<operation> \- the reduction operator to use
<volume\-out> \- output \- the output volume
.IP
[\-exclude\-outliers] \- exclude outliers from each timeseries by standard
.IP
deviation
<sigma\-below> \- number of standard deviations below the mean to
.IP
include
.IP
<sigma\-above> \- number of standard deviations above the mean to
.IP
include
.PP
\fB\-volume\-remove\-islands\fR
REMOVE ISLANDS FROM AN ROI VOLUME
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-remove\-islands\fR
.IP
<volume\-in>
<volume\-out>
.IP
Finds all face\-connected parts of the ROI, and zeros out all but the
largest one.
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- the input ROI volume
<volume\-out> \- output \- the output ROI volume
.PP
\fB\-volume\-reorient\fR
CHANGE VOXEL ORDER OF A VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-reorient\fR
.IP
<volume>
<orient\-string>
<volume\-out>
.IP
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:
.TP
L
left to right
.TP
R
right to left
.TP
P
posterior to anterior
.TP
A
anterior to posterior
.TP
I
inferior to superior
.TP
S
superior to inferior
.IP
Descriptions of parameters and options:
.IP
<volume> \- the volume to reorient
<orient\-string> \- the desired orientation
<volume\-out> \- out \- the reoriented volume
.PP
\fB\-volume\-rois\-from\-extrema\fR
CREATE VOLUME ROI MAPS FROM EXTREMA MAPS
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-rois\-from\-extrema\fR
.IP
<volume\-in>
<limit>
<volume\-out>
[\-gaussian]
.IP
<sigma>
.IP
[\-roi]
.IP
<roi\-volume>
.IP
[\-overlap\-logic]
.IP
<method>
.IP
[\-subvolume]
.IP
<subvol>
.IP
For each nonzero value in each map, make a map with an ROI around that
location.  If the \fB\-gaussian\fR option is specified, then normalized gaussian
kernels are output instead of ROIs.  The <method> argument to
\fB\-overlap\-logic\fR 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.
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- the input volume
<limit> \- distance limit from voxel center, in mm
<volume\-out> \- output \- the output volume
.IP
[\-gaussian] \- generate a gaussian kernel instead of a flat ROI
.IP
<sigma> \- the sigma for the gaussian kernel, in mm
.IP
[\-roi] \- select a region of interest to use
.IP
<roi\-volume> \- the region to use
.IP
[\-overlap\-logic] \- how to handle overlapping ROIs, default ALLOW
.IP
<method> \- the method of resolving overlaps
.IP
[\-subvolume] \- select a single subvolume to take the gradient of
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-set\-space\fR
CHANGE VOLUME SPACE INFORMATION
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-set\-space\fR
.IP
<volume\-in>
<volume\-out>
[\-plumb]
.IP
<axis\-order>
<x\-spacing>
<y\-spacing>
<z\-spacing>
<x\-offset>
<y\-offset>
<z\-offset>
.IP
[\-sform]
.IP
<xi\-spacing>
<xj\-spacing>
<xk\-spacing>
<x\-offset>
<yi\-spacing>
<yj\-spacing>
<yk\-spacing>
<y\-offset>
<zi\-spacing>
<zj\-spacing>
<zk\-spacing>
<z\-offset>
.IP
Writes a copy of the volume file, with the spacing information changed as
specified.  No reordering of the voxel data occurs.  Exactly one of
\fB\-plumb\fR or \fB\-sform\fR must be specified.
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- the input volume
<volume\-out> \- output \- the output volume
.IP
[\-plumb] \- set via axis order and spacing/offset
.IP
<axis\-order> \- a string like 'XYZ' that specifies which index is along
.IP
which spatial dimension
.IP
<x\-spacing> \- change in x\-coordinate from incrementing the relevant
.IP
index
.IP
<y\-spacing> \- change in y\-coordinate from incrementing the relevant
.IP
index
.IP
<z\-spacing> \- change in z\-coordinate from incrementing the relevant
.IP
index
.IP
<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
.IP
[\-sform] \- set via a nifti sform
.IP
<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
.PP
\fB\-volume\-smoothing\fR
SMOOTH A VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-smoothing\fR
.IP
<volume\-in>
<kernel>
<volume\-out>
[\-roi]
.IP
<roivol>
.IP
[\-fix\-zeros]
[\-subvolume]
.IP
<subvol>
.TP
Gaussian smoothing for volumes.
By default, smooths all subvolumes with
.IP
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.
.IP
The \fB\-fix\-zeros\fR 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.
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- the volume to smooth
<kernel> \- the gaussian smoothing kernel sigma, in mm
<volume\-out> \- output \- the output volume
.IP
[\-roi] \- smooth only from data within an ROI
.IP
<roivol> \- the volume to use as an ROI
.IP
[\-fix\-zeros] \- treat zero values as not being data
.IP
[\-subvolume] \- select a single subvolume to smooth
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-tfce\fR
DO TFCE ON A VOLUME FILE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-tfce\fR
.IP
<volume\-in>
<volume\-out>
[\-presmooth]
.IP
<kernel>
.IP
[\-roi]
.IP
<roi\-volume>
.IP
[\-parameters]
.IP
<E>
<H>
.IP
[\-subvolume]
.IP
<subvolume>
.IP
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:
.IP
e(h, p)^E * h^H * dh
.IP
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.
.IP
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
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- the volume to run TFCE on
<volume\-out> \- output \- the output volume
.IP
[\-presmooth] \- smooth the volume before running TFCE
.IP
<kernel> \- the sigma for the gaussian smoothing kernel, in mm
.IP
[\-roi] \- select a region of interest to run TFCE on
.IP
<roi\-volume> \- the area to run TFCE on, as a volume
.IP
[\-parameters] \- set parameters for TFCE integral
.IP
<E> \- exponent for cluster volume (default 0.5)
<H> \- exponent for threshold value (default 2.0)
.IP
[\-subvolume] \- select a single subvolume
.IP
<subvolume> \- the subvolume number or name
.PP
\fB\-volume\-to\-surface\-mapping\fR
MAP VOLUME TO SURFACE
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-to\-surface\-mapping\fR
.IP
<volume>
<surface>
<metric\-out>
[\-trilinear]
[\-enclosing]
[\-cubic]
[\-ribbon\-constrained]
.IP
<inner\-surf>
<outer\-surf>
[\-volume\-roi]
.IP
<roi\-volume>
.IP
[\-voxel\-subdiv]
.IP
<subdiv\-num>
.IP
[\-output\-weights]
.IP
<vertex>
<weights\-out>
.IP
[\-myelin\-style]
.IP
<ribbon\-roi>
<thickness>
<sigma>
.IP
[\-subvol\-select]
.IP
<subvol>
.TP
You must specify exactly one mapping method.
Enclosing voxel uses the
.IP
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.
.IP
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.  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.
.IP
The myelin style method uses part of the caret5 myelin mapping command to
do the mapping: for each surface vertex, take all voxels closer than the
thickness at the vertex that are within the ribbon ROI, and less than
half the thickness value away from the vertex along the direction of the
surface normal, and apply a gaussian kernel with the specified sigma to
them to get the weights to use.
.IP
Descriptions of parameters and options:
.IP
<volume> \- the volume to map data from
<surface> \- the surface to map the data onto
<metric\-out> \- output \- the output metric file
.IP
[\-trilinear] \- use trilinear volume interpolation
.IP
[\-enclosing] \- use value of the enclosing voxel
.IP
[\-cubic] \- use cubic splines
.IP
[\-ribbon\-constrained] \- use ribbon constrained mapping algorithm
.IP
<inner\-surf> \- the inner surface of the ribbon
<outer\-surf> \- the outer surface of the ribbon
.IP
[\-volume\-roi] \- use a volume roi
.IP
<roi\-volume> \- the volume file
.IP
[\-voxel\-subdiv] \- voxel divisions while estimating voxel weights
.IP
<subdiv\-num> \- number of subdivisions, default 3
.IP
[\-output\-weights] \- write the voxel weights for a vertex to a volume
.IP
file
<vertex> \- the vertex number to get the voxel weights for, 0\-based
<weights\-out> \- output \- volume to write the weights to
.IP
[\-myelin\-style] \- use the method from myelin mapping
.IP
<ribbon\-roi> \- an roi volume of the cortical ribbon for this
.IP
hemisphere
.IP
<thickness> \- a metric file of cortical thickness
<sigma> \- guassian kernel in mm for weighting voxels within range
.IP
[\-subvol\-select] \- select a single subvolume to map
.IP
<subvol> \- the subvolume number or name
.PP
\fB\-volume\-warpfield\-resample\fR
RESAMPLE VOLUME USING WARPFIELD
.IP
debian/tmp/usr/bin/wb_command \fB\-volume\-warpfield\-resample\fR
.IP
<volume\-in>
<warpfield>
<volume\-space>
<method>
<volume\-out>
[\-fnirt]
.IP
<source\-volume>
.TP
Resample a volume file with a warpfield.
The parameter <method> must be
.IP
one of:
.IP
CUBIC
ENCLOSING_VOXEL
TRILINEAR
.IP
Descriptions of parameters and options:
.IP
<volume\-in> \- volume to resample
<warpfield> \- the warpfield to apply
<volume\-space> \- a volume file in the volume space you want for the
.IP
output
.IP
<method> \- the resampling method
<volume\-out> \- output \- the output volume
.IP
[\-fnirt] \- MUST be used if using a fnirt warpfield
.IP
<source\-volume> \- the source volume used when generating the warpfield
.PP
\fB\-wbsparse\-merge\-dense\fR
MERGE WBSPARSE FILES ALONG DENSE DIMENSION
.IP
debian/tmp/usr/bin/wb_command \fB\-wbsparse\-merge\-dense\fR
.IP
<direction>
<wbsparse\-out>
[\-wbsparse] (repeatable)
.IP
<wbsparse\-in>
.IP
The input wbsparse files must have matching mappings along the direction
not specified, and the mapping along the specified direction must be
brain models.
.IP
Descriptions of parameters and options:
.IP
<direction> \- which dimension to merge along, ROW or COLUMN
<wbsparse\-out> \- output \- the output wbsparse file
.IP
[\-wbsparse] \- repeatable \- specify an input wbsparse file
.IP
<wbsparse\-in> \- a wbsparse file to merge
.PP
\fB\-zip\-scene\-file\fR
ZIP A SCENE FILE AND ITS DATA FILES
.IP
debian/tmp/usr/bin/wb_command \fB\-zip\-scene\-file\fR
.IP
<scene\-file>
<extract\-dir>
<zip\-file>
[\-base\-dir]
.IP
<directory>
.IP
If zip\-file already exists, it will be overwritten.
.IP
Descriptions of parameters and options:
.IP
<scene\-file> \- the scene file to make the zip file from
<extract\-dir> \- the directory created when the zip file is unzipped
<zip\-file> \- out \- the zip file that will be created
.IP
[\-base\-dir] \- specify a directory that all data files are somewhere
.IP
within
<directory> \- the directory that will become the root of the zipfile's
.IP
directory structure
.PP
\fB\-zip\-spec\-file\fR
ZIP A SPEC FILE AND ITS DATA FILES
.IP
debian/tmp/usr/bin/wb_command \fB\-zip\-spec\-file\fR
.IP
<spec\-file>
<extract\-dir>
<zip\-file>
[\-base\-dir]
.IP
<directory>
.TP
If zip\-file already exists, it will be overwritten.
If \fB\-base\-dir\fR is not
.IP
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.
.IP
Descriptions of parameters and options:
.IP
<spec\-file> \- the specification file to add to zip file
<extract\-dir> \- the directory created when the zip file is unzipped
<zip\-file> \- out \- the zip file that will be created
.IP
[\-base\-dir] \- specify a directory that all data files are somewhere
.IP
within
<directory> \- the directory that will become the root of the zipfile's
.IP
directory structure