Provided by: connectome-workbench_1.3.1-1_amd64 bug

NAME

       wb_command  -  command-line  program  for  performing a variety of algorithmic tasks using
       volume, surface, and grayordinate data

SYNOPSIS

       <class-name>

DESCRIPTION

       -add-to-spec-file ADD A FILE TO A SPECIFICATION FILE

              wb_command -add-to-spec-file

              <specfile> - the specification file to add to <structure> - the  structure  of  the
              data file <filename> - the path to the file

       The resulting spec file overwrites the existing spec file.
              If the spec

       file doesn't exist, it is created with default metadata.
              The structure

              argument must be one of the following:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -backend-average-dense-roi CONNECTOME DB BACKEND COMMAND FOR CIFTI AVERAGE DENSE ROI

              wb_command -backend-average-dense-roi

              <index-list>  -  comma separated list of cifti indexes to average <out-file> - file
              to write the average row to

              This   command   is   probably   not   the   one   you   are   looking   for,   try
              -cifti-average-dense-roi.   It  takes  the  list  of  cifti  files  to average from
              standard input, and writes its output as little endian, 32-bit integer of row  size
              followed by the row as 32-bit floats.

       -backend-average-roi-correlation  CONNECTOME  DB  BACKEND  COMMAND  FOR  CIFTI AVERAGE ROI
       CORRELATION

              wb_command -backend-average-roi-correlation

              <index-list> - comma separated list of cifti indexes to average and then

              correlate

              <out-file> - file to write the average row to

              This   command   is   probably   not   the   one   you   are   looking   for,   try
              -cifti-average-roi-correlation.   It  takes the list of cifti files to average from
              standard input, and writes its output as little endian, 32-bit integer of row  size
              followed by the row as 32-bit floats.

       -border-export-color-table WRITE BORDER NAMES AND COLORS AS TEXT

              wb_command -border-export-color-table

              <border-file> - the input border file <table-out> - output - the output text file

              [-class-colors] - use class colors instead of the name colors

              Takes  the  names  and  colors  of each border, and writes it to the same format as
              -metric-label-import expects.  By default, the borders are colored by border  name,
              specify  -class-colors  to  color them by class instead.  The key values start at 1
              and follow the order of the borders in the file.

       -border-file-export-to-caret5 EXPORT BORDER FILE TO CARET5 FILE FORMAT

              wb_command -border-file-export-to-caret5

              <border-file> - workbench border file <output-file-prefix> -  prefix  for  name  of
              output caret5

              border/borderproj/bordercolor files

              [-surface] - repeatable - specify an input surface

              <surface-in> - a surface file for unprojection of borders

              A  Workbench  border  file  may contain borders for multiple structures and borders
              that are both projected and unprojected.  It also contains a color  table  for  the
              borders.

              Caret5  has  both border (unprojected) and border projection (projected) files.  In
              addition, each Caret5 border or border projection file typically contains data  for
              a  single  structure.  Caret5  also uses a border color file that associates colors
              with the names of the borders.

              This command will try to output both Caret5 border  and  border  projection  files.
              Each  output  border/border projection file will contains data for one structure so
              there may be many files created.  The structure name is included  in  the  name  of
              each border or border projection file that is created.

              One Caret5 border color file will also be produced by this command.

              Providing  surface(s)  as  input parameters is optional, but recommended.  Surfaces
              may be needed to create both projected and/or unprojected coordinates  of  borders.
              If  there  is  a  failure to produce an output border or border projection due to a
              missing surface with the matching structure, an error message will be displayed and
              some output files will not be created.

              When writing new files, this command will overwrite a file with the same name.

       -border-length REPORT LENGTH OF BORDERS

              wb_command -border-length

              <border> - the input border file <surface> - the surface to measure the borders on

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

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

              [-separate-pieces] - report lengths for multi-part borders as separate

              numbers

              [-hide-border-name] - don't print border name before each output

       For each border, print its length along the surface, in mm.
              If a border

              has   multiple   parts,   their   lengths   are   summed  before  printing,  unless
              -separate-pieces is specified.

              The -corrected-areas option is intended for when the  length  is  not  meaningfully
              measurable  on  individual  surfaces,  it is only an approximate correction for the
              reduction in structure of a group average surface.

       -border-merge MERGE BORDER FILES INTO A NEW FILE

              wb_command -border-merge

              <border-file-out> - output - the output border file

              [-border] - repeatable - specify an input border file

              <border-file-in> - a border file to use borders from

              [-select] - repeatable - select a single border to use

              <border> - the border number or name

              [-up-to] - use an inclusive range of borders

              <last-border> - the number or name of the last column to include

              [-reverse] - use the range in reverse order

              Takes one or more border files and makes a new border  file  from  the  borders  in
              them.

              Example: wb_command -border-merge out.border -border first.border -select 1 -border
              second.border

              This example would take the first border from first.border, followed by all borders
              from second.border, and write these to out.border.

       -border-resample RESAMPLE A BORDER FILE TO A DIFFERENT MESH

              wb_command -border-resample

              <border-in>  - the border file to resample <current-sphere> - a sphere surface with
              the mesh that the metric is

              currently on

              <new-sphere> - a sphere surface that is in register with <current-sphere>

              and has the desired output mesh

              <border-out> - output - the output border file

              Resamples a border file, given two spherical surfaces that are in  register.   Only
              borders that have the same structure as current-sphere will be resampled.

       -border-to-rois MAKE METRIC ROIS FROM BORDERS

              wb_command -border-to-rois

              <surface>  -  the  surface the borders are drawn on <border-file> - the border file
              <metric-out> - output - the output metric file

              [-border] - create ROI for only one border

              <name> - the name of the border

              [-inverse] - use inverse selection (outside border)

              By default, draws ROIs inside all borders in the border file,  as  separate  metric
              columns.

       -border-to-vertices DRAW BORDERS AS VERTICES IN A METRIC FILE

              wb_command -border-to-vertices

              <surface>  -  the  surface the borders are drawn on <border-file> - the border file
              <metric-out> - output - the output metric file

              [-border] - create ROI for only one border

              <name> - the name of the border

              Outputs a metric with 1s on vertices that follow a border, and  0s  elsewhere.   By
              default, a separate metric column is created for each border.

       -cifti-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A CIFTI LABEL MAP

              wb_command -cifti-all-labels-to-rois

              <label-in> - the input cifti label file <map> - the number or name of the label map
              to use <cifti-out> - output - the output cifti file

              The output cifti file is a dscalar file with a column (map) for each label  in  the
              specified  input map, other than the ??? label, each of which contains a binary ROI
              of all brainordinates that are set to the corresponding label.

              Most of the time, specifying '1' for the <map> argument will do what is desired.

       -cifti-average AVERAGE CIFTI FILES

              wb_command -cifti-average

              <cifti-out> - output - output cifti file

              [-exclude-outliers] - exclude outliers by standard deviation of each

              element across files <sigma-below> - number of standard deviations below  the  mean
              to

              include

              <sigma-above> - number of standard deviations above the mean to

              include

              [-cifti] - repeatable - specify an input file

              <cifti-in> - the input cifti file

              [-weight] - give a weight for this file

              <weight> - the weight to use

       Averages cifti files together.
              Files without -weight specified are given

       a weight of 1.
              If -exclude-outliers is specified, at each element, the

              data  across  all  files is taken as a set, its unweighted mean and sample standard
              deviation are found, and values outside the specified number of standard deviations
              are excluded from the (potentially weighted) average at that element.

       -cifti-average-dense-roi AVERAGE CIFTI ROWS ACROSS SUBJECTS BY ROI

              wb_command -cifti-average-dense-roi

              <cifti-out> - output - output cifti dscalar file

              [-cifti-roi] - cifti file containing combined weights

              <roi-cifti> - the roi cifti file

              [-in-memory] - cache the roi in memory so that it isn't re-read for

              each input cifti

              [-left-roi] - weights to use for left hempsphere

              <roi-metric> - the left roi as a metric file

              [-right-roi] - weights to use for right hempsphere

              <roi-metric> - the right roi as a metric file

              [-cerebellum-roi] - weights to use for cerebellum surface

              <roi-metric> - the cerebellum roi as a metric file

              [-vol-roi] - voxel weights to use

              <roi-vol> - the roi volume file

              [-left-area-surf] - specify the left surface for vertex area correction

              <left-surf> - the left surface file

              [-right-area-surf] - specify the right surface for vertex area correction

              <right-surf> - the right surface file

              [-cerebellum-area-surf] - specify the cerebellum surface for vertex area

              correction <cerebellum-surf> - the cerebellum surface file

              [-cifti] - repeatable - specify an input cifti file

              <cifti-in> - a cifti file to average across

       Averages rows for each map of the ROI(s), across all files.
              ROI maps are

       treated as weighting functions, including negative values.
              For

              efficiency,  ensure  that everything that is not intended to be used is zero in the
              ROI map.  If -cifti-roi is specified, -left-roi, -right-roi,  -cerebellum-roi,  and
              -vol-roi  must  not  be  specified.  If multiple non-cifti ROI files are specified,
              they must have the same number of columns.

       -cifti-average-roi-correlation CORRELATE ROI AVERAGE WITH ALL  ROWS  THEN  AVERAGE  ACROSS
       SUBJECTS

              wb_command -cifti-average-roi-correlation

              <cifti-out> - output - output cifti file

              [-cifti-roi] - cifti file containing combined weights

              <roi-cifti> - the roi cifti file

              [-in-memory] - cache the roi in memory so that it isn't re-read for

              each input cifti

              [-left-roi] - weights to use for left hempsphere

              <roi-metric> - the left roi as a metric file

              [-right-roi] - weights to use for right hempsphere

              <roi-metric> - the right roi as a metric file

              [-cerebellum-roi] - weights to use for cerebellum surface

              <roi-metric> - the cerebellum roi as a metric file

              [-vol-roi] - voxel weights to use

              <roi-vol> - the roi volume file

              [-left-area-surf] - specify the left surface for vertex area correction

              <left-surf> - the left surface file

              [-right-area-surf] - specify the right surface for vertex area correction

              <right-surf> - the right surface file

              [-cerebellum-area-surf] - specify the cerebellum surface for vertex area

              correction <cerebellum-surf> - the cerebellum surface file

              [-cifti] - repeatable - specify an input cifti file

              <cifti-in> - a cifti file to average across

              Averages rows for each map of the ROI(s), takes the correlation of each ROI average
              to the rest of the rows in the same file, then  averages  the  results  across  all
              files.   ROIs are always treated as weighting functions, including negative values.
              For efficiency, ensure that everything that is not intended to be used is  zero  in
              the  ROI  map.  If -cifti-roi is specified, -left-roi, -right-roi, -cerebellum-roi,
              and -vol-roi must not be specified.  If multiple non-cifti ROI files are specified,
              they must have the same number of columns.

       -cifti-change-mapping CONVERT TO SCALAR, COPY MAPPING, ETC

              wb_command -cifti-change-mapping

              <data-cifti> - the cifti file to use the data from <direction> - which direction on
              <data-cifti> to replace the mapping <cifti-out> - output - the output cifti file

              [-series] - set the mapping to series

              <step> - increment between series points <start> - start value of the series

              [-unit] - select unit for series (default SECOND)

              <unit> - unit identifier

              [-scalar] - set the mapping to scalar

              [-name-file] - specify names for the maps

              <file> - text file containing map names, one per line

              [-from-cifti] - copy mapping from another cifti file

              <template-cifti> - a cifti file containing the desired mapping <direction> -  which
              direction to copy the mapping from

       Take an existing cifti file and change one of the mappings.
              Exactly one

       of -series, -scalar, or -from-cifti must be specified.
              The direction can

              be either an integer starting from 1, or the strings 'ROW' or 'COLUMN'.

              The argument to -unit must be one of the following:

              SECOND HERTZ METER RADIAN

       -cifti-convert DUMP CIFTI MATRIX INTO OTHER FORMATS

              wb_command -cifti-convert

              [-to-gifti-ext] - convert to GIFTI external binary

              <cifti-in> - the input cifti file <gifti-out> - output - the output gifti file

              [-from-gifti-ext] - convert a GIFTI made with this command back into a

              CIFTI  <gifti-in>  -  the  input gifti file <cifti-out> - output - the output cifti
              file

              [-reset-timepoints] - reset the mapping along rows to timepoints,

              taking length from the gifti file <timestep> -  the  desired  time  between  frames
              <timestart> - the desired time offset of the initial frame

              [-unit] - use a unit other than time

              <unit> - unit identifier (default SECOND)

              [-reset-scalars] - reset mapping along rows to scalars, taking length

              from the gifti file

              [-replace-binary] - replace data with a binary file

              <binary-in> - the binary file that contains replacement data

              [-flip-endian] - byteswap the binary file

              [-transpose] - transpose the binary file

              [-to-nifti] - convert to NIFTI1

              <cifti-in> - the input cifti file <nifti-out> - output - the output nifti file

              [-smaller-file] - use better-fitting dimension lengths

              [-from-nifti] - convert a NIFTI (1 or 2) file made with this command back

              into  CIFTI  <nifti-in> - the input nifti file <cifti-template> - a cifti file with
              the dimension(s) and mapping(s)

              that should be used

              <cifti-out> - output - the output cifti file

              [-reset-timepoints] - reset the mapping along rows to timepoints,

              taking length from the nifti file <timestep> -  the  desired  time  between  frames
              <timestart> - the desired time offset of the initial frame

              [-unit] - use a unit other than time

              <unit> - unit identifier (default SECOND)

              [-reset-scalars] - reset mapping along rows to scalars, taking length

              from the nifti file

              [-to-text] - convert to a plain text file

              <cifti-in> - the input cifti file <text-out> - output - the output text file

              [-col-delim] - choose string to put between elements in a row

              <delim-string> - the string to use (default is a tab character)

              [-from-text] - convert from plain text to cifti

              <text-in>  -  the  input  text  file  <cifti-template>  -  a  cifti  file  with the
              dimension(s) and mapping(s)

              that should be used

              <cifti-out> - output - the output cifti file

              [-col-delim] - specify string that is between elements in a row

              <delim-string> - the string to use (default is any whitespace)

              [-reset-timepoints] - reset the mapping along rows to timepoints,

              taking length from the text file <timestep>  -  the  desired  time  between  frames
              <timestart> - the desired time offset of the initial frame

              [-unit] - use a unit other than time

              <unit> - unit identifier (default SECOND)

              [-reset-scalars] - reset mapping along rows to scalars, taking length

              from the text file

              This  command  is  used  to convert a full CIFTI matrix to/from formats that can be
              used by programs that don't understand CIFTI.  You  must  specify  exactly  one  of
              -to-gifti-ext, -from-gifti-ext, -to-nifti, -from-nifti, -to-text, or -from-text.

              If  you  want  to  write an existing CIFTI file with a different CIFTI version, see
              -file-convert, and its -cifti-version-convert option.

              If you want part of the CIFTI  file  as  a  metric,  label,  or  volume  file,  see
              -cifti-separate.   If  you  want  to  create a CIFTI file from metric and/or volume
              files, see the -cifti-create-* commands.

              If you want to import a matrix that  is  restricted  to  an  ROI,  first  create  a
              template  CIFTI  file  matching  that  ROI  using a -cifti-create-* command.  After
              importing to CIFTI, you can then expand the file  into  a  standard  brainordinates
              space with -cifti-create-dense-from-template.  If you want to export only part of a
              CIFTI    file,    first    create    an    roi-restricted    CIFTI    file     with
              -cifti-restrict-dense-mapping.

              The  -transpose  option to -from-gifti-ext is needed if the replacement binary file
              is in column-major order.

              The -unit options accept these values:

              SECOND HERTZ METER RADIAN

       -cifti-correlation GENERATE CORRELATION OF ROWS IN A CIFTI FILE

              wb_command -cifti-correlation

              <cifti> - input cifti file <cifti-out> - output - output cifti file

              [-roi-override] - perform correlation from a subset of rows to all rows

              [-left-roi] - use an roi for left hempsphere

              <roi-metric> - the left roi as a metric file

              [-right-roi] - use an roi for right hempsphere

              <roi-metric> - the right roi as a metric file

              [-cerebellum-roi] - use an roi for cerebellum

              <roi-metric> - the cerebellum roi as a metric file

              [-vol-roi] - use an roi for volume

              <roi-vol> - the volume roi file

              [-cifti-roi] - use a cifti file for combined rois

              <roi-cifti> - the cifti roi file

              [-weights] - specify column weights

              <weight-file> - text file containing one weight per column

              [-fisher-z] - apply fisher small z transform (ie, artanh) to correlation

              [-no-demean] - instead of correlation, do dot product of rows, then

              normalize by diagonal

              [-covariance] - compute covariance instead of correlation

              [-mem-limit] - restrict memory usage

              <limit-GB> - memory limit in gigabytes

              For each row (or each row inside an roi if -roi-override is  specified),  correlate
              to  all other rows.  The -cifti-roi suboption to -roi-override may not be specified
              with any other -*-roi suboption, but you may specify the  other  -*-roi  suboptions
              together.

              When  using  the -fisher-z option, the output is NOT a Z-score, it is artanh(r), to
              do further math on this output, consider using -cifti-math.

              Restricting the memory usage will make it calculate the output in  chunks,  and  if
              the input file size is more than 70% of the memory limit, it will also read through
              the input file as rows are required, resulting in several passes through the  input
              file  (once  per chunk).  Memory limit does not need to be an integer, you may also
              specify 0 to calculate a single output row at a time (this may be very slow).

       -cifti-correlation-gradient CORRELATE CIFTI ROWS AND TAKE GRADIENT

              wb_command -cifti-correlation-gradient

              <cifti> - the input cifti <cifti-out> - output - the output cifti

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-left-corrected-areas] - vertex areas to use instead of computing

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

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-right-corrected-areas] - vertex areas to use instead of computing

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

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              [-cerebellum-corrected-areas] - vertex areas to use instead of

              computing them from the cerebellum surface <area-metric>  -  the  corrected  vertex
              areas, as a metric

              [-surface-presmooth] - smooth on the surface before computing the

              gradient <surface-kernel> - the sigma for the gaussian surface smoothing

              kernel, in mm

              [-volume-presmooth] - smooth the volume before computing the gradient

              <volume-kernel> - the sigma for the gaussian volume smoothing kernel,

              in mm

              [-undo-fisher-z] - apply the inverse fisher small z transform to the

              input

              [-fisher-z] - apply the fisher small z transform to the correlations

              before taking the gradient

              [-surface-exclude] - exclude vertices near each seed vertex from

              computation <distance> - geodesic distance from seed vertex for the exclusion

              zone, in mm

              [-volume-exclude] - exclude voxels near each seed voxel from computation

              <distance> - distance from seed voxel for the exclusion zone, in mm

              [-covariance] - compute covariance instead of correlation

              [-mem-limit] - restrict memory usage

              <limit-GB> - memory limit in gigabytes

              For  each structure, compute the correlation of the rows in the structure, and take
              the gradients of the resulting rows, then average them.  Memory limit does not need
              to  be an integer, you may also specify 0 to use as little memory as possible (this
              may be very slow).

       -cifti-create-dense-from-template CREATE CIFTI WITH MATCHING DENSE MAP

              wb_command -cifti-create-dense-from-template

              <template-cifti> - file to match brainordinates  of  <cifti-out>  -  output  -  the
              output cifti file

              [-series] - make a dtseries file instead of a dscalar

              <step> - increment between series points <start> - start value of the series

              [-unit] - select unit for series (default SECOND)

              <unit> - unit identifier

              [-volume-all] - specify an input volume file for all voxel data

              <volume-in> - the input volume file

              [-from-cropped] - the input is cropped to the size of the voxel data

              in the template file

              [-cifti] - repeatable - use input data from a cifti file

              <cifti-in> - cifti file containing input data

              [-metric] - repeatable - use input data from a metric file

              <structure>  -  which  structure  to  put  the metric file into <metric-in> - input
              metric file

              [-label] - repeatable - use input data from surface label files

              <structure> - which structure to put the label file into <label-in> -  input  label
              file

              [-volume] - repeatable - use a volume file for a single volume

              structure's  data  <structure>  -  which  structure  to  put  the  volume file into
              <volume-in> - the input volume file

              [-from-cropped] - the input is cropped to the size of the volume

              structure

              This command helps you make a new dscalar, dtseries,  or  dlabel  cifti  file  that
              matches the brainordinate space used in another cifti file.  The template file must
              have the desired brainordinate space in the mapping along the column direction (for
              dtseries, dscalar, dlabel, and symmetric dconn this is always the case).  All input
              cifti files must have a brain models mapping along column and use the  same  volume
              space and/or surface vertex count as the template for structures that they contain.
              If any input files contain label data, then input files with non-label data are not
              allowed, and the -series option may not be used.

              Any  structure that isn't covered by an input is filled with zeros or the unlabeled
              key.

              The <structure> argument  of  -metric,  -label  or  -volume  must  be  one  of  the
              following:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

              The argument to -unit must be one of the following:

              SECOND HERTZ METER RADIAN

       -cifti-create-dense-scalar CREATE A CIFTI DENSE SCALAR FILE

              wb_command -cifti-create-dense-scalar

              <cifti-out> - output - the output cifti file

              [-volume] - volume component

              <volume-data> - volume file containing all voxel data for all volume

              structures

              <label-volume> - label volume file containing labels for cifti

              structures

              [-left-metric] - metric for left surface

              <metric> - the metric file

              [-roi-left] - roi of vertices to use from left surface

              <roi-metric> - the ROI as a metric file

              [-right-metric] - metric for left surface

              <metric> - the metric file

              [-roi-right] - roi of vertices to use from right surface

              <roi-metric> - the ROI as a metric file

              [-cerebellum-metric] - metric for the cerebellum

              <metric> - the metric file

              [-roi-cerebellum] - roi of vertices to use from right surface

              <roi-metric> - the ROI as a metric file

              [-name-file] - use a text file to set all map names

              <file> - text file containing map names, one per line

       All input files must have the same number of columns/subvolumes.
              Only

       the specified components will be in the output cifti.
              Map names will be

       taken from one of the input files.
              At least one component must be

       specified.
              The label volume should have some of the label names from

              this list, all other label names will be ignored:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -cifti-create-dense-timeseries CREATE A CIFTI DENSE TIMESERIES

              wb_command -cifti-create-dense-timeseries

              <cifti-out> - output - the output cifti file

              [-volume] - volume component

              <volume-data> - volume file containing all voxel data for all volume

              structures

              <label-volume> - label volume file containing labels for cifti

              structures

              [-left-metric] - metric for left surface

              <metric> - the metric file

              [-roi-left] - roi of vertices to use from left surface

              <roi-metric> - the ROI as a metric file

              [-right-metric] - metric for left surface

              <metric> - the metric file

              [-roi-right] - roi of vertices to use from right surface

              <roi-metric> - the ROI as a metric file

              [-cerebellum-metric] - metric for the cerebellum

              <metric> - the metric file

              [-roi-cerebellum] - roi of vertices to use from right surface

              <roi-metric> - the ROI as a metric file

              [-timestep] - set the timestep

              <interval> - the timestep, in seconds (default 1.0)

              [-timestart] - set the start time

              <start> - the time at the first frame, in seconds (default 0.0)

              [-unit] - use a unit other than time

              <unit> - unit identifier (default SECOND)

       All input files must have the same number of columns/subvolumes.
              Only

       the specified components will be in the output cifti.
              At least one

       component must be specified.
              The label volume should have some of the

              label names from this list, all other label names will be ignored:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

              The -unit option accepts these values:

              SECOND HERTZ METER RADIAN

       -cifti-create-label CREATE A CIFTI LABEL FILE

              wb_command -cifti-create-label

              <cifti-out> - output - the output cifti file

              [-volume] - volume component

              <label-volume>  -  volume  file  containing  the label data <parcel-volume> - label
              volume file with cifti structure names to

              define the volume parcels

              [-left-label] - label file for left surface

              <label> - the label file

              [-roi-left] - roi of vertices to use from left surface

              <roi-metric> - the ROI as a metric file

              [-right-label] - label for left surface

              <label> - the label file

              [-roi-right] - roi of vertices to use from right surface

              <roi-metric> - the ROI as a metric file

              [-cerebellum-label] - label for the cerebellum

              <label> - the label file

              [-roi-cerebellum] - roi of vertices to use from right surface

              <roi-metric> - the ROI as a metric file

       All input files must have the same number of columns/subvolumes.
              Only

       the specified components will be in the output cifti.
              At least one

              component must be specified.

              The -volume option  of  -cifti-create-label  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:

              CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT  ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT     CEREBELLAR_WHITE_MATTER_RIGHT      CEREBELLUM_LEFT
              CEREBELLUM_RIGHT   CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT  CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT  INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -cifti-create-parcellated-from-template MATCH PARCELS TO TEMPLATE BY NAME

              wb_command -cifti-create-parcellated-from-template

              <cifti-template> - a cifti file with the template parcel mapping along

              column

              <modify-direction> - which dimension of the output file should match the

              template (integer, 'ROW', or 'COLUMN')

              <cifti-out> - output - the output cifti file

              [-fill-value] - specify value to be used in parcels that don't match

              <value> - value to use (default 0)

              [-cifti] - repeatable - specify an input cifti file

              <cifti-in> - the input parcellated cifti file

              For each parcel name in the template mapping, find that name in an input cifti file
              and  use  its  data  in the output file.  All input cifti files must have a parcels
              mapping along <modify-direction> and matching mappings along other dimensions.  The
              direction  can  be  either  an  integer  starting  from  1, or the strings 'ROW' or
              'COLUMN'.

       -cifti-create-scalar-series IMPORT SERIES DATA INTO CIFTI

              wb_command -cifti-create-scalar-series

              <input> - input file <cifti-out> - output - output cifti file

              [-transpose] - use if the rows of the text file are along the scalar

              dimension

              [-name-file] - use a text file to set names on scalar dimension

              <file> - text file containing names, one per line

              [-series] - set the units and values of the series

              <unit> - the unit to use <start> - the value at the first series point <step> - the
              interval between series points

              Convert  a text file containing series of equal length into a cifti file.  The text
              file should have lines made up of numbers separated by whitespace,  with  no  extra
              newlines between lines.

              The <unit> argument must be one of the following:

              SECOND HERTZ METER RADIAN

       -cifti-cross-correlation CORRELATE A CIFTI FILE WITH ANOTHER CIFTI FILE

              wb_command -cifti-cross-correlation

              <cifti-a>  - first input cifti file <cifti-b> - second input cifti file <cifti-out>
              - output - output cifti file

              [-weights] - specify column weights

              <weight-file> - text file containing one weight per column

              [-fisher-z] - apply fisher small z transform (ie, artanh) to correlation

              [-mem-limit] - restrict memory usage

              <limit-GB> - memory limit in gigabytes

       Correlates every row in <cifti-a> with every row in <cifti-b>.
              The

              mapping along columns in <cifti-b> becomes the mapping along rows in the output.

              When using the -fisher-z option, the output is NOT a Z-score, it is  artanh(r),  to
              do further math on this output, consider using -cifti-math.

              Restricting  the  memory  usage  will  make  it  calculate the output in chunks, by
              reading through <cifti-b> multiple times.

       -cifti-dilate DILATE A CIFTI FILE

              wb_command -cifti-dilate

              <cifti-in> - the input cifti file <direction> - which dimension  to  dilate  along,
              ROW  or  COLUMN  <surface-distance>  -  the  distance  to dilate on surfaces, in mm
              <volume-distance> - the distance to dilate in  the  volume,  in  mm  <cifti-out>  -
              output - the output cifti file

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-left-corrected-areas] - vertex areas to use instead of computing

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

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-right-corrected-areas] - vertex areas to use instead of computing

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

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              [-cerebellum-corrected-areas] - vertex areas to use instead of

              computing  them  from  the  cerebellum surface <area-metric> - the corrected vertex
              areas, as a metric

              [-bad-brainordinate-roi] - specify an roi of brainordinates to overwrite,

              rather than zeros <roi-cifti> - cifti dscalar or  dtseries  file,  positive  values
              denote

              brainordinates to have their values replaced

              [-nearest] - use nearest value

              [-merged-volume] - treat volume components as if they were a single

              component

              For  all data values designated as bad, if they neighbor a good value or are within
              the specified distance of a good value in the same kind of model, replace the value
              with  a distance weighted average of nearby good values, otherwise set the value to
              zero.  If -nearest is specified, it will use the value from the closest good  value
              within  range  instead  of  a weighted average.  When the input file contains label
              data, nearest dilation is used on the surface, and weighted popularity is  used  in
              the volume.

              The -*-corrected-areas options are intended for dilating on group average surfaces,
              but it is only an approximate correction for the reduction of structure in a  group
              average surface.

              If  -bad-brainordinate-roi  is  specified,  all  values, including those with value
              zero, are good, except for locations with a positive value in the ROI.   If  it  is
              not specified, only values equal to zero are bad.

       -cifti-erode ERODE A CIFTI FILE

              wb_command -cifti-erode

              <cifti-in>  -  the  input cifti file <direction> - which dimension to dilate along,
              ROW or COLUMN <surface-distance> - the  distance  to  dilate  on  surfaces,  in  mm
              <volume-distance>  -  the  distance  to  dilate  in the volume, in mm <cifti-out> -
              output - the output cifti file

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-left-corrected-areas] - vertex areas to use instead of computing

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

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-right-corrected-areas] - vertex areas to use instead of computing

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

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              [-cerebellum-corrected-areas] - vertex areas to use instead of

              computing them from the cerebellum surface <area-metric>  -  the  corrected  vertex
              areas, as a metric

              [-merged-volume] - treat volume components as if they were a single

              component

              For  all  data  values  that  are empty (for label data, unlabeled, for other data,
              zero), set the surrounding values to empty.  The surrounding values are defined  as
              the  immediate  neighbors and all values in the same structure within the specified
              distance (-merged-volume treats all voxels as one structure).

              The -*-corrected-areas options are intended for eroding on group average  surfaces,
              but it is only an approximate correction.

       -cifti-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A CIFTI FILE

              wb_command -cifti-estimate-fwhm

              <cifti> - the input cifti file

              [-merged-volume] - treat volume components as if they were a single

              component

              [-column] - only output estimates for one column

              <column> - the column number

              [-surface] - repeatable - specify an input surface

              <structure> - what structure to use this surface for <surface> - the surface file

              Estimate the smoothness of the components of the cifti file, printing the estimates
              to standard output.  If -merged-volume is used, all voxels are  used  as  a  single
              component, rather than separated by structure.

              <structure> must be one of the following:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -cifti-export-dense-mapping WRITE INDEX TO ELEMENT MAPPING AS TEXT

              wb_command -cifti-export-dense-mapping

              <cifti>  - the cifti file <direction> - which direction to export the mapping from,
              ROW or COLUMN

              [-volume-all] - export the the mapping of all voxels

              <text-out> - output - the output text file

              [-no-cifti-index] - don't write the cifti index in the output file

              [-structure] - write the structure each voxel belongs to in the output

              file

              [-surface] - repeatable - export the the mapping of one surface structure

              <structure> - the structure to output <text-out> - output - the output text file

              [-no-cifti-index] - don't write the cifti index in the output file

              [-volume] - repeatable - export the the mapping of one volume structure

              <structure> - the structure to output <text-out> - output - the output text file

              [-no-cifti-index] - don't write the cifti index in the output file

              This command produces text files that describe the mapping from  cifti  indices  to
              surface  vertices  or  voxels.  All indices are zero-based.  The default format for
              -surface is lines of the form:

              <cifti-index> <vertex>

              The default format for -volume and -volume-all is lines of the form:

              <cifti-index> <i> <j> <k>

              For each <structure> argument, use one of the following strings:

              CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT  ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT     CEREBELLAR_WHITE_MATTER_RIGHT      CEREBELLUM_LEFT
              CEREBELLUM_RIGHT   CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT  CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT  INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -cifti-extrema FIND EXTREMA IN A CIFTI FILE

              wb_command -cifti-extrema

              <cifti> - the input cifti <surface-distance> - the minimum distance between extrema
              of the same

              type, for surface components

              <volume-distance> - the minimum distance between extrema of the same

              type, for volume components

              <direction>  -  which  dimension to find extrema along, ROW or COLUMN <cifti-out> -
              output - the output cifti

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              [-surface-presmooth] - smooth on the surface before finding extrema

              <surface-kernel> - the sigma for the gaussian surface smoothing

              kernel, in mm

              [-volume-presmooth] - smooth volume components before finding extrema

              <volume-kernel> - the sigma for the gaussian volume smoothing kernel,

              in mm

              [-threshold] - ignore small extrema

              <low> - the largest value to consider for being a minimum  <high>  -  the  smallest
              value to consider for being a maximum

              [-merged-volume] - treat volume components as if they were a single

              component

              [-sum-maps] - output the sum of the extrema maps instead of each map

              separately

              [-consolidate-mode] - use consolidation of local minima instead of a

              large neighborhood

              [-only-maxima] - only find the maxima

              [-only-minima] - only find the minima

              Finds  spatial  locations  in  a  cifti file that have more extreme values than all
              nearby locations in the same component (surface or volume  structure).   The  input
              cifti  file must have a brain models mapping along the specified direction.  COLUMN
              is the direction that works on dtseries and dscalar.  For dconn, if it is symmetric
              use COLUMN, otherwise use ROW.

       -cifti-false-correlation COMPARE CORRELATION LOCALLY AND ACROSS/THROUGH SULCI/GYRI

              wb_command -cifti-false-correlation

              <cifti-in>  - the cifti file to use for correlation <3D-dist> - maximum 3D distance
              to check around each vertex <geo-outer> - maximum  geodesic  distance  to  use  for
              neighboring

              correlation

              <geo-inner> - minimum geodesic distance to use for neighboring

              correlation

              <cifti-out> - output - the output cifti dscalar file

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-dump-text] - dump the raw measures used to a text file

              <text-out> - the output text file

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-dump-text] - dump the raw measures used to a text file

              <text-out> - the output text file

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              [-dump-text] - dump the raw measures used to a text file

              <text-out> - the output text file

              For  each  vertex,  compute  the  average  correlation  within  a range of geodesic
              distances that don't cross a sulcus/gyrus,  and  the  correlation  to  the  closest
              vertex  crossing a sulcus/gyrus.  A vertex is considered to cross a sulcus/gyrus if
              the 3D distance is less than a third of the geodesic  distance.   The  output  file
              contains  the  ratio  between  these correlations, and some additional maps to help
              explain the ratio.

       -cifti-find-clusters FILTER CLUSTERS BY AREA/VOLUME

              wb_command -cifti-find-clusters

              <cifti> - the input cifti <surface-value-threshold> - threshold  for  surface  data
              values  <surface-minimum-area>  -  threshold  for  surface  cluster  area,  in mm^2
              <volume-value-threshold> - threshold for volume data values <volume-minimum-size> -
              threshold for volume cluster size, in mm^3 <direction> - which dimension to use for
              spatial information, ROW or

              COLUMN

              <cifti-out> - output - the output cifti

              [-less-than] - find values less than <value-threshold>, rather than

              greater

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

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

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

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

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

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

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

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

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

              [-cifti-roi] - search only within regions of interest

              <roi-cifti> - the regions to search within, as a cifti file

              [-merged-volume] - treat volume components as if they were a single

              component

              [-size-ratio] - ignore clusters smaller than a given fraction of the

              largest cluster in the structure <surface-ratio>  -  fraction  of  the  structure's
              largest  cluster  area <volume-ratio> - fraction of the structure's largest cluster
              volume

              [-distance] - ignore clusters further than a given distance from the

              largest cluster in the structure <surface-distance> -  how  far  from  the  largest
              cluster a cluster can

              be, edge to edge, in mm

              <volume-distance> - how far from the largest cluster a cluster can be,

              edge to edge, in mm

              [-start] - start labeling clusters from a value other than 1

              <startval> - the value to give the first cluster found

              Outputs  a  cifti  file with nonzero integers for all brainordinates within a large
              enough cluster, and zeros elsewhere.  The integers denote  cluster  membership  (by
              default,  first  cluster found will use value 1, second cluster 2, etc).  The input
              cifti file must have a brain models mapping on the chosen  dimension,  columns  for
              .dtseries, and either for .dconn.  The ROI should have a brain models mapping along
              columns, exactly matching the mapping of the chosen direction in  the  input  file.
              Data outside the ROI is ignored.

       -cifti-gradient TAKE GRADIENT OF A CIFTI FILE

              wb_command -cifti-gradient

              <cifti> - the input cifti <direction> - which dimension to take the gradient along,
              ROW or COLUMN <cifti-out> - output - the output cifti

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-left-corrected-areas] - vertex areas to use instead of computing

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

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-right-corrected-areas] - vertex areas to use instead of computing

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

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              [-cerebellum-corrected-areas] - vertex areas to use instead of

              computing them from the cerebellum surface <area-metric>  -  the  corrected  vertex
              areas, as a metric

              [-surface-presmooth] - smooth on the surface before computing the

              gradient <surface-kernel> - the sigma for the gaussian surface smoothing

              kernel, in mm

              [-volume-presmooth] - smooth on the surface before computing the gradient

              <volume-kernel> - the sigma for the gaussian volume smoothing kernel,

              in mm

              [-average-output] - output the average of the gradient magnitude maps

              instead of each gradient map separately

              [-vectors] - output gradient vectors

              <vectors-out> - output - the vectors, as a dscalar file

              Performs  gradient  calculation on each component of the cifti file, and optionally
              averages the resulting gradients.  The -vectors and -average-output options may not
              be  used  together.   You  must specify a surface for each surface structure in the
              cifti file.  The COLUMN direction should be faster, and is the direction that works
              on   dtseries.    For   dconn,   you  probably  want  ROW,  unless  you  are  using
              -average-output.

       -cifti-label-adjacency MAKE ADJACENCY MATRIX OF A CIFTI LABEL FILE

              wb_command -cifti-label-adjacency

              <label-in> - the input cifti label file <adjacency-out> - output - the output cifti
              pconn adjacency matrix

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              Find  face-adjacent voxels and connected vertices that have different label values,
              and count them for  each  pair.   Put  the  resulting  counts  into  a  parcellated
              connectivity  file,  with  the diagonal being zero.  This gives a rough estimate of
              how long or expansive the border between two labels is.

       -cifti-label-export-table EXPORT LABEL TABLE FROM CIFTI AS TEXT

              wb_command -cifti-label-export-table

              <label-in> - the input cifti label file <map> - the number or name of the label map
              to use <table-out> - output - the output text file

              Takes  the  label  table  from  the cifti label map, and writes it to a text format
              matching what is expected by -cifti-label-import.

       -cifti-label-import MAKE A CIFTI LABEL FILE FROM A CIFTI FILE

              wb_command -cifti-label-import

              <input> - the input cifti file <label-list-file> - text file containing the  values
              and names for labels <output> - output - the output cifti label file

              [-discard-others] - set any values not mentioned in the label list to the

              ??? label

              [-unlabeled-value] - set the value that will be interpreted as unlabeled

              <value> - the numeric value for unlabeled (default 0)

              [-drop-unused-labels] - remove any unused label values from the label

              table

       Creates a cifti label file from a cifti file with label-like values.
              You

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

              The label list file must have the following format (2 lines per label):

              <labelname> <key> <red> <green> <blue> <alpha> ...

              Label names are specified on a separate line from their value and color,  in  order
              to  let  label  names  contain spaces.  Whitespace is trimmed from both ends of the
              label name, but is kept if it is in the middle of a  label.   The  value  of  <key>
              specifies what value in the imported file should be used as this label.  The values
              of <red>, <green>, <blue> and <alpha> must be integers from  0  to  255,  and  will
              specify  the color the label is drawn as (alpha of 255 means fully opaque, which is
              probably what you want).

              By default, it will create new label names with names like LABEL_5 for  any  values
              encountered  that  are  not  mentioned in the list file, specify -discard-others to
              instead set these values to the "unlabeled" key.

       -cifti-label-probability FIND FREQUENCY OF CIFTI LABELS

              wb_command -cifti-label-probability

              <label-maps> - cifti dlabel file containing individual label maps from

              many subjects

              <probability-dscalar-out> - output - the relative frequencies of each

              label at each vertex/voxel

              [-exclude-unlabeled] - don't make a probability map of the unlabeled key

              This command outputs a set of soft ROIs, one for each label in the input, where the
              value is how many of the input maps had that label at that vertex/voxel, divided by
              the number of input maps.

       -cifti-label-to-border DRAW BORDERS AROUND CIFTI LABELS

              wb_command -cifti-label-to-border

              <cifti-in> - the input cifti dlabel file

              [-placement] - set how far along the edge border points are drawn

              <fraction> - fraction along edge from inside vertex (default 0.33)

              [-column] - select a single column

              <column> - the column number or name

              [-border] - repeatable - specify output file for a surface structure

              <surface> - the surface to use for neighbor and structure information  <border-out>
              - output - the output border file

              For  each  surface,  takes  the  labels on the matching structure and draws borders
              around the labels.  Use -column to only draw borders around one label map.

       -cifti-label-to-roi MAKE A CIFTI LABEL INTO AN ROI

              wb_command -cifti-label-to-roi

              <label-in> - the input cifti label file <scalar-out> - output -  the  output  cifti
              scalar file

              [-name] - select label by name

              <label-name> - the label name that you want an roi of

              [-key] - select label by key

              <label-key> - the label key that you want an roi of

              [-map] - select a single label map to use

              <map> - the map number or name

              For  each  map  in <label-in>, a map is created in <scalar-out> where all locations
              labeled with <label-name> or with a key of <label-key> are given a value of 1,  and
              all  other locations are given 0.  Exactly one of -name and -key must be specified.
              Specify -map to use only one map from <label-in>.

       -cifti-math EVALUATE EXPRESSION ON CIFTI FILES

              wb_command -cifti-math

              <expression> - the expression to evaluate, in quotes <cifti-out>  -  output  -  the
              output cifti file

              [-fixnan] - replace NaN results with a value

              <replace> - value to replace NaN with

              [-override-mapping-check] - don't check the mappings for compatibility,

              only check length

              [-var] - repeatable - a cifti file to use as a variable

              <name>  -  the  name of the variable, as used in the expression <cifti> - the cifti
              file to use as this variable

              [-select] - repeatable - select a single index from a dimension

              <dim> - the dimension to select from (1-based) <index> - the index to use (1-based)

              [-repeat] - repeat the selected values for each index of output in

              this dimension

              This command evaluates <expression> at each matrix  element  independently.   There
              must  be  at  least  one  -var  option (to get the output layout from), even if the
              <name> specified in it isn't used in <expression>.

              To select a single column from a 2D file (most cifti files are 2D), use  -select  1
              <index>,  where  <index>  is  1-based.   To select a single row from a 2D file, use
              -select 2 <index>.  Where -select is not used, the cifti files must have compatible
              mappings  (e.g.,  brain  models  and parcels mappings must match exactly except for
              parcel names).  Use -override-mapping-check to skip this checking.

              Filenames are not valid in <expression>, use a variable name and a -var option with
              matching  <name>  to  specify  an  input  file.   The  format of <expression> is as
              follows:

              Expressions consist of constants, variables, operators, parentheses, and functions,
              in  infix  notation,  such  as 'exp(-x + 3) * scale'.  Variables are strings of any
              length, using the characters a-z, A-Z, 0-9, and _, but may not take the name  of  a
              named  constant.   Currently,  there is only one named constant, PI.  The operators
              are +, -, *, /, ^, >, <, >=, <=, ==, !=, !, &&, ||.  These behave as in  C,  except
              that  ^  is  exponentiation, i.e. pow(x, y), and takes higher precedence than other
              binary operators (also, '-3^-4^-5' means '-(3^(-(4^-5)))').  The <=, >=, ==, and !=
              operators  are  given  a small amount of wiggle room, equal to one millionth of the
              smaller of the absolute values of the values being compared.

              Comparison and logical operators return 0 or 1, you can do masking with expressions
              like  'x * (mask > 0)'.  For all logical operators, an input is considered true iff
              it is greater than 0.  The expression '0 < x < 5' is not syntactically  wrong,  but
              it  will NOT do what is desired, because it is evaluated left to right, i.e. '((0 <
              x) < 5)', which will always return 1, as both possible results of a comparison  are
              less  than  5.   A  warning is generated if an expression of this type is detected.
              Use something like 'x > 0 && x < 5' to get the desired behavior.

              Whitespace between elements is ignored, ' sin  (  2  *  x  )  '  is  equivalent  to
              'sin(2*x)',  but  's  in(2*x)' is an error.  Implied multiplication is not allowed,
              the expression '2x' will be parsed as a variable.  Parentheses are (), do  not  use
              [] or {}.  Functions require parentheses, the expression 'sin x' is an error.

              The following functions are supported:

              sin:  1 argument, the sine of the argument (units are radians) cos: 1 argument, the
              cosine of the argument (units are radians) tan: 1  argument,  the  tangent  of  the
              argument (units are radians) asin: 1 argument, the inverse of sine of the argument,
              in radians acos: 1 argument, the inverse of cosine  of  the  argument,  in  radians
              atan:  1  argument,  the  inverse  of  tangent of the argument, in radians atan2: 2
              arguments, atan2(y, x) returns the inverse of tangent of

              (y/x), in radians, determining quadrant by the sign of both arguments

              sinh: 1 argument, the hyperbolic  sine  of  the  argument  cosh:  1  argument,  the
              hyperbolic  cosine  of the argument tanh: 1 argument, the hyperboloc tangent of the
              argument asinh: 1 argument, the inverse hyperbolic sine of the  argument  acosh:  1
              argument,  the  inverse  hyperbolic  cosine  of the argument atanh: 1 argument, the
              inverse hyperboloc tangent of the argument ln: 1 argument, the natural logarithm of
              the  argument  exp:  1 argument, the constant e raised to the power of the argument
              log: 1 argument, the base 10 logarithm of the argument sqrt: 1 argument, the square
              root  of  the argument abs: 1 argument, the absolute value of the argument floor: 1
              argument, the largest integer not greater than the argument round: 1 argument,  the
              nearest integer, with ties rounded away from

              zero

              ceil: 1 argument, the smallest integer not less than the argument min: 2 arguments,
              min(x, y) returns y if (x > y), x otherwise max: 2 arguments, max(x, y)  returns  y
              if (x < y), x otherwise mod: 2 arguments, mod(x, y) = x - y * floor(x / y), or 0 if
              y == 0 clamp: 3 arguments, clamp(x, low, high) = min(max(x, low), high)

       -cifti-merge MERGE CIFTI TIMESERIES, SCALAR, OR LABEL FILES

              wb_command -cifti-merge

              <cifti-out> - output - output cifti file

              [-cifti] - repeatable - specify an input cifti file

              <cifti-in> - a cifti file to use columns from

              [-column] - repeatable - select a single column to use

              <column> - the column number (starting from 1) or name

              [-up-to] - use an inclusive range of columns

              <last-column> - the number or name of the last column to include

              [-reverse] - use the range in reverse order

              Given input CIFTI files which have matching mappings along columns, and  for  which
              mappings  along rows are the same type, all either series, scalars, or labels, this
              command concatenates the specified columns horizontally (rows become longer).

              Example: wb_command -cifti-merge out.dtseries.nii -cifti first.dtseries.nii -column
              1 -cifti second.dtseries.nii

              This  example  would take the first column from first.dtseries.nii, followed by all
              columns from second.dtseries.nii, and write these columns to out.dtseries.nii.

       -cifti-merge-dense MERGE CIFTI FILES ALONG DENSE DIMENSION

              wb_command -cifti-merge-dense

              <direction> - which dimension to merge along, ROW or COLUMN <cifti-out> - output  -
              the output cifti file

              [-cifti] - repeatable - specify an input cifti file

              <cifti-in> - a cifti file to merge

              The  input  cifti  files  must  have  matching  mappings  along  the  direction not
              specified, and the mapping along the specified direction must be brain models.

       -cifti-merge-parcels MERGE CIFTI FILES ALONG PARCELS DIMENSION

              wb_command -cifti-merge-parcels

              <direction> - which dimension to merge along (integer, 'ROW', or

              'COLUMN')

              <cifti-out> - output - the output cifti file

              [-cifti] - repeatable - specify an input cifti file

              <cifti-in> - a cifti file to merge

              The input  cifti  files  must  have  matching  mappings  along  the  direction  not
              specified,  and  the  mapping  along  the specified direction must be parcels.  The
              direction can be either an integer  starting  from  1,  or  the  strings  'ROW'  or
              'COLUMN'.

       -cifti-pairwise-correlation CORRELATE PAIRED ROWS BETWEEN TWO CIFTI FILES

              wb_command -cifti-pairwise-correlation

              <cifti-a>  - first input cifti file <cifti-b> - second input cifti file <cifti-out>
              - output - output cifti file

              [-fisher-z] - apply fisher small z transform (ie, artanh) to correlation

              [-override-mapping-check] - don't check the mappings for compatibility,

              only check length

              For each row in <cifti-a>, correlate it with the same row in <cifti-b>, and put the
              result in the same row of <cifti-out>, which has only one column.

       -cifti-palette SET PALETTE ON A CIFTI FILE

              wb_command -cifti-palette

              <cifti-in>  -  the cifti input <mode> - the mapping mode <cifti-out> - output - the
              output cifti file

              [-column] - select a single column for scalar maps

              <column> - the column number or name

              [-pos-percent] - percentage min/max for positive data coloring

              <pos-min-%> - the  percentile  for  the  least  positive  data  <pos-max-%>  -  the
              percentile for the most positive data

              [-neg-percent] - percentage min/max for negative data coloring

              <neg-min-%>  -  the  percentile  for  the  least  negative  data  <neg-max-%> - the
              percentile for the most negative data

              [-pos-user] - user min/max values for positive data coloring

              <pos-min-user> - the value for the least positive data <pos-max-user> -  the  value
              for the most positive data

              [-neg-user] - user min/max values for negative data coloring

              <neg-min-user>  -  the value for the least negative data <neg-max-user> - the value
              for the most negative data

              [-interpolate] - interpolate colors

              <interpolate> - boolean, whether to interpolate

              [-disp-pos] - display positive data

              <display> - boolean, whether to display

              [-disp-neg] - display positive data

              <display> - boolean, whether to display

              [-disp-zero] - display data closer to zero than the min cutoff

              <display> - boolean, whether to display

              [-palette-name] - set the palette used

              <name> - the name of the palette

              [-thresholding] - set the thresholding

              <type> - thresholding setting <test> - show values  inside  or  outside  thresholds
              <min> - lower threshold <max> - upper threshold

              [-inversion] - specify palette inversion

              <type> - the type of inversion

              NOTE: The output file must be a different file than the input file.

              For  scalar  maps, by default the palette is changed for every map, specify -column
              to change only one map.  Palette settings not specified  will  be  taken  from  the
              first  column for scalar maps, and from the existing file palette for other mapping
              types.  The <mode> argument must be one of the following:

              MODE_AUTO_SCALE   MODE_AUTO_SCALE_ABSOLUTE_PERCENTAGE    MODE_AUTO_SCALE_PERCENTAGE
              MODE_USER_SCALE

              The <name> argument to -palette-name must be one of the following:

              ROY-BIG-BL   videen_style   Gray_Interp_Positive  Gray_Interp  PSYCH-FIXED  RBGYR20
              RBGYR20P RYGBR4_positive RGRBR_mirror90_pos Orange-Yellow  POS_NEG_ZERO  red-yellow
              blue-lightblue  FSL  power_surf  fsl_red fsl_green fsl_blue fsl_yellow RedWhiteBlue
              cool-warm spectral RY-BC-BL magma JET256 PSYCH  PSYCH-NO-NONE  ROY-BIG  clear_brain
              fidl raich4_clrmid raich6_clrmid HSB8_clrmid POS_NEG

              The <type> argument to -thresholding must be one of the following:

              THRESHOLD_TYPE_OFF THRESHOLD_TYPE_NORMAL THRESHOLD_TYPE_FILE

              The <test> argument to -thresholding must be one of the following:

              THRESHOLD_TEST_SHOW_OUTSIDE THRESHOLD_TEST_SHOW_INSIDE

              The <type> argument to -inversion must be one of the following:

              OFF POSITIVE_WITH_NEGATIVE POSITIVE_NEGATIVE_SEPARATE

       -cifti-parcel-mapping-to-label CREATE DLABEL FROM PARCELLATED FILE

              wb_command -cifti-parcel-mapping-to-label

              <cifti-in>  -  the input parcellated file <direction> - which dimension to take the
              parcel map from, ROW or COLUMN <template-cifti> - a cifti  file  with  the  desired
              dense mapping along

              column

              <dlabel-out> - output - the output dense label file

              This  command  will output a dlabel file, useful for doing the same parcellation to
              another dense file.

              For ptseries, pscalar, plabel, pconn, and pdconn, using COLUMN for <direction> will
              work.

       -cifti-parcellate PARCELLATE A CIFTI FILE

              wb_command -cifti-parcellate

              <cifti-in> - the cifti file to parcellate <cifti-label> - a cifti label file to use
              for the parcellation <direction> - which mapping to parcellate  (integer,  ROW,  or
              COLUMN) <cifti-out> - output - output cifti file

              [-spatial-weights] - use voxel volume and either vertex areas or metric

              files as weights

              [-left-area-surf] - use a surface for left vertex areas

              <left-surf> - the left surface to use, areas are in mm^2

              [-right-area-surf] - use a surface for right vertex areas

              <right-surf> - the right surface to use, areas are in mm^2

              [-cerebellum-area-surf] - use a surface for cerebellum vertex areas

              <cerebellum-surf> - the cerebellum surface to use, areas are in

              mm^2

              [-left-area-metric] - use a metric file for left vertex weights

              <left-metric> - metric file containing left vertex weights

              [-right-area-metric] - use a metric file for right vertex weights

              <right-metric> - metric file containing right vertex weights

              [-cerebellum-area-metric] - use a metric file for cerebellum vertex

              weights <cerebellum-metric> - metric file containing cerebellum vertex

              weights

              [-cifti-weights] - use a cifti file containing weights

              <weight-cifti> - the weights to use, as a cifti file

              [-method] - specify method of parcellation (default MEAN, or MODE if

              label data) <method> - the method to use to assign parcel values from the values

              of member brainordinates

              [-exclude-outliers] - exclude non-numeric values and outliers from each

              parcel  by  standard  deviation <sigma-below> - number of standard deviations below
              the mean to

              include

              <sigma-above> - number of standard deviations above the mean to

              include

              [-only-numeric] - exclude non-numeric values

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

              voxels

              [-fill-value] - specify value to use in empty parcels (default 0)

              <value> - the value to fill empty parcels with

              [-nonempty-mask-out] - output a matching pscalar file that has 0s in

              empty parcels, and 1s elsewhere <mask-out> - output - the output mask file

              Each non-empty label (other than the unlabeled key) in the cifti label file will be
              treated  as  a  parcel,  and  all  rows  or  columns within the parcel are averaged
              together to form the output row or column.  If -include-empty is  specified,  empty
              labels  will  be  treated  as  parcels with no elements, and filled with a constant
              value.  The direction can be either an integer starting  from  1,  or  the  strings
              'ROW' or 'COLUMN'.  For dtseries or dscalar, use COLUMN.  If you are parcellating a
              dconn in both directions, parcellating by ROW first will use much less memory.

              The parameter to the -method option must be one of the following:

              MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based  index  of  the
              maximum  value INDEXMIN: the 1-based index of the minimum value SUM: add all values
              PRODUCT: multiply all values MEAN:  the  mean  of  the  data  STDEV:  the  standard
              deviation   (N   denominator)   SAMPSTDEV:   the  sample  standard  deviation  (N-1
              denominator) VARIANCE: the variance of  the  data  TSNR:  mean  divided  by  sample
              standard   deviation   (N-1   denominator)  COV:  sample  standard  deviation  (N-1
              denominator) divided by mean MEDIAN: the median of the data MODE: the mode  of  the
              data COUNT_NONZERO: the number of nonzero elements in the data

              The  -*-weights options are mutually exclusive and may only be used with MEAN, SUM,
              STDEV, SAMPSTDEV, VARIANCE, MEDIAN, or MODE.

       -cifti-reduce PERFORM REDUCTION OPERATION ON A CIFTI FILE

              wb_command -cifti-reduce

              <cifti-in> - the cifti file to reduce <operation> - the reduction operator  to  use
              <cifti-out> - output - the output cifti file

              [-direction] - specify what direction to reduce along

              <direction> - the direction (default ROW)

              [-exclude-outliers] - exclude non-numeric values and outliers by standard

              deviation <sigma-below> - number of standard deviations below the mean to

              include

              <sigma-above> - number of standard deviations above the mean to

              include

              [-only-numeric] - exclude non-numeric values

              For the specified direction (default ROW), perform a reduction operation along that
              direction.  The direction can be either an integer starting from 1, or the  strings
              'ROW' or 'COLUMN'.  The reduction operators are as follows:

              MAX:  the  maximum  value MIN: the minimum value INDEXMAX: the 1-based index of the
              maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all  values
              PRODUCT:  multiply  all  values  MEAN:  the  mean  of  the data STDEV: the standard
              deviation  (N  denominator)  SAMPSTDEV:  the   sample   standard   deviation   (N-1
              denominator)  VARIANCE:  the  variance  of  the  data  TSNR: mean divided by sample
              standard  deviation  (N-1  denominator)  COV:  sample   standard   deviation   (N-1
              denominator)  divided  by mean MEDIAN: the median of the data MODE: the mode of the
              data COUNT_NONZERO: the number of nonzero elements in the data

       -cifti-reorder REORDER THE PARCELS OR SCALAR/LABEL MAPS IN A CIFTI FILE

              wb_command -cifti-reorder

              <cifti-in> - input cifti file <direction> - which dimension to reorder  along,  ROW
              or  COLUMN <reorder-list> - a text file containing the desired order transformation
              <cifti-out> - output - the reordered cifti file

              The mapping along the specified direction must be parcels, scalars, or labels.  For
              pscalar  or ptseries, use COLUMN to reorder the parcels.  For dlabel, use ROW.  The
              <reorder-list> file must contain 1-based indices separated by  whitespace  (spaces,
              newlines,  tabs,  etc),  with as many indices as <cifti-in> has along the specified
              dimension.  These indices specify  which  current  index  should  end  up  in  that
              position, for instance, if the current order is 'A B C D', and the desired order is
              'D A B C', the text file should contain '4 1 2 3'.

       -cifti-replace-structure REPLACE DATA IN A STRUCTURE IN A CIFTI FILE

              wb_command -cifti-replace-structure

              <cifti> - the cifti to modify <direction> -  which  dimension  to  interpret  as  a
              single map, ROW or COLUMN

              [-volume-all] - replace the data in all volume components

              <volume> - the input volume

              [-from-cropped] - the input is cropped to the size of the data

              [-discard-unused-labels] - when operating on a dlabel file, drop any

              unused label keys from the label table

              [-label] - repeatable - replace the data in a surface label component

              <structure> - the structure to replace the data of <label> - the input label file

              [-metric] - repeatable - replace the data in a surface component

              <structure> - the structure to replace the data of <metric> - the input metric

              [-volume] - repeatable - replace the data in a volume component

              <structure> - the structure to replace the data of <volume> - the input volume

              [-from-cropped] - the input is cropped to the size of the component

              You  must specify at least one of -metric, -label, -volume, or -volume-all for this
              command  to  do  anything.   Input  volumes  must  line  up  with  the  output   of
              -cifti-separate.   For  dtseries/dscalar,  use  COLUMN,  and if your matrix will be
              fully symmetric, COLUMN is more efficient.  The structure argument must be  one  of
              the following:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -cifti-resample RESAMPLE A CIFTI FILE TO A NEW CIFTI SPACE

              wb_command -cifti-resample

              <cifti-in>  -  the  cifti file to resample <direction> - the direction of the input
              that should be resampled, ROW or

              COLUMN

              <cifti-template> -  a  cifti  file  containing  the  cifti  space  to  resample  to
              <template-direction> - the direction of the template to use as the

              resampling space, ROW or COLUMN

              <surface-method>  - specify a surface resampling method <volume-method> - specify a
              volume interpolation method <cifti-out> - output - the output cifti file

              [-surface-largest] - use largest weight instead of weighted average or

              popularity when doing surface resampling

              [-volume-predilate] - dilate the volume components before resampling

              <dilate-mm> - distance, in mm, to dilate

              [-nearest] - use nearest value dilation

              [-weighted] - use weighted dilation (default)

              [-exponent] - specify exponent in weighting function

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

              weighting function (default 2)

              [-surface-postdilate] - dilate the surface components after resampling

              <dilate-mm> - distance, in mm, to dilate

              [-nearest] - use nearest value dilation

              [-linear] - use linear dilation

              [-weighted] - use weighted dilation (default for non-label data)

              [-exponent] - specify exponent in weighting function

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

              the weighting function (default 2)

              [-affine] - use an affine transformation on the volume components

              <affine-file> - the affine file to use

              [-flirt] - MUST be used if affine is a flirt affine

              <source-volume> - the source volume used when generating the affine <target-volume>
              - the target volume used when generating the affine

              [-warpfield] - use a warpfield on the volume components

              <warpfield> - the warpfield to use

              [-fnirt] - MUST be used if using a fnirt warpfield

              <source-volume> - the source volume used when generating the

              warpfield

              [-left-spheres] - specify spheres for left surface resampling

              <current-sphere> - a sphere with the same mesh as the current left

              surface

              <new-sphere> - a sphere with the new left mesh that is in register

              with the current sphere

              [-left-area-surfs] - specify left surfaces to do vertex area

              correction  based  on  <current-area>  -  a  relevant  left anatomical surface with
              current

              mesh

              <new-area> - a relevant left anatomical surface with new mesh

              [-left-area-metrics] - specify left vertex area metrics to do area

              correction based on <current-area> - a  metric  file  with  vertex  areas  for  the
              current

              mesh

              <new-area> - a metric file with vertex areas for the new mesh

              [-right-spheres] - specify spheres for right surface resampling

              <current-sphere> - a sphere with the same mesh as the current right

              surface

              <new-sphere> - a sphere with the new right mesh that is in register

              with the current sphere

              [-right-area-surfs] - specify right surfaces to do vertex area

              correction  based  on  <current-area>  -  a  relevant right anatomical surface with
              current

              mesh

              <new-area> - a relevant right anatomical surface with new mesh

              [-right-area-metrics] - specify right vertex area metrics to do area

              correction based on <current-area> - a  metric  file  with  vertex  areas  for  the
              current

              mesh

              <new-area> - a metric file with vertex areas for the new mesh

              [-cerebellum-spheres] - specify spheres for cerebellum surface resampling

              <current-sphere> - a sphere with the same mesh as the current

              cerebellum surface

              <new-sphere> - a sphere with the new cerebellum mesh that is in

              register with the current sphere

              [-cerebellum-area-surfs] - specify cerebellum surfaces to do vertex

              area  correction based on <current-area> - a relevant cerebellum anatomical surface
              with

              current mesh

              <new-area> - a relevant cerebellum anatomical surface with new mesh

              [-cerebellum-area-metrics] - specify cerebellum vertex area metrics to

              do area correction based on <current-area> - a metric file with  vertex  areas  for
              the current

              mesh

              <new-area> - a metric file with vertex areas for the new mesh

       Resample cifti data to a different brainordinate space.
              Use COLUMN for

       the direction to resample dscalar, dlabel, or dtseries.
              Resampling both

              dimensions  of  a  dconn  requires running this command twice, once with COLUMN and
              once with ROW.  If you are resampling a dconn and your machine has a  large  amount
              of  memory,  you might consider using -cifti-resample-dconn-memory to avoid writing
              and rereading an  intermediate  file.   The  <template-direction>  argument  should
              usually be COLUMN, as dtseries, dscalar, and dlabel all have brainordinates on that
              direction.  If spheres are not specified for a surface structure  which  exists  in
              the  cifti  files,  its data is copied without resampling or dilation.  Dilation is
              done with the 'nearest' method, and is  done  on  <new-sphere>  for  surface  data.
              Volume  components are padded before dilation so that dilation doesn't run into the
              edge of the  component  bounding  box.   If  neither  -affine  nor  -warpfield  are
              specified, the identity transform is assumed for the volume data.

              The  recommended  resampling  methods  are ADAP_BARY_AREA and CUBIC (cubic spline),
              except for label data which should use ADAP_BARY_AREA and  ENCLOSING_VOXEL.   Using
              ADAP_BARY_AREA requires specifying an area option to each used -*-spheres option.

              The <volume-method> argument must be one of the following:

              CUBIC ENCLOSING_VOXEL TRILINEAR

              The <surface-method> argument must be one of the following:

              ADAP_BARY_AREA BARYCENTRIC

       -cifti-resample-dconn-memory USE LOTS OF MEMORY TO RESAMPLE DCONN

              wb_command -cifti-resample-dconn-memory

              <cifti-in>  - the cifti file to resample <cifti-template> - a cifti file containing
              the cifti space to resample to <template-direction> - the direction of the template
              to use as the

              resampling space, ROW or COLUMN

              <surface-method>  - specify a surface resampling method <volume-method> - specify a
              volume interpolation method <cifti-out> - output - the output cifti file

              [-surface-largest] - use largest weight instead of weighted average when

              doing surface resampling

              [-volume-predilate] - dilate the volume components before resampling

              <dilate-mm> - distance, in mm, to dilate

              [-nearest] - use nearest value dilation

              [-weighted] - use weighted dilation

              [-exponent] - specify exponent in weighting function

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

              weighting function (default 2)

              [-surface-postdilate] - dilate the surface components after resampling

              <dilate-mm> - distance, in mm, to dilate

              [-nearest] - use nearest value dilation

              [-linear] - use linear dilation

              [-weighted] - use weighted dilation

              [-exponent] - specify exponent in weighting function

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

              the weighting function (default 2)

              [-affine] - use an affine transformation on the volume components

              <affine-file> - the affine file to use

              [-flirt] - MUST be used if affine is a flirt affine

              <source-volume> - the source volume used when generating the affine <target-volume>
              - the target volume used when generating the affine

              [-warpfield] - use a warpfield on the volume components

              <warpfield> - the warpfield to use

              [-fnirt] - MUST be used if using a fnirt warpfield

              <source-volume> - the source volume used when generating the

              warpfield

              [-left-spheres] - specify spheres for left surface resampling

              <current-sphere> - a sphere with the same mesh as the current left

              surface

              <new-sphere> - a sphere with the new left mesh that is in register

              with the current sphere

              [-left-area-surfs] - specify left surfaces to do vertex area

              correction  based  on  <current-area>  -  a  relevant  left anatomical surface with
              current

              mesh

              <new-area> - a relevant left anatomical surface with new mesh

              [-left-area-metrics] - specify left vertex area metrics to do area

              correction based on <current-area> - a  metric  file  with  vertex  areas  for  the
              current

              mesh

              <new-area> - a metric file with vertex areas for the new mesh

              [-right-spheres] - specify spheres for right surface resampling

              <current-sphere> - a sphere with the same mesh as the current right

              surface

              <new-sphere> - a sphere with the new right mesh that is in register

              with the current sphere

              [-right-area-surfs] - specify right surfaces to do vertex area

              correction  based  on  <current-area>  -  a  relevant right anatomical surface with
              current

              mesh

              <new-area> - a relevant right anatomical surface with new mesh

              [-right-area-metrics] - specify right vertex area metrics to do area

              correction based on <current-area> - a  metric  file  with  vertex  areas  for  the
              current

              mesh

              <new-area> - a metric file with vertex areas for the new mesh

              [-cerebellum-spheres] - specify spheres for cerebellum surface resampling

              <current-sphere> - a sphere with the same mesh as the current

              cerebellum surface

              <new-sphere> - a sphere with the new cerebellum mesh that is in

              register with the current sphere

              [-cerebellum-area-surfs] - specify cerebellum surfaces to do vertex

              area  correction based on <current-area> - a relevant cerebellum anatomical surface
              with

              current mesh

              <new-area> - a relevant cerebellum anatomical surface with new mesh

              [-cerebellum-area-metrics] - specify cerebellum vertex area metrics to

              do area correction based on <current-area> - a metric file with  vertex  areas  for
              the current

              mesh

              <new-area> - a metric file with vertex areas for the new mesh

              This  command does the same thing as running -cifti-resample twice, but uses memory
              up to approximately 2x the size that the  intermediate  file  would  be.   This  is
              because  the intermediate dconn is kept in memory, rather than written to disk, and
              the components before and after resampling/dilation have to be  in  memory  at  the
              same  time  during  the  relevant  computation.   The <template-direction> argument
              should usually be COLUMN, as dtseries, dscalar, and dlabel all have  brainordinates
              on  that  direction.   If  spheres  are not specified for a surface structure which
              exists in the cifti files, its data  is  copied  without  resampling  or  dilation.
              Dilation is done with the 'nearest' method, and is done on <new-sphere> for surface
              data.  Volume components are padded before dilation so that  dilation  doesn't  run
              into the edge of the component bounding box.

              The <volume-method> argument must be one of the following:

              CUBIC ENCLOSING_VOXEL TRILINEAR

              The <surface-method> argument must be one of the following:

              ADAP_BARY_AREA BARYCENTRIC

       -cifti-restrict-dense-map EXCLUDE BRAINORDINATES FROM A CIFTI FILE

              wb_command -cifti-restrict-dense-map

              <cifti-in> - the input cifti <direction> - which dimension to change the mapping on
              (integer, 'ROW',

              or 'COLUMN')

              <cifti-out> - output - the output cifti

              [-cifti-roi] - cifti file containing combined rois

              <roi-cifti> - the rois as a cifti file

              [-left-roi] - vertices to use from left hemisphere

              <roi-metric> - the left roi as a metric file

              [-right-roi] - vertices to use from right hemisphere

              <roi-metric> - the right roi as a metric file

              [-cerebellum-roi] - vertices to use from cerebellum

              <roi-metric> - the cerebellum roi as a metric file

              [-vol-roi] - voxels to use

              <roi-vol> - the roi volume file

              Writes a modified version of  <cifti-in>,  where  all  brainordinates  outside  the
              specified roi(s) are removed from the file.  The direction can be either an integer
              starting from 1, or the strings 'ROW' or 'COLUMN'.  If -cifti-roi is specified,  no
              other  -*-roi option may be specified.  If not using -cifti-roi, any -*-roi options
              not present will discard the relevant structure, if present in the input file.

       -cifti-roi-average AVERAGE ROWS IN A SINGLE CIFTI FILE

              wb_command -cifti-roi-average

              <cifti-in> - the cifti file to average rows from <text-out> - output text  file  of
              the average values

              [-cifti-roi] - cifti file containing combined rois

              <roi-cifti> - the rois as a cifti file

              [-left-roi] - vertices to use from left hemisphere

              <roi-metric> - the left roi as a metric file

              [-right-roi] - vertices to use from right hemisphere

              <roi-metric> - the right roi as a metric file

              [-cerebellum-roi] - vertices to use from cerebellum

              <roi-metric> - the cerebellum roi as a metric file

              [-vol-roi] - voxels to use

              <roi-vol> - the roi volume file

              Average  the  rows  that  are  within  the  specified ROIs, and write the resulting
              average row to a text file, separated by newlines.   If  -cifti-roi  is  specified,
              -left-roi, -right-roi, -cerebellum-roi, and -vol-roi must not be specified.

       -cifti-rois-from-extrema CREATE CIFTI ROI MAPS FROM EXTREMA MAPS

              wb_command -cifti-rois-from-extrema

              <cifti> - the input cifti <surf-limit> - geodesic distance limit from vertex, in mm
              <vol-limit> - euclidean distance limit from voxel center, in mm <direction> - which
              dimension  an extrema map is along, ROW or COLUMN <cifti-out> - output - the output
              cifti

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              [-gaussian] - generate gaussian kernels instead of flat ROIs

              <surf-sigma> - the sigma for the surface gaussian kernel, in mm <vol-sigma>  -  the
              sigma for the volume gaussian kernel, in mm

              [-overlap-logic] - how to handle overlapping ROIs, default ALLOW

              <method> - the method of resolving overlaps

              [-merged-volume] - treat volume components as if they were a single

              component

              For  each  nonzero  value in each map, make a map with an ROI around that location.
              If the -gaussian option is specified, then normalized gaussian kernels  are  output
              instead  of  ROIs.   The  <method> argument to -overlap-logic must be one of ALLOW,
              CLOSEST, or EXCLUDE.  ALLOW is  the  default,  and  means  that  ROIs  are  treated
              independently  and  may overlap.  CLOSEST means that ROIs may not overlap, and that
              no ROI contains vertices that are closer to a different seed vertex.  EXCLUDE means
              that  ROIs  may  not overlap, and that any vertex within range of more than one ROI
              does not belong to any ROI.

       -cifti-separate WRITE A CIFTI STRUCTURE AS METRIC, LABEL OR VOLUME

              wb_command -cifti-separate

              <cifti-in> - the cifti to separate a component of <direction> - which direction  to
              separate into components, ROW or COLUMN

              [-volume-all] - separate all volume structures into a volume file

              <volume-out> - output - the output volume

              [-roi] - also output the roi of which voxels have data

              <roi-out> - output - the roi output volume

              [-label] - output a volume label file indicating the location of

              structures <label-out> - output - the label output volume

              [-crop] - crop volume to the size of the data rather than using the

              original volume size

              [-label] - repeatable - separate a surface model into a surface label

              file  <structure> - the structure to output <label-out> - output - the output label
              file

              [-roi] - also output the roi of which vertices have data

              <roi-out> - output - the roi output metric

              [-metric] - repeatable - separate a surface model into a metric file

              <structure> - the structure to output <metric-out> - output - the output metric

              [-roi] - also output the roi of which vertices have data

              <roi-out> - output - the roi output metric

              [-volume] - repeatable - separate a volume structure into a volume file

              <structure> - the structure to output <volume-out> - output - the output volume

              [-roi] - also output the roi of which voxels have data

              <roi-out> - output - the roi output volume

              [-crop] - crop volume to the size of the component rather than using

              the original volume size

              For dtseries, dscalar, and dlabel, use COLUMN for <direction>, and if  you  have  a
              symmetric dconn, COLUMN is more efficient.

              You  must specify at least one of -metric, -volume-all, -volume, or -label for this
              command to do anything.  Output volumes will spatially line up with their  original
              positions, whether or not they are cropped.

              For each <structure> argument, use one of the following strings:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -cifti-smoothing SMOOTH A CIFTI FILE

              wb_command -cifti-smoothing

              <cifti>  -  the  input  cifti <surface-kernel> - the sigma for the gaussian surface
              smoothing kernel,

              in mm

              <volume-kernel> - the sigma for the gaussian volume smoothing kernel, in

              mm

              <direction> - which dimension to smooth along, ROW or COLUMN <cifti-out> - output -
              the output cifti

              [-left-surface] - specify the left surface to use

              <surface> - the left surface file

              [-left-corrected-areas] - vertex areas to use instead of computing

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

              [-right-surface] - specify the right surface to use

              <surface> - the right surface file

              [-right-corrected-areas] - vertex areas to use instead of computing

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

              [-cerebellum-surface] - specify the cerebellum surface to use

              <surface> - the cerebellum surface file

              [-cerebellum-corrected-areas] - vertex areas to use instead of

              computing  them  from  the  cerebellum surface <area-metric> - the corrected vertex
              areas, as a metric

              [-cifti-roi] - smooth only within regions of interest

              <roi-cifti> - the regions to smooth within, as a cifti file

              [-fix-zeros-volume] - treat values of zero in the volume as missing data

              [-fix-zeros-surface] - treat values of zero on the surface as missing

              data

              [-merged-volume] - smooth across subcortical structure boundaries

              The input cifti file must have a brain models  mapping  on  the  chosen  dimension,
              columns  for  .dtseries,  and  either  for  .dconn.   By default, data in different
              structures is smoothed independently (i.e.,  "parcel  constrained"  smoothing),  so
              volume  structures  that  touch  do  not  smooth  across  this  boundary.   Specify
              -merged-volume  to  ignore  these   boundaries.    Surface   smoothing   uses   the
              GEO_GAUSS_AREA smoothing method.

              The -*-corrected-areas options are intended for when it is unavoidable to smooth on
              group average surfaces, it is only an approximate correction for the  reduction  of
              structure  in  a  group  average  surface.   It  is  better  to  smooth the data on
              individuals before averaging, when feasible.

              The -fix-zeros-* options will treat values of zero as lack of  data,  and  not  use
              that  value  when  generating  the  smoothed  values,  but  will  fill  zeros  with
              extrapolated values.  The ROI should have a brain  models  mapping  along  columns,
              exactly  matching  the  mapping  of  the  chosen direction in the input file.  Data
              outside the ROI is ignored.

       -cifti-stats STATISTICS ALONG CIFTI COLUMNS

              wb_command -cifti-stats

              <cifti-in> - the input cifti

              [-reduce] - use a reduction operation

              <operation> - the reduction operation

              [-percentile] - give the value at a percentile

              <percent> - the percentile to find

              [-column] - only display output for one column

              <column> - the column index (starting from 1)

              [-roi] - only consider data inside an roi

              <roi-cifti> - the roi, as a cifti file

              [-match-maps] - each column of input uses the corresponding column

              from the roi file

              [-show-map-name] - print column index and name before each output

              For each column of the input,  a  row  of  text  is  printed,  resulting  from  the
              specified  reduction  or  percentile  operation.   If  -roi  is  specified  without
              -match-maps, then each row contains as many numbers as there are maps  in  the  ROI
              file,  separated  by  tab characters.  Use -column to only give output for a single
              data column.  Exactly one of -reduce or -percentile must be specified.

              The argument to the -reduce option must be one of the following:

              MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based  index  of  the
              maximum  value INDEXMIN: the 1-based index of the minimum value SUM: add all values
              PRODUCT: multiply all values MEAN:  the  mean  of  the  data  STDEV:  the  standard
              deviation   (N   denominator)   SAMPSTDEV:   the  sample  standard  deviation  (N-1
              denominator) VARIANCE: the variance of  the  data  TSNR:  mean  divided  by  sample
              standard   deviation   (N-1   denominator)  COV:  sample  standard  deviation  (N-1
              denominator) divided by mean MEDIAN: the median of the data MODE: the mode  of  the
              data COUNT_NONZERO: the number of nonzero elements in the data

       -cifti-transpose TRANSPOSE A CIFTI FILE

              wb_command -cifti-transpose

              <cifti-in> - the input cifti file <cifti-out> - output - the output cifti file

              [-mem-limit] - restrict memory usage

              <limit-GB> - memory limit in gigabytes

       The input must be a 2-dimensional cifti file.
              The output is a cifti file

              where every row in the input is a column in the output.

       -cifti-vector-operation DO A VECTOR OPERATION ON CIFTI FILES

              wb_command -cifti-vector-operation

              <vectors-a>  -  first  vector  input  file  <vectors-b>  - second vector input file
              <operation> - what vector operation to do <cifti-out> - output - the output file

              [-normalize-a] - normalize vectors of first input

              [-normalize-b] - normalize vectors of second input

              [-normalize-output] - normalize output vectors (not valid for dot

              product)

              [-magnitude] - output the magnitude of the result (not valid for dot

              product)

              Does a vector operation on two  cifti  files  (that  must  have  a  multiple  of  3
              columns).   Either  of  the inputs may have multiple vectors (more than 3 columns),
              but not both (at least one must  have  exactly  3  columns).   The  -magnitude  and
              -normalize-output  options may not be specified together, or with an operation that
              returns a scalar (dot product).  The <operation>  parameter  must  be  one  of  the
              following:

              DOT CROSS ADD SUBTRACT

       -cifti-weighted-stats WEIGHTED STATISTICS ALONG CIFTI COLUMNS

              wb_command -cifti-weighted-stats

              <cifti-in> - the input cifti

              [-spatial-weights] - use vertex area and voxel volume as weights

              [-left-area-surf] - use a surface for left vertex areas

              <left-surf> - the left surface to use, areas are in mm^2

              [-right-area-surf] - use a surface for right vertex areas

              <right-surf> - the right surface to use, areas are in mm^2

              [-cerebellum-area-surf] - use a surface for cerebellum vertex areas

              <cerebellum-surf> - the cerebellum surface to use, areas are in

              mm^2

              [-left-area-metric] - use a metric file for left vertex areas

              <left-metric> - metric file containing left vertex areas

              [-right-area-metric] - use a metric file for right vertex areas

              <right-metric> - metric file containing right vertex areas

              [-cerebellum-area-metric] - use a metric file for cerebellum vertex

              areas <cerebellum-metric> - metric file containing cerebellum vertex

              areas

              [-cifti-weights] - use a cifti file containing weights

              <weight-cifti> - the weights to use, as a cifti file

              [-column] - only display output for one column

              <column> - the column to use (1-based)

              [-roi] - only consider data inside an roi

              <roi-cifti> - the roi, as a cifti file

              [-match-maps] - each column of input uses the corresponding column

              from the roi file

              [-mean] - compute weighted mean

              [-stdev] - compute weighted standard deviation

              [-sample] - estimate population stdev from the sample

              [-percentile] - compute weighted percentile

              <percent> - the percentile to find

              [-sum] - compute weighted sum

              [-show-map-name] - print map index and name before each output

              If  the  mapping  along  column  is brain models, for each column of the input, the
              specified operation is done on each surface and across all voxels, and the  results
              are  printed  separately.   For  other mapping types, the operation is done on each
              column, and one number per map is printed.   Exactly  one  of  -spatial-weights  or
              -cifti-weights  must  be  specified.   Use -column to only give output for a single
              column.  Use -roi to consider only the data within a region.  Exactly one of -mean,
              -stdev, -percentile or -sum must be specified.

              Using  -sum  with  -spatial-weights  (or with -cifti-weights and a cifti containing
              weights of similar meaning) is equivalent to integrating with respect to  area  and
              volume.   When  the  input  is  binary ROIs, this will therefore output the area or
              volume of each ROI.

       -class-add-member

       Add members to class header (.h) and implementation (.cxx) files.

              [-add-to-files] [-m <member-name> <data-type> <description>]...

              If the -add-to-files is not specified, the code for the header  and  implementation
              files is printed to the terminal.

              If  the  -add-to-files  is  specified,  the  class  files are expected to be in the
              current directory and named <class-name>.h and <class-name>.cxx.  The  header  file
              must contain this text in its private section:

              // ADD_NEW_MEMBERS_HERE

              The implementation file must contain this text in its public section:

              // ADD_NEW_METHODS_HERE

              If  either of these text string are missing, the code that would have been added to
              the file(s) is printed to the terminal.

              For each member, three text strings separated by a space must be provided and  they
              are  the name of the member its data type, and a description of the member.  If the
              description contains spaces the description must be enclosed in double quotes ("").

              If the data type begins with a capital letter, it is assumed to be the  name  of  a
              class.   In  this case, both const and non-const getters are created but not setter
              is created.  Otherwise, the data type is expected to be a primitive type and both a
              getter  and  a  setter  are  created.  Note that AString and QString are treated as
              primitive types.

       -class-create

       Create class header (.h) and implementation (.cxx) files.

       Usage:  <class-name>

              [-copy] [-equal] [-event-class  <event-type-enum>]  [-event-listener]  [-no-parent]
              [-parent <parent-class-name>] [-scene] [-scene-sub-class]

OPTIONS

       -copy

              Adds copy constructor and assignment operator

       -equal

              Adds equality operator.

       -event-class <event-type-enum>

              When  creating  an  Event  subclass,  using  this option will automatically set the
              parent class to Event and place the given event  enumerated  type  value  into  the
              parameter for the Event class constructor.

              For the <event-type-enum> there is no need to prepend it with "EventTypeEnum::".

       -event-listener

              Implement the EventListenerInterface so that the class may listen for events.

       -no-parent

              Created class is not derived from any other class.  By default, the parent class is
              CaretObject.

       -parent <parent-class-name>

              Specify the  parent  (derived  from)  class.   By  default,  the  parent  class  is
              CaretObject.

       -scene

              Implement  the  SceneableInterface  so  that instances of the class can be restored
              from and saved to scenes.

       -scene-sub-class

              Adds methods that can be called by the superclass so that this sub-class  can  save
              and restore data to and from scenes.

              This  option should only be used when creating a class whose super class implements
              the SceneableInterface

       -class-create-algorithm

       Create Algorithm Class header (.h) and implementation (.cxx) files.

       Usage:  <algorithm-class-name>

              <command-line-switch> <short-description>

              algorithm-class-name

              Required name of the algorithm class that MUST start with "Algorithm"

              command-line-switch

              Required command line switch for algorithm.

              short-description

              Required short description within double quotes.

       -class-create-enum

       Create enumerated type header (.h) and implementation (.cxx) files.

       Usage:  <enum-class-name>

              <number-of-values> <auto-number>

              enum-class-name

       Name of the enumerated type.
              Must end in "Enum"

              number-of-values

              Number of values in the enumerated type.

              auto-number

              Automatically generated integer  codes  corresponding  to  the  enumerated  values.
              Value for this parameter are "true" and "false".

              [enum-name-1] [enum-name-2]...[enum-name-N]

              Optional names for the enumerated values.

              If the number of names listed is greater than the "number-of-values" parameter, the
              "number-of-values" will become the number of names.  If the number of names  is  is
              less than the "number-of-values", empty entries will be created.

       -class-create-operation

       Create Operation Class header (.h) and implementation (.cxx) files.

       Usage:  <operation-class-name>

              <command-line-switch> <short-description> [-no-parameters]

              operation-class-name

              Required name of the operation class that MUST start with "Operation"

              command-line-switch

              Required command line switch for operation.

              short-description

              Required short description within double quotes.

       -no-parameters

              Optional parameter if the operation does not use parameters.

       -convert-affine CONVERT AN AFFINE FILE BETWEEN CONVENTIONS

              wb_command -convert-affine

              [-from-world] - input is a NIFTI 'world' affine

              <input> - the input affine

              [-inverse] - for files that use 'target to source' convention

              [-from-itk] - input is an ITK matrix

              <input> - the input affine

              [-from-flirt] - input is a flirt matrix

              <input> - the input affine <source-volume> - the source volume used when generating
              the input

              affine

              <target-volume> - the target volume used when generating the input

              affine

              [-to-world] - write output as a NIFTI 'world' affine

              <output> - output - the output affine

              [-inverse] - write file using 'target to source' convention

              [-to-itk] - write output as an ITK affine

              <output> - output - the output affine

              [-to-flirt] - repeatable - write output as a flirt matrix

              <output> - output - the output affine <source-volume> -  the  volume  you  want  to
              apply  the transform to <target-volume> - the target space you want the transformed
              volume to

              match

              NIFTI  world  matrices  can  be  used  directly  on  mm  coordinates   via   matrix
              multiplication, they use the NIFTI coordinate system, that is, positive X is right,
              positive Y is anterior, and positive Z is superior.  Note that  wb_command  assumes
              that world matrices transform source coordinates to target coordinates, while other
              tools may use affines that transform target coordinates to source coordinates.

              The ITK format is used by ANTS.

              You must specify exactly one  -from  option,  but  you  may  specify  multiple  -to
              options, and -to-flirt may be specified more than once.

       -convert-fiber-orientations CONVERT BINGHAM PARAMETER VOLUMES TO FIBER ORIENTATION FILE

              wb_command -convert-fiber-orientations

              <label-volume> - volume of cifti structure labels <fiber-out> - output - the output
              fiber orientation file

              [-fiber] - repeatable - specify the parameter volumes for a fiber

              <mean-f> - mean fiber strength <stdev-f> - standard  deviation  of  fiber  strength
              <theta>  -  theta  angle  <phi>  -  phi  angle  <psi> - psi angle <ka> - ka bingham
              parameter <kb> - kb bingham parameter

              Takes precomputed bingham parameters from volume files and  converts  them  to  the
              format  workbench  uses  for  display.  The <label-volume> argument must be a label
              volume, where the labels use these strings:

              CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT  ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT     CEREBELLAR_WHITE_MATTER_RIGHT      CEREBELLUM_LEFT
              CEREBELLUM_RIGHT   CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT  CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT  INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -convert-matrix4-to-matrix2 GENERATES A MATRIX2 CIFTI FROM MATRIX4 WBSPARSE

              wb_command -convert-matrix4-to-matrix2

              <matrix4-wbsparse> - a wbsparse matrix4 file <counts-out>  -  output  -  the  total
              fiber counts, as a cifti file

              [-distances] - output average trajectory distance

              <distance-out> - output - the distances, as a cifti file

              [-individual-fibers] - output files for each fiber direction

              <fiber-1>  -  output - output file for first fiber <fiber-2> - output - output file
              for second fiber <fiber-3> - output - output file for third fiber

              This command makes a cifti file from the fiber counts in a matrix4  wbsparse  file,
              and  optionally  a second cifti file from the distances.  Note that while the total
              count is stored exactly, the per-fiber counts are stored as approximate  fractions,
              so the output of -individual-fibers will contain nonintegers.

       -convert-matrix4-to-workbench-sparse CONVERT A 3-FILE MATRIX4 TO A WORKBENCH SPARSE FILE

              wb_command -convert-matrix4-to-workbench-sparse

              <matrix4_1>  -  the  first  matrix4  file  <matrix4_2>  -  the  second matrix4 file
              <matrix4_3> - the third matrix4 file <orientation-file> - the  .fiberTEMP.nii  file
              this trajectory file applies

              to

              <voxel-list> - list of white matter voxel index triplets as used in the

              trajectory matrix

              <wb-sparse-out> - output - the output workbench sparse file

              [-surface-seeds] - specify the surface seed space

              <seed-roi> - metric roi file of all vertices used in the seed space

              [-volume-seeds] - specify the volume seed space

              <cifti-template>  -  cifti  file  to  use  the  volume  mappings from <direction> -
              dimension along the cifti file to take the mapping from,

              ROW or COLUMN

              Converts the matrix 4  output  of  probtrackx  to  workbench  sparse  file  format.
              Exactly one of -surface-seeds and -volume-seeds must be specified.

       -convert-warpfield CONVERT A WARPFIELD BETWEEN CONVENTIONS

              wb_command -convert-warpfield

              [-from-world] - input is a NIFTI 'world' warpfield

              <input> - the input warpfield

              [-from-itk] - input is an ITK warpfield

              <input> - the input warpfield

              [-from-fnirt] - input is a fnirt warpfield

              <input>  -  the  input  warpfield  <source-volume>  -  the  source volume used when
              generating the input

              warpfield

              [-absolute] - warpfield was written in absolute convention, rather

              than relative

              [-to-world] - write output as a NIFTI 'world' warpfield

              <output> - output - the output warpfield

              [-to-itk] - write output as an ITK warpfield

              <output> - output - the output warpfield

              [-to-fnirt] - repeatable - write output as a fnirt warpfield

              <output> - output - the output warpfield <source-volume> - the volume you  want  to
              apply the warpfield to

              NIFTI  world  warpfields  can  be  used directly on mm coordinates via sampling the
              three subvolumes at the coordinate and adding the sampled values to the  coordinate
              vector.   They  use  the NIFTI coordinate system, that is, X is left to right, Y is
              posterior to anterior, and Z is inferior to superior.

              NOTE: this command does not invert the warpfield, and to warp a surface,  you  must
              use the inverse of the warpfield that warps the corresponding volume.

              The ITK format is used by ANTS.

              You  must  specify  exactly  one  -from  option,  but  you may specify multiple -to
              options, and -to-fnirt may be specified more than once.

       -create-signed-distance-volume CREATE SIGNED DISTANCE VOLUME FROM SURFACE

              wb_command -create-signed-distance-volume

              <surface> - the input surface <refspace> - a volume in  the  desired  output  space
              (dims, spacing, origin) <outvol> - output - the output volume

              [-roi-out] - output an roi volume of where the output has a computed

              value <roi-vol> - output - the output roi volume

              [-fill-value] - specify a value to put in all voxels that don't get

              assigned a distance <value> - value to fill with (default 0)

              [-exact-limit] - specify distance for exact output

              <dist> - distance in mm (default 5)

              [-approx-limit] - specify distance for approximate output

              <dist> - distance in mm (default 20)

              [-approx-neighborhood] - voxel neighborhood for approximate calculation

              <num> - size of neighborhood cube measured from center to face, in

              voxels (default 2 = 5x5x5)

              [-winding] - winding method for point inside surface test

              <method> - name of the method (default EVEN_ODD)

       Computes the signed distance function of the surface.
              Exact distance is

              calculated  by  finding  the closest point on any surface triangle to the center of
              the voxel.  Approximate distance is calculated starting with these distances, using
              dijkstra's  method with a neighborhood of voxels.  Specifying too small of an exact
              distance may produce unexpected results.  Valid specifiers for winding methods  are
              as follows:

              EVEN_ODD (default) NEGATIVE NONZERO NORMALS

              The NORMALS method uses the normals of triangles and edges, or the closest triangle
              hit by a ray from the point.  This method may  be  slightly  faster,  but  is  only
              reliable  for  a  closed  surface  that  does  not cross through itself.  All other
              methods count entry (positive) and exit (negative) crossings of a vertical ray from
              the  point,  then  counts  as  inside  if  the  total is odd, negative, or nonzero,
              respectively.

       -estimate-fiber-binghams ESTIMATE FIBER ORIENTATION DISTRIBUTIONS FROM BEDPOSTX SAMPLES

              wb_command -estimate-fiber-binghams

              <merged_f1samples> - fiber 1 strength samples <merged_th1samples> - fiber  1  theta
              samples  <merged_ph1samples>  -  fiber  1  phi samples <merged_f2samples> - fiber 2
              strength samples <merged_th2samples> - fiber 2 theta samples <merged_ph2samples>  -
              fiber   2   phi   samples   <merged_f3samples>   -   fiber   3   strength   samples
              <merged_th3samples> - fiber 3 theta  samples  <merged_ph3samples>  -  fiber  3  phi
              samples  <label-volume>  -  volume of cifti structure labels <cifti-out> - output -
              output cifti fiber distributons file

              This  command  does  an  estimation  of  a  bingham  distribution  for  each  fiber
              orientation in each voxel which is labeled a structure identifier.  These labelings
              come from the <label-volume> argument,  which  must  have  labels  that  match  the
              following strings:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -fiber-dot-products COMPUTE DOT PRODUCTS OF FIBER ORIENTATIONS WITH SURFACE NORMALS

              wb_command -fiber-dot-products

              <white-surf> - the white/gray boundary surface <fiber-file> - the fiber orientation
              file <max-dist> - the maximum distance from any surface vertex a fiber

              population may be, in mm

              <direction> - test against surface for whether a fiber population should

              be used

              <dot-metric> - output - the metric of dot products <f-metric> - output -  a  metric
              of the f values of the fiber distributions

              For each vertex, this command finds the closest fiber population that satisfies the
              <direction> test, and computes the absolute value of the dot product of the surface
              normal  and the normalized mean direction of each fiber.  The <direction> test must
              be one of INSIDE, OUTSIDE, or ANY, which causes  the  command  to  only  use  fiber
              populations  that are inside the surface, outside the surface, or to not care which
              direction it is from the surface.  Each fiber population is output  in  a  separate
              metric column.

       -file-convert CHANGE VERSION OF FILE FORMAT

              wb_command -file-convert

              [-border-version-convert] - write a border file with a different version

              <border-in> - the input border file <out-version> - the format version to write as,
              1 or 3 (2 doesn't

              exist)

              <border-out> - output - the output border file

              [-surface] - must be specified if the input is version 1

              <surface> - use this surface file for structure and number of

              vertices, ignore borders on other structures

              [-nifti-version-convert] - write a nifti file with a different version

              <input> - the input nifti file <version> - the nifti version to write as <output> -
              output - the output nifti file

              [-cifti-version-convert] - write a cifti file with a different version

              <cifti-in>  -  the  input  cifti  file  <version>  -  the cifti version to write as
              <cifti-out> - output - the output cifti file

              You may only specify one top-level option.

       -file-information LIST INFORMATION ABOUT A FILE'S CONTENT

              wb_command -file-information

              <data-file> - data file

              [-no-map-info] - do not show map information for files that support maps

              [-only-step-interval] - suppress normal output, print the interval

              between maps

              [-only-number-of-maps] - suppress normal output, print the number of maps

              [-only-map-names] - suppress normal output, print the names of all maps

              [-only-metadata] - suppress normal output, print file metadata

              [-key] - only print the metadata for one key, with no formatting

              <key> - the metadata key

              [-only-cifti-xml] - suppress normal output, print the cifti xml if the

              file type has it

       List information about the content of a data file.
              Only one -only option

       may be specified.
              The information listed when no -only option is present

              is dependent upon the type of data file.

       -foci-get-projection-vertex GET PROJECTION VERTEX FOR FOCI

              wb_command -foci-get-projection-vertex

              <foci> -  the  foci  file  <surface>  -  the  surface  related  to  the  foci  file
              <metric-out> - output - the output metric file

              [-name] - select a focus by name

              <name> - the name of the focus

              For  each  focus, a column is created in <metric-out>, and the vertex with the most
              influence on its projection is assigned a value of 1 in that column, with all other
              vertices 0.  If -name is used, only one focus will be used.

       -foci-list-coords OUTPUT FOCI COORDINATES IN A TEXT FILE

              wb_command -foci-list-coords

              <foci-file>  -  input  foci  file <coord-file-out> - output - the output coordinate
              text file

              [-names-out] - output the foci names

              <names-file-out> - output - text file to put foci names in

              Output the coordinates for every focus in the foci file, and optionally  the  focus
              names in a second text file.

       -foci-resample PROJECT FOCI TO A DIFFERENT SURFACE

              wb_command -foci-resample

              <foci-in> - the input foci file <foci-out> - output - the output foci file

              [-left-surfaces] - the left surfaces for resampling

              <current-surf>  -  the surface the foci are currently projected on <new-surf> - the
              surface to project the foci onto

              [-right-surfaces] - the right surfaces for resampling

              <current-surf> - the surface the foci are currently projected on <new-surf>  -  the
              surface to project the foci onto

              [-cerebellum-surfaces] - the cerebellum surfaces for resampling

              <current-surf>  -  the surface the foci are currently projected on <new-surf> - the
              surface to project the foci onto

              [-discard-distance-from-surface] - ignore the distance the foci are above

              or below the current surface

              [-restore-xyz] - put the original xyz coordinates into the foci, rather

              than the coordinates obtained from unprojection

              Unprojects foci from the <current-surf> for the structure, then  projects  them  to
              <new-surf>.   If the foci have meaningful distances above or below the surface, use
              anatomical surfaces.  If the foci should be on the surface, use registered  spheres
              and the options -discard-distance-from-surface and -restore-xyz.

       -gifti-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A GIFTI COLUMN

              wb_command -gifti-all-labels-to-rois

              <label-in> - the input gifti label file <map> - the number or name of the label map
              to use <metric-out> - output - the output metric file

              The output metric file has a column for each label  in  the  specified  input  map,
              other  than  the  ??? label, each of which contains an ROI of all vertices that are
              set to the corresponding label.

       -gifti-convert CONVERT A GIFTI FILE TO A DIFFERENT ENCODING

              wb_command -gifti-convert

              <gifti-encoding> - what the output encoding  should  be  <input-gifti-file>  -  the
              input gifti file <output-gifti-file> - output - the output gifti file

              The value of <gifti-encoding> must be one of the following:

              ASCII BASE64_BINARY GZIP_BASE64_BINARY EXTERNAL_FILE_BINARY

       -gifti-label-add-prefix ADD PREFIX TO ALL LABEL NAMES IN A GIFTI LABEL FILE

              wb_command -gifti-label-add-prefix

              <label-in> - the input label file <prefix> - the prefix string to add <label-out> -
              output - the output label file

              For each label other than '???', prepend <prefix> to the label name.

       -gifti-label-to-roi MAKE A GIFTI LABEL INTO AN ROI METRIC

              wb_command -gifti-label-to-roi

              <label-in> - the input gifti label file <metric-out> - output - the  output  metric
              file

              [-name] - select label by name

              <label-name> - the label name that you want an roi of

              [-key] - select label by key

              <label-key> - the label key that you want an roi of

              [-map] - select a single label map to use

              <map> - the map number or name

              For  each  map  in <label-in>, a map is created in <metric-out> where all locations
              labeled with <label-name> or with a key of <label-key> are given a value of 1,  and
              all  other locations are given 0.  Exactly one of -name and -key must be specified.
              Specify -map to use only one map from <label-in>.

       -label-dilate DILATE A LABEL FILE

              wb_command -label-dilate

              <label> - the input label <surface> - the surface  to  dilate  on  <dilate-dist>  -
              distance in mm to dilate the labels <label-out> - output - the output label file

              [-bad-vertex-roi] - specify an roi of vertices to overwrite, rather than

              vertices  with the unlabeled key <roi-metric> - metric file, positive values denote
              vertices to have

              their values replaced

              [-column] - select a single column to dilate

              <column> - the column number or name

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

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

              Fills in label information for all vertices designated as bad, up to the  specified
              distance  away  from  other labels.  If -bad-vertex-roi is specified, all vertices,
              including those with the unlabeled key,  are  good,  except  for  vertices  with  a
              positive  value  in  the  ROI.   If  it  is  not  specified, only vertices with the
              unlabeled key are bad.

       -label-erode ERODE A LABEL FILE

              wb_command -label-erode

              <label> - the input label <surface> -  the  surface  to  erode  on  <erode-dist>  -
              distance in mm to erode the labels <label-out> - output - the output label file

              [-roi] - assume values outside this roi are labeled

              <roi-metric> - metric file, positive values denote vertices that have

              data

              [-column] - select a single column to erode

              <column> - the column number or name

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

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

              Around  each  vertex that is unlabeled, set surrounding vertices to unlabeled.  The
              surrounding vertices are all  immediate  neighbors  and  all  vertices  within  the
              specified distance.

              Note  that  the -corrected-areas option uses an approximate correction for distance
              along the surface.

       -label-export-table EXPORT LABEL TABLE FROM GIFTI AS TEXT

              wb_command -label-export-table

              <label-in> - the input label file <table-out> - output - the output text file

              Takes the label table from the gifti label file, and writes it  to  a  text  format
              matching what is expected by -metric-label-import.

       -label-mask MASK A LABEL FILE

              wb_command -label-mask

              <label>  -  the  label file to mask <mask> - the mask metric <label-out> - output -
              the output label file

              [-column] - select a single column

              <column> - the column number or name

              By default, the output label is a copy of the input label, but  with  the  'unused'
              label  wherever  the mask metric is zero or negative.  if -column is specified, the
              output contains only one column, the masked version of the specified input column.

       -label-merge MERGE LABEL FILES INTO A NEW FILE

              wb_command -label-merge

              <label-out> - output - the output label

              [-label] - repeatable - specify an input label

              <label-in> - a label file to use columns from

              [-column] - repeatable - select a single column to use

              <column> - the column number or name

              [-up-to] - use an inclusive range of columns

              <last-column> - the number or name of the last column to include

              [-reverse] - use the range in reverse order

              Takes one or more label files and constructs a  new  label  file  by  concatenating
              columns  from  them.  The input files must have the same number of vertices and the
              same structure.

              Example: wb_command -label-merge out.label.gii  -label  first.label.gii  -column  1
              -label second.label.gii

              This  example  would  take the first column from first.label.gii and all subvolumes
              from second.label.gii, and write these to out.label.gii.

       -label-modify-keys CHANGE KEY VALUES IN A LABEL FILE

              wb_command -label-modify-keys

              <label-in> - the input label file <remap-file> - text file with  old  and  new  key
              values <label-out> - output - output label file

              [-column] - select a single column to use

              <column> - the column number or name

              <remap-file> should have lines of the form 'oldkey newkey', like so:

              3 5 5 8 8 2

              This  would  change  the  current  label with key '3' to use the key '5' instead, 5
              would use 8, and 8 would use 2.  Any collision in key values results in  the  label
              that  was  not  specified in the remap file getting remapped to an otherwise unused
              key.  Remapping more than one key to the same new key, or the same key to more than
              one  new key, results in an error.  This will not change the appearance of the file
              when displayed, it will change the keys in the data at the same time.

       -label-probability FIND FREQUENCY OF SURFACE LABELS

              wb_command -label-probability

              <label-maps> - label file containing individual label maps from many

              subjects

              <probability-metric-out> - output - the relative frequencies of each

              label at each vertex

              [-exclude-unlabeled] - don't make a probability map of the unlabeled key

              This command outputs a set of soft ROIs, one for each label in the input, where the
              value  is  how many of the input maps had that label at that vertex, divided by the
              number of input maps.

       -label-resample RESAMPLE A LABEL FILE TO A DIFFERENT MESH

              wb_command -label-resample

              <label-in> - the label file to resample <current-sphere> - a  sphere  surface  with
              the mesh that the label file is

              currently on

              <new-sphere> - a sphere surface that is in register with <current-sphere>

              and has the desired output mesh

              <method> - the method name <label-out> - output - the output label file

              [-area-surfs] - specify surfaces to do vertex area correction based on

              <current-area> - a relevant anatomical surface with <current-sphere>

              mesh

              <new-area> - a relevant anatomical surface with <new-sphere> mesh

              [-area-metrics] - specify vertex area metrics to do area correction based

              on <current-area> - a metric file with vertex areas for <current-sphere>

              mesh

              <new-area> - a metric file with vertex areas for <new-sphere> mesh

              [-current-roi] - use an input roi on the current mesh to exclude non-data

              vertices <roi-metric> - the roi, as a metric file

              [-valid-roi-out] - output the ROI of vertices that got data from valid

              source vertices <roi-out> - output - the output roi as a metric

              [-largest] - use only the label of the vertex with the largest weight

              Resamples  a  label  file,  given  two spherical surfaces that are in register.  If
              ADAP_BARY_AREA is used,  exactly  one  of  -area-surfs  or  -area-metrics  must  be
              specified.

              The  ADAP_BARY_AREA  method  is  recommended  for  label data, because it should be
              better at resolving  vertices  that  are  near  multiple  labels,  or  in  case  of
              downsampling.   Midthickness surfaces are recommended for the vertex areas for most
              data.

              The -largest option results in nearest vertex behavior when used with  BARYCENTRIC,
              as it uses the value of the source vertex that has the largest weight.

              When  -largest  is  not specified, the vertex weights are summed according to which
              label they correspond to, and the label with the largest sum is used.

              The <method> argument must be one of the following:

              ADAP_BARY_AREA BARYCENTRIC

       -label-to-border DRAW BORDERS AROUND LABELS

              wb_command -label-to-border

              <surface> - the surface to use for neighbor  information  <label-in>  -  the  input
              label file <border-out> - output - the output border file

              [-placement] - set how far along the edge border points are drawn

              <fraction> - fraction along edge from inside vertex (default 0.33)

              [-column] - select a single column

              <column> - the column number or name

              For  each  label, finds all edges on the mesh that cross the boundary of the label,
              and draws borders through them.  By default, this is done on  all  columns  in  the
              input file, using the map name as the class name for the border.

       -label-to-volume-mapping MAP LABEL FILE TO VOLUME

              wb_command -label-to-volume-mapping

              <label>  -  the  input  label  file <surface> - the surface to use coordinates from
              <volume-space> - a volume file in the desired output volume  space  <volume-out>  -
              output - the output volume file

              [-nearest-vertex] - use the label from the vertex closest to the voxel

              center <distance> - how far from the surface to map labels to voxels, in mm

              [-ribbon-constrained] - use ribbon constrained mapping algorithm

              <inner-surf>  - the inner surface of the ribbon <outer-surf> - the outer surface of
              the ribbon

              [-voxel-subdiv] - voxel divisions while estimating voxel weights

              <subdiv-num> - number of subdivisions, default 3

              [-greedy] - also put labels in voxels with less than 50% partial

              volume (legacy behavior)

              [-thick-columns] - use overlapping columns (legacy method)

       Maps labels from a gifti label file into a volume file.
              You must specify

       exactly one mapping method option.
              The -nearest-vertex method uses the

       label from the vertex closest to the voxel center.
              The

       -ribbon-constrained method uses the same method as in

       -volume-to-surface-mapping, then uses the weights in reverse, with

              popularity logic to decide on a label to use.

       -metadata-remove-provenance REMOVE PROVENANCE INFORMATION FROM FILE METADATA

              wb_command -metadata-remove-provenance

              <input-file> - the file to  remove  provenance  information  from  <output-file>  -
              output - the name to save the modified file as

              Removes the provenance metadata fields added by workbench during processing.

       -metadata-string-replace REPLACE A STRING IN ALL METADATA OF A FILE

              wb_command -metadata-string-replace

              <input-file>  -  the file to replace metadata in <find-string> - the string to find
              <replace-string> - the string to replace <find-string> with <output-file> -  output
              - the name to save the modified file as

              [-case-insensitive] - match with case variation also

              Replaces  all  occurrences  of  <find-string>  in  the  metadata  and  map names of
              <input-file> with <replace-string>.

       -metric-convert CONVERT METRIC FILE TO FAKE NIFTI

              wb_command -metric-convert

              [-to-nifti] - convert metric to nifti

              <metric-in> - the metric to convert <nifti-out> - output - the output nifti file

              [-from-nifti] - convert nifti to metric

              <nifti-in> - the nifti file to convert <surface-in> - surface file to use number of
              vertices and structure

              from

              <metric-out> - output - the output metric file

              The  purpose  of this command is to convert between metric files and nifti1 so that
              gifti-unaware programs can operate on the data.  You must specify  exactly  one  of
              the options.

       -metric-dilate DILATE A METRIC FILE

              wb_command -metric-dilate

              <metric>  - the metric to dilate <surface> - the surface to compute on <distance> -
              distance in mm to dilate <metric-out> - output - the output metric

              [-bad-vertex-roi] - specify an roi of vertices to overwrite, rather than

              vertices with value  zero  <roi-metric>  -  metric  file,  positive  values  denote
              vertices to have

              their values replaced

              [-data-roi] - specify an roi of where there is data

              <roi-metric> - metric file, positive values denote vertices that have

              data

              [-column] - select a single column to dilate

              <column> - the column number or name

              [-nearest] - use the nearest good value instead of a weighted average

              [-linear] - fill in values with linear interpolation along strongest

              gradient

              [-exponent] - use a different exponent in the weighting function

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

              weighting function (default 2)

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

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

              For  all  metric  vertices  that  are designated as bad, if they neighbor a non-bad
              vertex with data or are within the specified distance of such a vertex, replace the
              value  with  a distance weighted average of nearby non-bad vertices that have data,
              otherwise set the value to zero.  No matter how small <distance> is, dilation  will
              always  use at least the immediate neighbor vertices.  If -nearest is specified, it
              will use the value from the closest non-bad vertex with data within  range  instead
              of a weighted average.

              If -bad-vertex-roi is specified, only vertices with a positive value in the ROI are
              bad.  If it is not specified, only vertices that have data, with a value  of  zero,
              are bad.  If -data-roi is not specified, all vertices are assumed to have data.

              Note that the -corrected-areas option uses an approximate correction for the change
              in distances along a group average surface.

       -metric-erode ERODE A METRIC FILE

              wb_command -metric-erode

              <metric> - the metric  file  to  erode  <surface>  -  the  surface  to  compute  on
              <distance> - distance in mm to erode <metric-out> - output - the output metric

              [-roi] - assume values outside this roi are nonzero

              <roi-metric> - metric file, positive values denote vertices that have

              data

              [-column] - select a single column to erode

              <column> - the column number or name

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

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

              Around  each  vertex  with  a value of zero, set surrounding vertices to zero.  The
              surrounding vertices are all  immediate  neighbors  and  all  vertices  within  the
              specified distance.

              Note  that  the -corrected-areas option uses an approximate correction for distance
              along the surface.

       -metric-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A METRIC FILE

              wb_command -metric-estimate-fwhm

              <surface> - the surface to use for distance and neighbor information <metric-in>  -
              the input metric

              [-roi] - use only data within an ROI

              <roi-metric> - the metric file to use as an ROI

              [-column] - select a single column to estimate smoothness of

              <column> - the column number or name

              Estimates  the smoothness of the metric columns, printing the estimates to standard
              output.  These estimates ignore variation in vertex spacing.

       -metric-extrema FIND EXTREMA IN A METRIC FILE

              wb_command -metric-extrema

              <surface> - the surface to use for distance information <metric-in> - the metric to
              find the extrema of <distance> - the minimum distance between identified extrema of
              the same

              type

              <metric-out> - output - the output extrema metric

              [-presmooth] - smooth the metric before finding extrema

              <kernel> - the sigma for the gaussian smoothing kernel, in mm

              [-roi] - ignore values outside the selected area

              <roi-metric> - the area to find extrema in, as a metric

              [-threshold] - ignore small extrema

              <low> - the largest value to consider for being a minimum  <high>  -  the  smallest
              value to consider for being a maximum

              [-sum-columns] - output the sum of the extrema columns instead of each

              column separately

              [-consolidate-mode] - use consolidation of local minima instead of a

              large neighborhood

              [-only-maxima] - only find the maxima

              [-only-minima] - only find the minima

              [-column] - select a single column to find extrema in

              <column> - the column number or name

              Finds  extrema  in  a  metric  file,  such that no two extrema of the same type are
              within <distance> of each other.  The extrema are labeled as -1 for minima,  1  for
              maxima,  0  otherwise.   If -only-maxima or -only-minima is specified, then it will
              ignore extrema not of the specified type.  These options are mutually exclusive.

              If -roi is specified, not only is data outside the roi not used, but any vertex  on
              the  edge  of  the  ROI  will  never be counted as an extrema, in case the ROI cuts
              across a gradient, which would otherwise generate extrema  where  there  should  be
              none.

              If  -sum-columns is specified, these extrema columns are summed, and the output has
              a single column with this result.

              By default, a datapoint is an extrema only if it is more extreme than  every  other
              datapoint  that  is  within  <distance>  from it.  If -consolidate-mode is used, it
              instead starts by finding all datapoints that are more extreme than their immediate
              neighbors,  then  while there are any extrema within <distance> of each other, take
              the two extrema closest to each other and merge them into one by a weighted average
              based on how many original extrema have been merged into each.

              By  default, all input columns are used with no smoothing, use -column to specify a
              single column to use, and  -presmooth  to  smooth  the  input  before  finding  the
              extrema.

       -metric-false-correlation COMPARE CORRELATION LOCALLY AND ACROSS/THROUGH SULCI/GYRI

              wb_command -metric-false-correlation

              <surface>  - the surface to compute geodesic and 3D distance with <metric-in> - the
              metric to correlate <3D-dist> - maximum 3D distance to  check  around  each  vertex
              <geo-outer> - maximum geodesic distance to use for neighboring

              correlation

              <geo-inner> - minimum geodesic distance to use for neighboring

              correlation

              <metric-out> - output - the output metric

              [-roi] - select a region of interest that has data

              <roi-metric> - the region, as a metric file

              [-dump-text] - dump the raw measures used to a text file

              <text-out> - the output text file

              For  each  vertex,  compute  the  average  correlation  within  a range of geodesic
              distances that don't cross a sulcus/gyrus,  and  the  correlation  to  the  closest
              vertex  crossing a sulcus/gyrus.  A vertex is considered to cross a sulcus/gyrus if
              the 3D distance is less than a third of the geodesic  distance.   The  output  file
              contains  the  ratio  between  these correlations, and some additional maps to help
              explain the ratio.

       -metric-fill-holes FILL HOLES IN AN ROI METRIC

              wb_command -metric-fill-holes

              <surface> - the surface to use for neighbor information <metric-in> - the input ROI
              metric <metric-out> - output - the output ROI metric

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

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

              Finds  all  connected  areas that are not included in the ROI, and writes ones into
              all but the largest one, in terms of surface area.

       -metric-find-clusters FILTER CLUSTERS BY SURFACE AREA

              wb_command -metric-find-clusters

              <surface>  -  the  surface  to  compute  on  <metric-in>   -   the   input   metric
              <value-threshold>  -  threshold  for  data  values  <minimum-area>  - threshold for
              cluster area, in mm^2 <metric-out> - output - the output metric

              [-less-than] - find values less than <value-threshold>, rather than

              greater

              [-roi] - select a region of interest

              <roi-metric> - the roi, as a metric

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

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

              [-column] - select a single column

              <column> - the column number or name

              [-size-ratio] - ignore clusters smaller than a given fraction of the

              largest cluster in map <ratio> - fraction of the largest cluster's area

              [-distance] - ignore clusters further than a given distance from the

              largest cluster <distance> - how far from the largest cluster  a  cluster  can  be,
              edge

              to edge, in mm

              [-start] - start labeling clusters from a value other than 1

              <startval> - the value to give the first cluster found

              Outputs  a  metric  with  nonzero  integers  for all vertices within a large enough
              cluster, and zeros elsewhere.  The integers denote cluster membership (by  default,
              first  cluster  found will use value 1, second cluster 2, etc).  By default, values
              greater than <value-threshold> are considered to be in a cluster, use -less-than to
              test  for  values less than the threshold.  To apply this as a mask to the data, or
              to do more complicated thresholding, see -metric-math.

       -metric-gradient SURFACE GRADIENT OF A METRIC FILE

              wb_command -metric-gradient

              <surface> - the surface to compute the gradient on  <metric-in>  -  the  metric  to
              compute the gradient of <metric-out> - output - the magnitude of the gradient

              [-presmooth] - smooth the metric before computing the gradient

              <kernel> - the sigma for the gaussian smoothing kernel, in mm

              [-roi] - select a region of interest to take the gradient of

              <roi-metric> - the area to take the gradient within, as a metric

              [-match-columns] - for each input column, use the corresponding column

              from the roi

              [-vectors] - output gradient vectors

              <vector-metric-out> - output - the vectors as a metric file

              [-column] - select a single column to compute the gradient of

              <column> - the column number or name

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

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

              [-average-normals] - average the normals of each vertex with its

              neighbors before using them to compute the gradient

              At  each  vertex,  the immediate neighbors are unfolded onto a plane tangent to the
              surface at the vertex (specifically, perpendicular to the normal).  The gradient is
              computed  using  a  regression  between  the unfolded positions of the vertices and
              their values.  The gradient is then given by the  slopes  of  the  regression,  and
              reconstructed  as  a  3D  gradient  vector.   By default, takes the gradient of all
              columns, with no presmoothing, across the  whole  surface,  without  averaging  the
              normals of the surface among neighbors.

              When  using  -corrected-areas,  note  that  it is an approximate correction.  Doing
              smoothing on individual  surfaces  before  averaging/gradient  is  preferred,  when
              possible, in order to make use of the original surface structure.

              Specifying  an  ROI  will restrict the gradient to only use data from where the ROI
              metric is positive, and output zeros anywhere the ROI metric is not positive.

              By default, the first column of the roi metric is used for all input columns.  When
              -match-columns is specified to the -roi option, the input and roi metrics must have
              the same number of columns, and for each input  column's  index,  the  same  column
              index  is  used  in  the  roi metric.  If the -match-columns option to -roi is used
              while the -column option is also used, the number of columns of the roi metric must
              match  the  input  metric,  and  it  will  use the roi column with the index of the
              selected input column.

              The vector output metric is organized such that the X, Y, and Z components  from  a
              single input column are consecutive columns.

       -metric-label-import IMPORT A GIFTI LABEL FILE FROM A METRIC FILE

              wb_command -metric-label-import

              <input> - the input metric file <label-list-file> - text file containing the values
              and names for labels <output> - output - the output gifti label file

              [-discard-others] - set any values not mentioned in the label list to the

              ??? label

              [-unlabeled-value] - set the value that will be interpreted as unlabeled

              <value> - the numeric value for unlabeled (default 0)

              [-column] - select a single column to import

              <column> - the column number or name

              [-drop-unused-labels] - remove any unused label values from the label

              table

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

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

              Do  not  specify  the  "unlabeled"  key in the file, it is assumed that 0 means not
              labeled unless -unlabeled-value is specified.  Label names must be  on  a  separate
              line,  but  may  contain  spaces  or  other  unusual  characters (but not newline).
              Whitespace is trimmed from both ends of the label name, but is kept if it is in the
              middle  of a label.  The values of red, green, blue and alpha must be integers from
              0 to 255, and will specify the color the label is drawn  as  (alpha  of  255  means
              opaque,  which is probably what you want).  By default, it will set new label names
              with names of LABEL_# for any values encountered that are not mentioned in the list
              file, specify -discard-others to instead set these voxels to the "unlabeled" key.

       -metric-mask MASK A METRIC FILE

              wb_command -metric-mask

              <metric>  -  the  input metric <mask> - the mask metric <metric-out> - output - the
              output metric

              [-column] - select a single column

              <column> - the column number or name

              By default, the output metric is a  copy  of  the  input  metric,  but  with  zeros
              wherever  the mask metric is zero or negative.  if -column is specified, the output
              contains only one column, the masked version of the specified input column.

       -metric-math EVALUATE EXPRESSION ON METRIC FILES

              wb_command -metric-math

              <expression> - the expression to evaluate, in quotes <metric-out> -  output  -  the
              output metric

              [-fixnan] - replace NaN results with a value

              <replace> - value to replace NaN with

              [-var] - repeatable - a metric to use as a variable

              <name>  - the name of the variable, as used in the expression <metric> - the metric
              file to use as this variable

              [-column] - select a single column

              <column> - the column number or name

              [-repeat] - reuse a single column for each column of calculation

              This command evaluates <expression> at each surface  vertex  independently.   There
              must  be  at  least  one -var option (to get the structure, number of vertices, and
              number of columns from),  even  if  the  <name>  specified  in  it  isn't  used  in
              <expression>.   All  metrics  must have the same number of vertices.  Filenames are
              not valid in <expression>, use a variable name and  a  -var  option  with  matching
              <name>  to  specify  an  input  file.   If  the -column option is given to any -var
              option, only one column is used from that file.  If -repeat is specified, the  file
              must  either have only one column, or have the -column option specified.  All files
              that don't use -repeat must have the same number of columns requested to  be  used.
              The format of <expression> is as follows:

              Expressions consist of constants, variables, operators, parentheses, and functions,
              in infix notation, such as 'exp(-x + 3) * scale'.  Variables  are  strings  of  any
              length,  using  the characters a-z, A-Z, 0-9, and _, but may not take the name of a
              named constant.  Currently, there is only one named constant,  PI.   The  operators
              are  +,  -, *, /, ^, >, <, >=, <=, ==, !=, !, &&, ||.  These behave as in C, except
              that ^ is exponentiation, i.e. pow(x, y), and takes higher  precedence  than  other
              binary operators (also, '-3^-4^-5' means '-(3^(-(4^-5)))').  The <=, >=, ==, and !=
              operators are given a small amount of wiggle room, equal to one  millionth  of  the
              smaller of the absolute values of the values being compared.

              Comparison and logical operators return 0 or 1, you can do masking with expressions
              like 'x * (mask > 0)'.  For all logical operators, an input is considered true  iff
              it  is  greater than 0.  The expression '0 < x < 5' is not syntactically wrong, but
              it will NOT do what is desired, because it is evaluated left to right, i.e. '((0  <
              x)  < 5)', which will always return 1, as both possible results of a comparison are
              less than 5.  A warning is generated if an expression of  this  type  is  detected.
              Use something like 'x > 0 && x < 5' to get the desired behavior.

              Whitespace  between  elements  is  ignored,  '  sin  (  2  * x ) ' is equivalent to
              'sin(2*x)', but 's in(2*x)' is an error.  Implied multiplication  is  not  allowed,
              the  expression  '2x' will be parsed as a variable.  Parentheses are (), do not use
              [] or {}.  Functions require parentheses, the expression 'sin x' is an error.

              The following functions are supported:

              sin: 1 argument, the sine of the argument (units are radians) cos: 1 argument,  the
              cosine  of  the  argument  (units  are radians) tan: 1 argument, the tangent of the
              argument (units are radians) asin: 1 argument, the inverse of sine of the argument,
              in  radians  acos:  1  argument,  the inverse of cosine of the argument, in radians
              atan: 1 argument, the inverse of tangent of  the  argument,  in  radians  atan2:  2
              arguments, atan2(y, x) returns the inverse of tangent of

              (y/x), in radians, determining quadrant by the sign of both arguments

              sinh:  1  argument,  the  hyperbolic  sine  of  the  argument cosh: 1 argument, the
              hyperbolic cosine of the argument tanh: 1 argument, the hyperboloc tangent  of  the
              argument  asinh:  1  argument, the inverse hyperbolic sine of the argument acosh: 1
              argument, the inverse hyperbolic cosine of the  argument  atanh:  1  argument,  the
              inverse hyperboloc tangent of the argument ln: 1 argument, the natural logarithm of
              the argument exp: 1 argument, the constant e raised to the power  of  the  argument
              log: 1 argument, the base 10 logarithm of the argument sqrt: 1 argument, the square
              root of the argument abs: 1 argument, the absolute value of the argument  floor:  1
              argument,  the largest integer not greater than the argument round: 1 argument, the
              nearest integer, with ties rounded away from

              zero

              ceil: 1 argument, the smallest integer not less than the argument min: 2 arguments,
              min(x,  y)  returns y if (x > y), x otherwise max: 2 arguments, max(x, y) returns y
              if (x < y), x otherwise mod: 2 arguments, mod(x, y) = x - y * floor(x / y), or 0 if
              y == 0 clamp: 3 arguments, clamp(x, low, high) = min(max(x, low), high)

       -metric-merge MERGE METRIC FILES INTO A NEW FILE

              wb_command -metric-merge

              <metric-out> - output - the output metric

              [-metric] - repeatable - specify an input metric

              <metric-in> - a metric file to use columns from

              [-column] - repeatable - select a single column to use

              <column> - the column number or name

              [-up-to] - use an inclusive range of columns

              <last-column> - the number or name of the last column to include

              [-reverse] - use the range in reverse order

              Takes  one  or  more metric files and constructs a new metric file by concatenating
              columns from them.  The input metric files must have the same  number  of  vertices
              and same structure.

              Example:  wb_command  -metric-merge  out.func.gii  -metric first.func.gii -column 1
              -metric second.func.gii

              This example would take the first  column  from  first.func.gii,  followed  by  all
              columns from second.func.gii, and write these columns to out.func.gii.

       -metric-palette SET THE PALETTE OF A METRIC FILE

              wb_command -metric-palette

              <metric> - the metric to modify <mode> - the mapping mode

              [-column] - select a single column

              <column> - the column number or name

              [-pos-percent] - percentage min/max for positive data coloring

              <pos-min-%>  -  the  percentile  for  the  least  positive  data  <pos-max-%> - the
              percentile for the most positive data

              [-neg-percent] - percentage min/max for negative data coloring

              <neg-min-%> - the  percentile  for  the  least  negative  data  <neg-max-%>  -  the
              percentile for the most negative data

              [-pos-user] - user min/max values for positive data coloring

              <pos-min-user>  -  the value for the least positive data <pos-max-user> - the value
              for the most positive data

              [-neg-user] - user min/max values for negative data coloring

              <neg-min-user> - the value for the least negative data <neg-max-user> -  the  value
              for the most negative data

              [-interpolate] - interpolate colors

              <interpolate> - boolean, whether to interpolate

              [-disp-pos] - display positive data

              <display> - boolean, whether to display

              [-disp-neg] - display positive data

              <display> - boolean, whether to display

              [-disp-zero] - display data closer to zero than the min cutoff

              <display> - boolean, whether to display

              [-palette-name] - set the palette used

              <name> - the name of the palette

              [-thresholding] - set the thresholding

              <type>  -  thresholding  setting  <test> - show values inside or outside thresholds
              <min> - lower threshold <max> - upper threshold

              [-inversion] - specify palette inversion

              <type> - the type of inversion

       The original metric file is overwritten with the modified version.
              By

              default, all columns of the metric file are adjusted to the new settings,  use  the
              -column  option  to  change  only  one  column.   Mapping settings not specified in
              options will be taken from the first column.  The <mode> argument must  be  one  of
              the following:

              MODE_AUTO_SCALE    MODE_AUTO_SCALE_ABSOLUTE_PERCENTAGE   MODE_AUTO_SCALE_PERCENTAGE
              MODE_USER_SCALE

              The <name> argument to -palette-name must be one of the following:

              ROY-BIG-BL  videen_style  Gray_Interp_Positive  Gray_Interp   PSYCH-FIXED   RBGYR20
              RBGYR20P  RYGBR4_positive  RGRBR_mirror90_pos Orange-Yellow POS_NEG_ZERO red-yellow
              blue-lightblue FSL power_surf fsl_red fsl_green  fsl_blue  fsl_yellow  RedWhiteBlue
              cool-warm  spectral  RY-BC-BL  magma JET256 PSYCH PSYCH-NO-NONE ROY-BIG clear_brain
              fidl raich4_clrmid raich6_clrmid HSB8_clrmid POS_NEG

              The <type> argument to -thresholding must be one of the following:

              THRESHOLD_TYPE_OFF THRESHOLD_TYPE_NORMAL THRESHOLD_TYPE_FILE

              The <test> argument to -thresholding must be one of the following:

              THRESHOLD_TEST_SHOW_OUTSIDE THRESHOLD_TEST_SHOW_INSIDE

              The <type> argument to -inversion must be one of the following:

              OFF POSITIVE_WITH_NEGATIVE POSITIVE_NEGATIVE_SEPARATE

       -metric-reduce PERFORM REDUCTION OPERATION ACROSS METRIC COLUMNS

              wb_command -metric-reduce

              <metric-in> - the metric to reduce <operation> -  the  reduction  operator  to  use
              <metric-out> - output - the output metric

              [-exclude-outliers] - exclude non-numeric values and outliers by standard

              deviation <sigma-below> - number of standard deviations below the mean to

              include

              <sigma-above> - number of standard deviations above the mean to

              include

              [-only-numeric] - exclude non-numeric values

              For  each  surface  vertex, takes the data across columns as a vector, and performs
              the specified reduction on it, putting the result into the single output column  at
              that vertex.  The reduction operators are as follows:

              MAX:  the  maximum  value MIN: the minimum value INDEXMAX: the 1-based index of the
              maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all  values
              PRODUCT:  multiply  all  values  MEAN:  the  mean  of  the data STDEV: the standard
              deviation  (N  denominator)  SAMPSTDEV:  the   sample   standard   deviation   (N-1
              denominator)  VARIANCE:  the  variance  of  the  data  TSNR: mean divided by sample
              standard  deviation  (N-1  denominator)  COV:  sample   standard   deviation   (N-1
              denominator)  divided  by mean MEDIAN: the median of the data MODE: the mode of the
              data COUNT_NONZERO: the number of nonzero elements in the data

       -metric-regression REGRESS METRICS OUT OF A METRIC FILE

              wb_command -metric-regression

              <metric-in> - the metric to regress from <metric-out> - output - the output metric

              [-roi] - only regress inside an roi

              <roi-metric> - the area to use for regression, as a metric

              [-column] - select a single column to regress from

              <column> - the column number or name

              [-remove] - repeatable - specify a metric to regress out

              <metric> - the metric file to use

              [-remove-column] - select a column to use, rather than all

              <column> - the column number or name

              [-keep] - repeatable - specify a metric to include in regression, but not

              remove <metric> - the metric file to use

              [-keep-column] - select a column to use, rather than all

              <column> - the column number or name

              For each regressor, its mean across the surface is subtracted from its data.   Each
              input  map  is  then  regressed  against these, and a constant term.  The resulting
              regressed slopes of all regressors specified with -remove are multiplied with their
              respective regressor maps, and these are subtracted from the input map.

       -metric-remove-islands REMOVE ISLANDS FROM AN ROI METRIC

              wb_command -metric-remove-islands

              <surface> - the surface to use for neighbor information <metric-in> - the input ROI
              metric <metric-out> - output - the output ROI metric

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

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

              Finds all connected areas in the ROI, and zeros out all but  the  largest  one,  in
              terms of surface area.

       -metric-resample RESAMPLE A METRIC FILE TO A DIFFERENT MESH

              wb_command -metric-resample

              <metric-in>  - the metric file to resample <current-sphere> - a sphere surface with
              the mesh that the metric is

              currently on

              <new-sphere> - a sphere surface that is in register with <current-sphere>

              and has the desired output mesh

              <method> - the method name <metric-out> - output - the output metric

              [-area-surfs] - specify surfaces to do vertex area correction based on

              <current-area> - a relevant anatomical surface with <current-sphere>

              mesh

              <new-area> - a relevant anatomical surface with <new-sphere> mesh

              [-area-metrics] - specify vertex area metrics to do area correction based

              on <current-area> - a metric file with vertex areas for <current-sphere>

              mesh

              <new-area> - a metric file with vertex areas for <new-sphere> mesh

              [-current-roi] - use an input roi on the current mesh to exclude non-data

              vertices <roi-metric> - the roi, as a metric file

              [-valid-roi-out] - output the ROI of vertices that got data from valid

              source vertices <roi-out> - output - the output roi as a metric

              [-largest] - use only the value of the vertex with the largest weight

              Resamples a metric file, given two spherical surfaces that  are  in  register.   If
              ADAP_BARY_AREA  is  used,  exactly  one  of  -area-surfs  or  -area-metrics must be
              specified.

              The ADAP_BARY_AREA method is recommended  for  ordinary  metric  data,  because  it
              should  use all data while downsampling, unlike BARYCENTRIC.  The recommended areas
              option for most data is individual midthicknesses for individual data, and averaged
              vertex area metrics from individual midthicknesses for group average data.

              The -current-roi option only masks the input, the output may be slightly dilated in
              comparison, consider using -metric-mask on the output when using -current-roi.

              The -largest option results in nearest vertex behavior when used with  BARYCENTRIC.
              When  resampling  a  binary  metric,  consider thresholding at 0.5 after resampling
              rather than using -largest.

              The <method> argument must be one of the following:

              ADAP_BARY_AREA BARYCENTRIC

       -metric-rois-from-extrema CREATE METRIC ROI MAPS FROM EXTREMA MAPS

              wb_command -metric-rois-from-extrema

              <surface> - the surface to use for geodesic distance <metric> -  the  input  metric
              file  <limit>  - geodesic distance limit from vertex, in mm <metric-out> - output -
              the output metric file

              [-gaussian] - generate a gaussian kernel instead of a flat ROI

              <sigma> - the sigma for the gaussian kernel, in mm

              [-roi] - select a region of interest to use

              <roi-metric> - the area to use, as a metric

              [-overlap-logic] - how to handle overlapping ROIs, default ALLOW

              <method> - the method of resolving overlaps

              [-column] - select a single input column to use

              <column> - the column number or name

              For each nonzero value in each map, make a map with an ROI  around  that  location.
              If  the  -gaussian option is specified, then normalized gaussian kernels are output
              instead of ROIs.  The <method> argument to -overlap-logic must  be  one  of  ALLOW,
              CLOSEST,  or  EXCLUDE.   ALLOW  is  the  default,  and  means that ROIs are treated
              independently and may overlap.  CLOSEST means that ROIs may not overlap,  and  that
              no ROI contains vertices that are closer to a different seed vertex.  EXCLUDE means
              that ROIs may not overlap, and that any vertex within range of more  than  one  ROI
              does not belong to any ROI.

       -metric-rois-to-border DRAW BORDERS AROUND METRIC ROIS

              wb_command -metric-rois-to-border

              <surface> - the surface to use for neighbor information <metric> - the input metric
              containing ROIs <class-name> - the name to use for the class of the output  borders
              <border-out> - output - the output border file

              [-placement] - set how far along the edge border points are drawn

              <fraction> - fraction along edge from inside vertex (default 0.33)

              [-column] - select a single column

              <column> - the column number or name

              For  each  ROI  column,  finds all edges on the mesh that cross the boundary of the
              ROI, and draws borders through them.  By default, this is done on  all  columns  in
              the input file, using the map name as the name for the border.

       -metric-smoothing SMOOTH A METRIC FILE

              wb_command -metric-smoothing

              <surface>  -  the  surface  to  smooth  on  <metric-in>  -  the  metric  to  smooth
              <smoothing-kernel> - the sigma for the gaussian kernel function, in mm <metric-out>
              - output - the output metric

              [-roi] - select a region of interest to smooth

              <roi-metric> - the roi to smooth within, as a metric

              [-match-columns] - for each input column, use the corresponding column

              from the roi

              [-fix-zeros] - treat zero values as not being data

              [-column] - select a single column to smooth

              <column> - the column number or name

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

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

              [-method] - select smoothing method, default GEO_GAUSS_AREA

              <method> - the name of the smoothing method

       Smooth a metric file on a surface.
              By default, smooths all input columns

              on  the  entire  surface, specify -column to use only one input column, and -roi to
              smooth only where the roi metric is greater than 0, outputting zeros elsewhere.

              When using -roi, input data outside the ROI is not used  to  compute  the  smoothed
              values.   By  default,  the  first  column  of the roi metric is used for all input
              columns.  When -match-columns is specified to the -roi option, the  input  and  roi
              metrics  must  have  the same number of columns, and for each input column's index,
              the same column index is used in the roi metric.  If the -match-columns  option  to
              -roi  is  used  while  the  -column option is also used, the number of columns must
              match between the roi and input metric, and it will use the  roi  column  with  the
              index of the selected input column.

              The -fix-zeros option causes the smoothing to not use an input value if it is zero,
              but still write a smoothed value to the vertex.  This  is  useful  for  zeros  that
              indicate  lack  of  information, preventing them from pulling down the intensity of
              nearby vertices, while giving the zero an extrapolated value.

              The -corrected-areas option is intended for when it is unavoidable to smooth  on  a
              group  average  surface,  it is only an approximate correction for the reduction of
              structure in a group  average  surface.   It  is  better  to  smooth  the  data  on
              individuals before averaging, when feasible.

              Valid values for <method> are:

              GEO_GAUSS_AREA  -  uses  a geodesic gaussian kernel, and normalizes based on vertex
              area in order to work more reliably on irregular surfaces

              GEO_GAUSS_EQUAL - uses a geodesic gaussian kernel,  and  normalizes  assuming  each
              vertex has equal importance

              GEO_GAUSS  -  matches  geodesic  gaussian smoothing from caret5, but does not check
              kernels for having unequal importance

              The GEO_GAUSS_AREA method is the default because it is usually the correct  choice.
              GEO_GAUSS_EQUAL  may  be  the  correct choice when the sum of vertex values is more
              meaningful then the surface integral (sum of values .* areas),  for  instance  when
              smoothing  vertex  areas  (the  sum  is  the  total surface area, while the surface
              integral is the sum of squares of the vertex areas).  The GEO_GAUSS method  is  not
              recommended,  it  exists  mainly to replicate methods of studies done with caret5's
              geodesic smoothing.

       -metric-stats SPATIAL STATISTICS ON A METRIC FILE

              wb_command -metric-stats

              <metric-in> - the input metric

              [-reduce] - use a reduction operation

              <operation> - the reduction operation

              [-percentile] - give the value at a percentile

              <percent> - the percentile to find

              [-column] - only display output for one column

              <column> - the column number or name

              [-roi] - only consider data inside an roi

              <roi-metric> - the roi, as a metric file

              [-match-maps] - each column of input uses the corresponding column

              from the roi file

              [-show-map-name] - print map index and name before each output

              For each column of the input, a  single  number  is  printed,  resulting  from  the
              specified reduction or percentile operation.  Use -column to only give output for a
              single column.  Use -roi to consider only the data within a region.  Exactly one of
              -reduce or -percentile must be specified.

              The argument to the -reduce option must be one of the following:

              MAX:  the  maximum  value MIN: the minimum value INDEXMAX: the 1-based index of the
              maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all  values
              PRODUCT:  multiply  all  values  MEAN:  the  mean  of  the data STDEV: the standard
              deviation  (N  denominator)  SAMPSTDEV:  the   sample   standard   deviation   (N-1
              denominator)  VARIANCE:  the  variance  of  the  data  TSNR: mean divided by sample
              standard  deviation  (N-1  denominator)  COV:  sample   standard   deviation   (N-1
              denominator)  divided  by mean MEDIAN: the median of the data MODE: the mode of the
              data COUNT_NONZERO: the number of nonzero elements in the data

       -metric-tfce DO TFCE ON A METRIC FILE

              wb_command -metric-tfce

              <surface> - the surface to compute on <metric-in> -  the  metric  to  run  TFCE  on
              <metric-out> - output - the output metric

              [-presmooth] - smooth the metric before running TFCE

              <kernel> - the sigma for the gaussian smoothing kernel, in mm

              [-roi] - select a region of interest to run TFCE on

              <roi-metric> - the area to run TFCE on, as a metric

              [-parameters] - set parameters for TFCE integral

              <E>  -  exponent  for cluster area (default 1.0) <H> - exponent for threshold value
              (default 2.0)

              [-column] - select a single column

              <column> - the column number or name

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

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

              Threshold-free cluster enhancement is a method to increase the  relative  value  of
              regions  that  would  form  clusters  in  a  standard  thresholding  test.  This is
              accomplished by evaluating the integral of:

              e(h, p)^E * h^H * dh

              at each vertex p, where h ranges from 0 to the maximum value in the data, and  e(h,
              p)  is  the  extent  of  the  cluster containing vertex p at threshold h.  Negative
              values are similarly enhanced by negating the data, running the same  process,  and
              negating the result.

              When  using  -presmooth  with  -corrected-areas,  note  that  it  is an approximate
              correction within the smoothing algorithm (the TFCE correction  is  exact).   Doing
              smoothing on individual surfaces before averaging/TFCE is preferred, when possible,
              in order to better tie the smoothing kernel size to the original feature size.

              The TFCE method is explained in: Smith SM,  Nichols  TE.,  "Threshold-free  cluster
              enhancement:   addressing   problems   of   smoothing,   threshold  dependence  and
              localisation in cluster  inference."  Neuroimage.  2009  Jan  1;44(1):83-98.  PMID:
              18501637

       -metric-to-volume-mapping MAP METRIC FILE TO VOLUME

              wb_command -metric-to-volume-mapping

              <metric>  -  the  input metric file <surface> - the surface to use coordinates from
              <volume-space> - a volume file in the desired output volume  space  <volume-out>  -
              output - the output volume file

              [-nearest-vertex] - use the value from the vertex closest to the voxel

              center <distance> - how far from the surface to map values to voxels, in mm

              [-ribbon-constrained] - use ribbon constrained mapping algorithm

              <inner-surf>  - the inner surface of the ribbon <outer-surf> - the outer surface of
              the ribbon

              [-voxel-subdiv] - voxel divisions while estimating voxel weights

              <subdiv-num> - number of subdivisions, default 3

              [-greedy] - instead of antialiasing partial-volumed voxels, put full

              metric values (legacy behavior)

              [-thick-columns] - use overlapping columns (legacy method)

       Maps values from a metric file into a volume file.
              You must specify

       exactly one mapping method option.
              The -nearest-vertex method uses the

              value from the vertex closest to the voxel center (useful for integer values).  The
              -ribbon-constrained  method  uses the same method as in -volume-to-surface-mapping,
              then uses the weights in reverse.  Mapping to lower resolutions than the  mesh  may
              require  a  larger  -voxel-subdiv  value  in  order to have all of the surface data
              participate.

       -metric-vector-operation DO A VECTOR OPERATION ON METRIC FILES

              wb_command -metric-vector-operation

              <vectors-a> - first vector input  file  <vectors-b>  -  second  vector  input  file
              <operation> - what vector operation to do <metric-out> - output - the output file

              [-normalize-a] - normalize vectors of first input

              [-normalize-b] - normalize vectors of second input

              [-normalize-output] - normalize output vectors (not valid for dot

              product)

              [-magnitude] - output the magnitude of the result (not valid for dot

              product)

              Does  a  vector  operation  on  two  metric  files  (that must have a multiple of 3
              columns).  Either of the inputs may have multiple vectors (more  than  3  columns),
              but  not  both  (at  least  one  must  have exactly 3 columns).  The -magnitude and
              -normalize-output options may not be specified together, or with an operation  that
              returns  a  scalar  (dot  product).   The  <operation> parameter must be one of the
              following:

              DOT CROSS ADD SUBTRACT

       -metric-vector-toward-roi FIND IF VECTORS POINT TOWARD AN ROI

              wb_command -metric-vector-toward-roi

              <surface> - the surface to compute on <target-roi> - the roi to find  the  shortest
              path to <metric-out> - output - the output metric

              [-roi] - don't compute for vertices outside an roi

              <roi-metric> - the region to compute inside, as a metric

              At each vertex, compute the vector along the start of the shortest path to the ROI.

       -metric-weighted-stats WEIGHTED SPATIAL STATISTICS ON A METRIC FILE

              wb_command -metric-weighted-stats

              <metric-in> - the input metric

              [-area-surface] - use vertex areas as weights

              <area-surface> - the surface to use for vertex areas

              [-weight-metric] - use weights from a metric file

              <weight-metric> - metric file containing the weights

              [-column] - only display output for one column

              <column> - the column number or name

              [-roi] - only consider data inside an roi

              <roi-metric> - the roi, as a metric file

              [-match-maps] - each column of input uses the corresponding column

              from the roi file

              [-mean] - compute weighted mean

              [-stdev] - compute weighted standard deviation

              [-sample] - estimate population stdev from the sample

              [-percentile] - compute weighted percentile

              <percent> - the percentile to find

              [-sum] - compute weighted sum

              [-show-map-name] - print map index and name before each output

              For  each  column  of  the  input,  a  single number is printed, resulting from the
              specified  operation.   You  must  specify  exactly   one   of   -area-surface   or
              -weight-metric.   Use -column to only give output for a single column.  Use -roi to
              consider only the data within a region.  Exactly one of -mean, -stdev,  -percentile
              or -sum must be specified.

              Using  -sum  with -area-surface (or -weight-metric with a metric containing similar
              data) is equivalent to integrating with respect to surface area.  For  example,  if
              you want to find the surface area within an roi, do this:

              $ wb_command -metric-weighted-stats roi.func.gii -sum -area-surface

              midthickness.surf.gii

       -nifti-information DISPLAY INFORMATION ABOUT A NIFTI/CIFTI FILE

              wb_command -nifti-information

              <nifti-file> - the nifti/cifti file to examine

              [-print-header] - display the header contents

              [-allow-truncated] - print the header even if the data is truncated

              [-print-matrix] - output the values in the matrix (cifti only)

              [-print-xml] - print the cifti XML (cifti only)

              [-version] - convert the XML to a specific CIFTI version (default is

              the file's cifti version) <version> - the CIFTI version to use

              You must specify at least one -print-* option.

       -probtrackx-dot-convert CONVERT A .DOT FILE FROM PROBTRACKX TO CIFTI

              wb_command -probtrackx-dot-convert

              <dot-file> - input .dot file <cifti-out> - output - output cifti file

              [-row-voxels] - the output mapping along a row will be voxels

              <voxel-list-file> - a text file containing IJK indices for the voxels

              used

              <label-vol> - a label volume with the dimensions and sform used, with

              structure labels

              [-row-surface] - the output mapping along a row will be surface vertices

              <roi-metric> - a metric file with positive values on all vertices used

              [-row-cifti] - take the mapping along a row from a cifti file

              <cifti>  - the cifti file to take the mapping from <direction> - which dimension to
              take the mapping along, ROW or COLUMN

              [-col-voxels] - the output mapping along a column will be voxels

              <voxel-list-file> - a text file containing IJK indices for the voxels

              used

              <label-vol> - a label volume with the dimensions and sform used, with

              structure labels

              [-col-surface] - the output mapping along a column will be surface

              vertices <roi-metric> - a metric file with positive values on all vertices used

              [-col-cifti] - take the mapping along a column from a cifti file

              <cifti> - the cifti file to take the mapping from <direction> - which dimension  to
              take the mapping along, ROW or COLUMN

              [-transpose] - transpose the input matrix

              [-make-symmetric] - transform half-square input into full matrix output

              NOTE: exactly one -row option and one -col option must be used.

              If  the  input  file does not have its indexes sorted in the correct ordering, this
              command may take longer than expected.  Specifying -transpose  will  transpose  the
              input  matrix  before  trying  to  put  its  values  into  the cifti file, which is
              currently needed for at least matrix2 in order to display it as intended.  How  the
              cifti  file is displayed is based on which -row option is specified: if -row-voxels
              is specified, then it will display data on volume slices.  The label names  in  the
              label volume(s) must have the following names, other names are ignored:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

       -scene-file-merge REARRANGE SCENES INTO A NEW FILE

              wb_command -scene-file-merge

              <scene-file-out> - output - the output scene file

              [-scene-file] - repeatable - specify a scene file to use scenes from

              <scene-file> - the input scene file

              [-scene] - repeatable - specify a scene to use

              <scene> - the scene number or name

              [-up-to] - use an inclusive range of scenes

              <last-column> - the number or name of the last scene to include

              [-reverse] - use the range in reverse order

              Takes  one  or  more  scene  files and constructs a new scene file by concatenating
              specified scenes from them.

              Example: wb_command -scene-file-merge out.scene -scene-file  first.scene  -scene  1
              -scene-file second.scene

              This  example  would  take the first scene from first.scene, followed by all scenes
              from second.scene, and write these scenes to out.scene.

       -scene-file-relocate RECREATE SCENE FILE IN NEW LOCATION

              wb_command -scene-file-relocate

              <input-scene> - the scene file to use <output-scene> - output - the new scene  file
              to create

              Scene  files  contain  internal relative paths, such that moving or copying a scene
              file will cause it to lose track of the files it refers to.  This command  makes  a
              modified  copy  of  the scene file, changing the relative paths to refer to the new
              relative locations of the files.

       -set-map-names SET THE NAME OF ONE OR MORE MAPS IN A FILE

              wb_command -set-map-names

              <data-file> - the file to set the map names of

              [-name-file] - use a text file to replace all map names

              <file> - text file containing map names, one per line

              [-map] - repeatable - specify a map to set the name of

              <index> - the map index to change the name of <new-name> - the name to set for  the
              map

              Sets the name of one or more maps for metric, shape, label, volume, cifti scalar or
              cifti label files.  If the -name-file option is not specified, the -map option must
              be  specified  at  least  once.   The -map option cannot be used when -name-file is
              specified.

       -set-structure SET STRUCTURE OF A DATA FILE

              wb_command -set-structure

              <data-file> - the file to set the structure of <structure> - the structure  to  set
              the file to

              [-surface-type] - set the type of a surface (only used if file is a

              surface file) <type> - name of surface type

              [-surface-secondary-type] - set the secondary type of a surface (only

              used if file is a surface file) <secondary type> - name of surface secondary type

       The existing file is modified and rewritten to the same filename.
              Valid

              values for the structure name are:

              CORTEX_LEFT  CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER
              ALL_WHITE_MATTER AMYGDALA_LEFT AMYGDALA_RIGHT BRAIN_STEM CAUDATE_LEFT CAUDATE_RIGHT
              CEREBELLAR_WHITE_MATTER_LEFT      CEREBELLAR_WHITE_MATTER_RIGHT     CEREBELLUM_LEFT
              CEREBELLUM_RIGHT  CEREBRAL_WHITE_MATTER_LEFT   CEREBRAL_WHITE_MATTER_RIGHT   CORTEX
              DIENCEPHALON_VENTRAL_LEFT        DIENCEPHALON_VENTRAL_RIGHT        HIPPOCAMPUS_LEFT
              HIPPOCAMPUS_RIGHT INVALID OTHER OTHER_GREY_MATTER OTHER_WHITE_MATTER  PALLIDUM_LEFT
              PALLIDUM_RIGHT PUTAMEN_LEFT PUTAMEN_RIGHT THALAMUS_LEFT THALAMUS_RIGHT

              Valid names for the surface type are:

              UNKNOWN  RECONSTRUCTION  ANATOMICAL INFLATED VERY_INFLATED SPHERICAL SEMI_SPHERICAL
              ELLIPSOID FLAT HULL

              Valid names for the surface secondary type are:

              INVALID GRAY_WHITE MIDTHICKNESS PIAL

       -show-scene OFFSCREEN RENDERING OF SCENE TO AN IMAGE FILE

              wb_command -show-scene

              <scene-file> - scene file <scene-name-or-number> - name or number (starting at one)
              of the scene in

              the scene file

              <image-file-name> - output image file name <image-width> - width of output image(s)
              <image-height> - height of output image(s)

              [-use-window-size] - Override image size with window size

              [-no-scene-colors] - Do not use background and foreground colors in scene

              [-set-map-yoke] - Override selected map index for a map yoking group.

              <Map Yoking Roman Numeral> - Roman numeral identifying the map yoking

              group (I, II, III, IV, V, VI, VII, VIII, IX, X)

       <Map Index> - Map index for yoking group.
              Indices start at 1 (one)

              [-conn-db-login] - Login for scenes with files in Connectome Database

              <Username> - Connectome DB Username <Password> - Connectome DB Password

              Render content of browser windows displayed in a scene  into  image  file(s).   The
              image  file name should be similar to "capture.png".  If there is only one image to
              render, the image name will not change.  If there is more than one image to render,
              an  index  will be inserted into the image name: "capture_01.png", "capture_02.png"
              etc.

              If the scene references files in  the  Connectome  Database,  the  "-conn-db-login"
              option  is  available  for providing the username and password.  If this options is
              not specified, the username and password stored in the user's preferences is used.

              The image format is determined by the image file extension.   The  available  image
              formats may vary by operating system.  Image formats available on this system are:

              bmp cur ico jpeg jpg pbm pgm png ppm xbm xpm

              The  result  of  using  the "-use-window-size" option is dependent upon the version
              used to create the scene.

              * Versions 1.2 and newer contain the width and

       height of the graphics region.
              The output image

              will be the width and height  from  the  scene  and  the  image  width  and  height
              specified on the command line is ignored.

              * If the scene does not contain the width and height

              of  the graphics region, the width and height specified on the command line is used
              for the size of the output image.

       -signed-distance-to-surface COMPUTE SIGNED DISTANCE FROM ONE SURFACE TO ANOTHER

              wb_command -signed-distance-to-surface

              <surface-comp>  -  the  comparison  surface  to  measure  the  signed  distance  on
              <surface-ref> - the reference surface that defines the signed distance

              function

              <metric> - output - the output metric

              [-winding] - winding method for point inside surface test

              <method> - name of the method (default EVEN_ODD)

              Compute  the  signed  distance function of the reference surface at every vertex on
              the comparison surface.  NOTE: this relation is NOT  symmetric,  the  line  from  a
              vertex  to  the closest point on the 'ref' surface (the one that defines the signed
              distance function) will only align with the normal of  the  'ref'  surface.   Valid
              specifiers for winding methods are as follows:

              EVEN_ODD (default) NEGATIVE NONZERO NORMALS

              The NORMALS method uses the normals of triangles and edges, or the closest triangle
              hit by a ray from the point.  This method may  be  slightly  faster,  but  is  only
              reliable  for  a  closed  surface  that  does  not cross through itself.  All other
              methods count entry (positive) and exit (negative) crossings of a vertical ray from
              the  point,  then  counts  as  inside  if  the  total is odd, negative, or nonzero,
              respectively.

       -spec-file-merge MERGE TWO SPEC FILES INTO ONE

              wb_command -spec-file-merge

              <spec-1> - first spec file to merge <spec-2> - second spec file to merge <out-spec>
              - output - output spec file

              The output spec file contains every file that is in either of the input spec files.

       -spec-file-relocate RECREATE SPEC FILE IN NEW LOCATION

              wb_command -spec-file-relocate

              <input-spec>  -  the spec file to use <output-spec> - output - the new spec file to
              create

              Spec files contain internal relative paths, such that moving or copying a spec file
              will  cause  it  to  lose  track  of  the files it refers to.  This command makes a
              modified copy of the spec file, changing the relative paths to  refer  to  the  new
              relative locations of the files.

       -surface-affine-regression REGRESS THE AFFINE TRANSFORM BETWEEN SURFACES ON THE SAME MESH

              wb_command -surface-affine-regression

              <source>  -  the surface to warp <target> - the surface to match the coordinates of
              <affine-out> - output - the output affine file

              Use linear regression to compute an affine that minimizes the sum of squares of the
              coordinate  differences  between  the target surface and the warped source surface.
              Note that this has a bias to shrink the surface that is being warped.   The  output
              is  written as a NIFTI 'world' matrix, see -convert-affine to convert it for use in
              other software.

       -surface-apply-affine APPLY AFFINE TRANSFORM TO SURFACE FILE

              wb_command -surface-apply-affine

              <in-surf> - the surface to transform <affine> - the affine file <out-surf> - output
              - the output transformed surface

              [-flirt] - MUST be used if affine is a flirt affine

              <source-volume> - the source volume used when generating the affine <target-volume>
              - the target volume used when generating the affine

              For flirt matrices, you must use the -flirt option, because flirt matrices are  not
              a  complete  description of the coordinate transform they represent.  If the -flirt
              option is not present, the affine must be a nifti  'world'  affine,  which  can  be
              obtained with the -convert-affine command, or aff_conv from the 4dfp suite.

       -surface-apply-warpfield APPLY WARPFIELD TO SURFACE FILE

              wb_command -surface-apply-warpfield

              <in-surf> - the surface to transform <warpfield> - the INVERSE warpfield <out-surf>
              - output - the output transformed surface

              [-fnirt] - MUST be used if using a fnirt warpfield

              <forward-warp> - the forward warpfield

              NOTE: warping a surface requires the INVERSE of the  warpfield  used  to  warp  the
              volume  it  lines  up with.  The header of the forward warp is needed by the -fnirt
              option in order to correctly interpret the displacements in the fnirt warpfield.

              If the -fnirt option is  not  present,  the  warpfield  must  be  a  nifti  'world'
              warpfield, which can be obtained with the -convert-warpfield command.

       -surface-average AVERAGE SURFACE FILES TOGETHER

              wb_command -surface-average

              <surface-out> - output - the output averaged surface

              [-stddev] - compute 3D sample standard deviation

              <stddev-metric-out> - output - the output metric for 3D sample

              standard deviation

              [-uncertainty] - compute caret5 'uncertainty'

              <uncert-metric-out> - output - the output metric for uncertainty

              [-surf] - repeatable - specify a surface to include in the average

              <surface> - a surface file to average

              [-weight] - specify a weighted average

              <weight> - the weight to use (default 1)

              The  3D  sample  standard  deviation  is  computed as 'sqrt(sum(squaredlength(xyz -
              mean(xyz)))/(n - 1))'.

              Uncertainty is a legacy measure used in caret5, and is computed as  'sum(length(xyz
              - mean(xyz)))/n'.

              When  weights are used, the 3D sample standard deviation treats them as reliability
              weights.

       -surface-closest-vertex FIND CLOSEST SURFACE VERTEX TO COORDINATES

              wb_command -surface-closest-vertex

              <surface> - the surface to use  <coord-list-file>  -  text  file  with  coordinates
              <vertex-list-out> - output - the output text file with vertex numbers

              For  each coordinate XYZ triple, find the closest vertex in the surface, and output
              its vertex number into a text file.  The input file should only use  whitespace  to
              separate coordinates (spaces, newlines, tabs), for instance:

              20 30 25 30 -20 10

       -surface-coordinates-to-metric MAKE METRIC FILE OF SURFACE COORDINATES

              wb_command -surface-coordinates-to-metric

              <surface>  -  the  surface  to  use  the coordinates of <metric-out> - output - the
              output metric

              Puts the coordinates of the surface into a 3-map metric file, as x, y, z.

       -surface-cortex-layer CREATE SURFACE APPROXIMATING A CORTICAL LAYER

              wb_command -surface-cortex-layer

              <white-surface> - the white  matter  surface  <pial-surface>  -  the  pial  surface
              <location>  -  what  volume fraction to place the layer at <out-surface> - output -
              the output surface

              [-placement-out] - output the placement as a distance fraction from pial

              to white <placement-metric> - output - output metric

       The input surfaces must have vertex correspondence.
              The output surface

              is generated by placing vertices between the two surfaces such  that  the  enclosed
              volume  within  any small patch of the new and white surfaces is the given fraction
              of the volume of the  same  patch  between  the  pial  and  white  surfaces  (i.e.,
              specifying 0 would give the white surface, 1 would give the pial surface).

       -surface-create-sphere GENERATE A SPHERE WITH CONSISTENT VERTEX AREAS

              wb_command -surface-create-sphere

              <num-vertices>  -  desired  number  of  vertices <sphere-out> - output - the output
              sphere

              Generates a sphere by regularly dividing the triangles of an icosahedron,  to  come
              as  close  to  the desired number of vertices as possible, and modifying it to have
              very similar vertex areas for all vertices.  To generate a pair  of  vertex-matched
              left  and  right  spheres,  use this command, then -surface-flip-lr to generate the
              other sphere, then -set-structure on each.  For example:

              $ wb_command -surface-create-sphere 6000 Sphere.6k.R.surf.gii
              $ wb_command -surface-flip-lr Sphere.6k.R.surf.gii Sphere.6k.L.surf.gii
              $ wb_command -set-structure Sphere.6k.R.surf.gii CORTEX_RIGHT
              $ wb_command -set-structure Sphere.6k.L.surf.gii CORTEX_LEFT

       -surface-curvature CALCULATE CURVATURE OF SURFACE

              wb_command -surface-curvature

              <surface> - the surface to compute the curvature of

              [-mean] - output mean curvature

              <mean-out> - output - mean curvature metric

              [-gauss] - output gaussian curvature

              <gauss-out> - output - gaussian curvature metric

              Compute the curvature of the surface, using the method  from:  Interactive  Texture
              Mapping by J. Maillot, Yahia, and Verroust, 1993.  ACM-0-98791-601-8/93/008

       -surface-cut-resample RESAMPLE A CUT SURFACE

              wb_command -surface-cut-resample

              <surface-in>  -  the  surface  file to resample <current-sphere> - a sphere surface
              with the mesh that the input surface

              is currently on

              <new-sphere> - a sphere surface that is in register with <current-sphere>

              and has the desired output mesh

              <surface-out> - output - the output surface file

              Resamples a surface file, given  two  spherical  surfaces  that  are  in  register.
              Barycentric  resampling  is  used,  because  it  is  usually  better for resampling
              surfaces, and because it is needed to figure out the new topology anyway.

       -surface-distortion MEASURE DISTORTION BETWEEN SURFACES

              wb_command -surface-distortion

              <surface-reference> - the reference surface  <surface-distorted>  -  the  distorted
              surface <metric-out> - output - the output distortion metric

              [-smooth] - smooth the area data

              <sigma> - the smoothing kernel sigma in mm

              [-caret5-method] - use the surface distortion method from caret5

              [-edge-method] - calculate distortion of edge lengths rather than areas

              [-local-affine-method] - calculate distortion by the local affines

              between triangles

              This command, when not using -caret5-method, -edge-method, or -local-affine-method,
              is equivalent to using -surface-vertex-areas on each surface, smoothing both output
              metrics with the GEO_GAUSS_EQUAL method on the surface they came from if -smooth is
              specified, and  then  using  the  formula  'ln(distorted/reference)/ln(2)'  on  the
              smoothed results.

              When using -caret5-method, it uses the surface distortion method from caret5, which
              takes the base 2 log of the ratio of tile areas, then  averages  those  results  at
              each vertex, and then smooths the result on the reference surface.

              When  using  -edge-method,  the  -smooth  option is ignored, and the output at each
              vertex is  the  average  of  'abs(ln(refEdge/distortEdge)/ln(2))'  over  all  edges
              connected to the vertex.

       When using -local-affine-method, the -smooth option is ignored.
              The

              output  is  two  columns, the first is the area distortion ratio, and the second is
              anisotropic strain.  These are calculated by an affine transform  between  matching
              triangles, and then averaged across the triangles of a vertex.

       -surface-flip-lr MIRROR A SURFACE THROUGH THE YZ PLANE

              wb_command -surface-flip-lr

              <surface> - the surface to flip <surface-out> - output - the output flipped surface

              This  command  negates  the  x  coordinate  of  each  vertex, and flips the surface
              normals, so that you have a surface of opposite handedness with the  same  features
              and vertex correspondence, with normals consistent with the original surface.  That
              is, if the input surface has normals facing outward, the output surface  will  also
              have normals facing outward.

       -surface-flip-normals FLIP ALL TILES ON A SURFACE

              wb_command -surface-flip-normals

              <surface>  - the surface to flip the normals of <surface-out> - output - the output
              surface

              Flips all triangles on a surface, resulting in surface normals  being  flipped  the
              other  direction  (inward  vs  outward).  If you transform a surface with an affine
              that has negative determinant, or a warpfield that similarly flips the surface, you
              may end up with a surface that has normals pointing inwards, which may have display
              problems.  Using this command will solve that problem.

       -surface-generate-inflated SURFACE GENERATE INFLATED

              wb_command -surface-generate-inflated

              <anatomical-surface-in> - the anatomical surface <inflated-surface-out> - output  -
              the  output inflated surface <very-inflated-surface-out> - output - the output very
              inflated surface

              [-iterations-scale] - optional iterations scaling

              <iterations-scale-value> - iterations-scale value

              Generate inflated and very inflated surfaces. The  output  surfaces  are  'matched'
              (have same XYZ range) to the anatomical surface. In most cases, an iterations-scale
              of 1.0 (default) is sufficient.  However, if the surface contains a large number of
              vertices (150,000), try an iterations-scale of 2.5.

       -surface-geodesic-distance COMPUTE GEODESIC DISTANCE FROM ONE VERTEX TO THE ENTIRE SURFACE

              wb_command -surface-geodesic-distance

              <surface>  -  the  surface  to compute on <vertex> - the vertex to compute geodesic
              distance from <metric-out> - output - the output metric

              [-naive] - use only neighbors, don't crawl triangles (not recommended)

              [-limit] - stop at a certain distance

              <limit-mm> - distance in mm to stop at

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

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

              Unless -limit is specified, computes  the  geodesic  distance  from  the  specified
              vertex  to all others.  The result is output as a single column metric file, with a
              value of -1 for vertices that the distance was not computed for.  If -naive is  not
              specified,  it  uses  not just immediate neighbors, but also neighbors derived from
              crawling across pairs of triangles that share an edge.

       -surface-geodesic-rois DRAW GEODESIC LIMITED ROIS AT VERTICES

              wb_command -surface-geodesic-rois

              <surface> - the surface to draw on <limit> - geodesic distance limit  from  vertex,
              in mm <vertex-list-file> - a text file containing the vertices to draw ROIs

              around

              <metric-out> - output - the output metric

              [-gaussian] - generate a gaussian kernel instead of a flat ROI

              <sigma> - the sigma for the gaussian kernel, in mm

              [-overlap-logic] - how to handle overlapping ROIs, default ALLOW

              <method> - the method of resolving overlaps

              [-names] - name the columns from text file

              <name-list-file> - a text file containing column names, one per line

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

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

              For  each vertex in the list file, a column in the output metric is created, and an
              ROI around that vertex is drawn in that column.  Each metric column will have zeros
              outside  the  geodesic  distance  spacified  by <limit>, and by default will have a
              value of 1.0 inside it.  If the -gaussian option is specified,  the  values  inside
              the  ROI will instead form a gaussian with the specified value of sigma, normalized
              so that the sum of the nonzero values in the metric column is  1.0.   The  <method>
              argument to -overlap-logic must be one of ALLOW, CLOSEST, or EXCLUDE.  ALLOW is the
              default, and means that ROIs are treated independently and  may  overlap.   CLOSEST
              means  that ROIs may not overlap, and that no ROI contains vertices that are closer
              to a different seed vertex.  EXCLUDE means that ROIs may not overlap, and that  any
              vertex within range of more than one ROI does not belong to any ROI.

       -surface-inflation SURFACE INFLATION

              wb_command -surface-inflation

              <anatomical-surface-in> - the anatomical surface <surface-in> - the surface file to
              inflate    <number-of-smoothing-cycles>    -    number    of    smoothing    cycles
              <smoothing-strength>    -    smoothing    strength    (ranges    [0.0    -    1.0])
              <smoothing-iterations> - smoothing iterations <inflation-factor> - inflation factor
              <surface-out> - output - output surface file

              Inflate  a  surface  by  performing  cycles  that  consist of smoothing followed by
              inflation (to correct shrinkage caused by smoothing).

       -surface-information DISPLAY INFORMATION ABOUT A SURFACE

              wb_command -surface-information

              <Surface File> - Surface for which information is displayed

              Information about surface is displayed including vertices, triangles, bounding box,
              and spacing.

       -surface-match SURFACE MATCH

              wb_command -surface-match

              <Match  Surface  File>  -  Match  (Reference)  Surface  <Input Surface File> - File
              containing surface that will be transformed <Output Surface Name>  -  Surface  File
              after transformation

              The  Input Surface File will be transformed so that its coordinate ranges (bounding
              box) match that of the Match Surface File

       -surface-modify-sphere CHANGE RADIUS AND OPTIONALLY RECENTER A SPHERE

              wb_command -surface-modify-sphere

              <sphere-in> - the sphere to modify <radius> - the radius the output  sphere  should
              have <sphere-out> - output - the output sphere

              [-recenter] - recenter the sphere by means of the bounding box

              This command may be useful if you have used -surface-resample to resample a sphere,
              which    can    suffer    from    problems     generally     not     present     in
              -surface-sphere-project-unproject.  If the sphere should already be centered around
              the origin, using -recenter may still shift it slightly before changing the radius,
              which is likely to be undesireable.

              If  <sphere-in>  is  not  close to spherical, or not centered around the origin and
              -recenter is not used, a warning is printed.

       -surface-normals OUTPUT VERTEX NORMALS AS METRIC FILE

              wb_command -surface-normals

              <surface> - the surface to output the normals of <metric-out> - output - the normal
              vectors

              Computes  the  normal  vectors  of the surface file, and outputs them as a 3 column
              metric file.

       -surface-resample RESAMPLE A SURFACE TO A DIFFERENT MESH

              wb_command -surface-resample

              <surface-in> - the surface file to resample <current-sphere>  -  a  sphere  surface
              with the mesh that the input surface

              is currently on

              <new-sphere> - a sphere surface that is in register with <current-sphere>

              and has the desired output mesh

              <method> - the method name <surface-out> - output - the output surface file

              [-area-surfs] - specify surfaces to do vertex area correction based on

              <current-area>  -  a  relevant  surface  with  <current-sphere> mesh <new-area> - a
              relevant surface with <new-sphere> mesh

              [-area-metrics] - specify vertex area metrics to do area correction based

              on <current-area> - a metric file with vertex areas for <current-sphere>

              mesh

              <new-area> - a metric file with vertex areas for <new-sphere> mesh

              Resamples a surface file, given two spherical surfaces that are  in  register.   If
              ADAP_BARY_AREA  is  used,  exactly  one  of  -area-surfs  or  -area-metrics must be
              specified.  This method is not generally recommended for surface resampling, but is
              provided for completeness.

              The  BARYCENTRIC  method is generally recommended for anatomical surfaces, in order
              to minimize smoothing.

              For cut surfaces (including flatmaps), use -surface-cut-resample.

              Instead of resampling a spherical  surface,  the  -surface-sphere-project-unproject
              command is recommended.

              The <method> argument must be one of the following:

              ADAP_BARY_AREA BARYCENTRIC

       -surface-set-coordinates MODIFY COORDINATES OF A SURFACE

              wb_command -surface-set-coordinates

              <surface-in>  -  the  surface  to  use  for  the  topology <coord-metric> - the new
              coordinates, as a 3-column metric file <surface-out> - output - the new surface

              Takes the topology from an existing surface file, and uses  values  from  a  metric
              file as coordinates to construct a new surface file.

              See  -surface-coordinates-to-metric  for how to get surface coordinates as a metric
              file, such that you can then modify them via metric commands, etc.

       -surface-smoothing SURFACE SMOOTHING

              wb_command -surface-smoothing

              <surface-in> - the surface file to smooth <smoothing-strength> - smoothing strength
              (ranges  [0.0 - 1.0]) <smoothing-iterations> - smoothing iterations <surface-out> -
              output - output surface file

              Smooths a surface by averaging vertex coordinates with  those  of  the  neighboring
              vertices.

       -surface-sphere-project-unproject DEFORM A SPHERE ACCORDING TO A REGISTRATION

              wb_command -surface-sphere-project-unproject

              <sphere-in>  -  the  sphere  with  the  desired output mesh <sphere-project-to> - a
              sphere that  aligns  with  sphere-in  <sphere-unproject-from>  -  sphere-project-to
              deformed to the output space <sphere-out> - output - the output sphere

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

       -surface-to-surface-3d-distance COMPUTE DISTANCE BETWEEN CORRESPONDING VERTICES

              wb_command -surface-to-surface-3d-distance

              <surface-comp> - the surface to  compare  to  the  reference  <surface-ref>  -  the
              surface to use as the reference <dists-out> - output - the output distances

              [-vectors] - output the displacement vectors

              <vectors-out> - output - the output vectors

              Computes  the  vector difference between the vertices of each surface with the same
              index, as (comp - ref), and output the magnitudes, and optionally the  displacement
              vectors.

       -surface-vertex-areas MEASURE SURFACE AREA EACH VERTEX IS RESPONSIBLE FOR

              wb_command -surface-vertex-areas

              <surface> - the surface to measure <metric> - output - the output metric

              Each vertex gets one third of the area of each triangle it is a part of.  Units are
              mm^2.

       -surface-wedge-volume MEASURE PER-VERTEX VOLUME BETWEEN SURFACES

              wb_command -surface-wedge-volume

              <inner-surface> - the inner surface <outer-surface> - the outer surface <metric>  -
              output - the output metric

              Compute the volume of each vertex's area from one surface to another.  The surfaces
              must have vertex correspondence.

       -unit-test

       -volume-affine-resample RESAMPLE VOLUME USING AFFINE TRANSFORM

              wb_command -volume-affine-resample

              <volume-in> - volume to resample <affine> - the affine file to apply <volume-space>
              - a volume file in the volume space you want for the

              output

              <method> - the resampling method <volume-out> - output - the output volume

              [-flirt] - MUST be used if affine is a flirt affine

              <source-volume> - the source volume used when generating the affine <target-volume>
              - the target volume used when generating the affine

       Resample a volume file with an affine transformation.
              The recommended

              methods are CUBIC (cubic spline) for most data, and ENCLOSING_VOXEL for label data.
              The parameter <method> must be one of:

              CUBIC ENCLOSING_VOXEL TRILINEAR

       -volume-all-labels-to-rois MAKE ROIS FROM ALL LABELS IN A VOLUME FRAME

              wb_command -volume-all-labels-to-rois

              <label-in>  -  the  input volume label file <map> - the number or name of the label
              map to use <volume-out> - output - the output volume file

              The output volume has a frame for each label in the specified  input  frame,  other
              than the ??? label, each of which contains an ROI of all voxels that are set to the
              corresponding label.

       -volume-capture-plane INTERPOLATE IMAGE FROM PLANE THROUGH VOLUME

              wb_command -volume-capture-plane

              <volume> - the volume file to interpolate from <subvolume> - the name or number  of
              the subvolume to use <interp> - interpolation type <h-dim> - width of output image,
              in pixels <v-dim> - height of output image, in pixels <scale-min> - value to render
              as  black  <scale-max> - value to render as white <bottom-left-x> - x-coordinate of
              the bottom left of the output image <bottom-left-y> - y-coordinate  of  the  bottom
              left  of  the output image <bottom-left-z> - z-coordinate of the bottom left of the
              output image <bottom-right-x> - x-coordinate of the  bottom  right  of  the  output
              image  <bottom-right-y>  -  y-coordinate  of  the  bottom right of the output image
              <bottom-right-z>  -  z-coordinate  of  the  bottom  right  of  the   output   image
              <top-left-x>  -  x-coordinate  of  the  top left of the output image <top-left-y> -
              y-coordinate of the top left of the output image <top-left-z> - z-coordinate of the
              top left of the output image <image> - output - the output image

              NOTE:  If  you  want  to  generate an image with all of the capabilities of the GUI
              rendering, see -show-scene.

              Renders an image of an arbitrary plane through  the  volume  file,  with  a  simple
              linear grayscale palette.  The parameter <interp> must be one of:

              CUBIC ENCLOSING_VOXEL TRILINEAR

       -volume-copy-extensions COPY EXTENDED DATA TO ANOTHER VOLUME FILE

              wb_command -volume-copy-extensions

              <data-volume> - the volume file containing the voxel data to use <extension-volume>
              - the volume file containing the extensions to use  <volume-out>  -  output  -  the
              output volume

              [-drop-unknown] - don't copy extensions that workbench doesn't understand

              This  command copies the information in a volume file that isn't a critical part of
              the standard header or data matrix, e.g. map names, palette settings, label tables.
              If  -drop-unknown is not specified, it also copies similar kinds of information set
              by other software.

       -volume-create CREATE A BLANK VOLUME FILE

              wb_command -volume-create

              <i-dim> - length of first dimension <j-dim> - length of second dimension <k-dim>  -
              length of third dimension <volume-out> - output - the output volume

              [-plumb] - set via axis order and spacing/offset

              <axis-order> - a string like 'XYZ' that specifies which index is along

              which spatial dimension

              <x-spacing> - change in x-coordinate from incrementing the relevant

              index

              <y-spacing> - change in y-coordinate from incrementing the relevant

              index

              <z-spacing> - change in z-coordinate from incrementing the relevant

              index

              <x-offset>  -  the x-coordinate of the first voxel <y-offset> - the y-coordinate of
              the first voxel <z-offset> - the z-coordinate of the first voxel

              [-sform] - set via a nifti sform

              <xi-spacing> - increase in x coordinate from incrementing the i index  <xj-spacing>
              - increase in x coordinate from incrementing the j index <xk-spacing> - increase in
              x coordinate from incrementing the k index <x-offset> - x coordinate of first voxel
              <yi-spacing>  - increase in y coordinate from incrementing the i index <yj-spacing>
              - increase in y coordinate from incrementing the j index <yk-spacing> - increase in
              y coordinate from incrementing the k index <y-offset> - y coordinate of first voxel
              <zi-spacing> - increase in z coordinate from incrementing the i index  <zj-spacing>
              - increase in z coordinate from incrementing the j index <zk-spacing> - increase in
              z coordinate from incrementing the k index <z-offset> - z coordinate of first voxel

       Creates a volume file full of zeros.
              Exactly one of -plumb or -sform

              must be specified.

       -volume-dilate DILATE A VOLUME FILE

              wb_command -volume-dilate

              <volume> - the volume to dilate <distance> - distance in mm to  dilate  <method>  -
              dilation method to use <volume-out> - output - the output volume

              [-exponent] - use a different exponent in the weighting function

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

              weighting function (default 2)

              [-bad-voxel-roi] - specify an roi of voxels to overwrite, rather than

              voxels with value zero <roi-volume> - volume file, positive values denote voxels to
              have

              their values replaced

              [-data-roi] - specify an roi of where there is data

              <roi-volume> - volume file, positive values denote voxels that have

              data

              [-subvolume] - select a single subvolume to dilate

              <subvol> - the subvolume number or name

              For all voxels that are designated as bad, if they neighbor a  non-bad  voxel  with
              data or are within the specified distance of such a voxel, replace the value in the
              bad voxel with a value calculated  from  nearby  non-bad  voxels  that  have  data,
              otherwise  set the value to zero.  No matter how small <distance> is, dilation will
              always use at least the face neighbor voxels.

              By default, voxels that have data with the value 0 are bad, specify  -bad-voxel-roi
              to  only  count voxels as bad if they are selected by the roi.  If -data-roi is not
              specified, all voxels are assumed to have data.

              Valid values for <method> are:

              NEAREST - use the value from the nearest good  voxel  WEIGHTED  -  use  a  weighted
              average based on distance

       -volume-distortion CALCULATE VOLUME WARPFIELD DISTORTION

              wb_command -volume-distortion

              <warpfield>  -  the  warpfield to compute the distortion of <volume-out> - output -
              the output distortion measures

              [-fnirt] - MUST be used if using a fnirt warpfield

              <source-volume> - the source volume used when generating the warpfield

              [-circular] - use the circle-based formula for the anisotropic measure

              Calculates isotropic and anisotropic distortions in the volume warpfield.  At  each
              voxel,  the  gradient  of  the  absolute  warpfield is computed to obtain the local
              affine transforms for each  voxel  (jacobian  matrices),  and  strain  tensors  are
              derived  from  them.   The  isotropic component (volumetric expansion ratio) is the
              product of the three principal strains.  The default measure ('elongation') for the
              anisotropic component is the largest principal strain divided by the smallest.

              The  -circular  option instead calculates the anisotropic component by transforming
              the principal strains into log space, considering them as x-values of points  on  a
              circle  120 degrees apart, finds the circle's diameter, and transforms that back to
              a ratio.

       -volume-erode ERODE A VOLUME FILE

              wb_command -volume-erode

              <volume> - the volume to erode <distance> - distance in mm to erode <volume-out>  -
              output - the output volume

              [-roi] - assume voxels outside this roi are nonzero

              <roi-volume> - volume file, positive values denote voxels that have

              data

              [-subvolume] - select a single subvolume to dilate

              <subvol> - the subvolume number or name

              Around  each  voxel  with  a  value  of  zero, set surrounding voxels to zero.  The
              surrounding voxels are all face neighbors  and  all  voxels  within  the  specified
              distance (center to center).

       -volume-estimate-fwhm ESTIMATE FWHM SMOOTHNESS OF A VOLUME

              wb_command -volume-estimate-fwhm

              <volume> - the input volume

              [-roi] - use only data within an ROI

              <roivol> - the volume to use as an ROI

              [-subvolume] - select a single subvolume to estimate smoothness of

              <subvol> - the subvolume number or name

              Estimates  the smoothness of the input volume in X, Y, and Z directions separately,
              printing the estimates to standard output.  If -subvolume is  not  specified,  each
              subvolume is estimated and displayed separately.

       -volume-extrema FIND EXTREMA IN A VOLUME FILE

              wb_command -volume-extrema

              <volume-in>  - volume file to find the extrema of <distance> - the minimum distance
              between identified extrema of the same

              type

              <volume-out> - output - the output extrema volume

              [-presmooth] - smooth the volume before finding extrema

              <kernel> - the sigma for the gaussian smoothing kernel, in mm

              [-roi] - ignore values outside the selected area

              <roi-volume> - the area to find extrema in

              [-threshold] - ignore small extrema

              <low> - the largest value to consider for being a minimum  <high>  -  the  smallest
              value to consider for being a maximum

              [-sum-subvols] - output the sum of the extrema subvolumes instead of each

              subvolume separately

              [-consolidate-mode] - use consolidation of local minima instead of a

              large neighborhood

              [-only-maxima] - only find the maxima

              [-only-minima] - only find the minima

              [-subvolume] - select a single subvolume to find extrema in

              <subvolume> - the subvolume number or name

              Finds  extrema  in  a  volume  file,  such that no two extrema of the same type are
              within <distance> of each other.  The extrema are labeled as -1 for minima,  1  for
              maxima,  0  otherwise.   If -only-maxima or -only-minima is specified, then it will
              ignore extrema not of the specified type.  These options are mutually exclusive.

              If -sum-subvols is specified, these extrema subvolumes are summed, and  the  output
              has a single subvolume with this result.

              By  default,  a datapoint is an extrema only if it is more extreme than every other
              datapoint that is within <distance> from it.   If  -consolidate-mode  is  used,  it
              instead starts by finding all datapoints that are more extreme than their immediate
              neighbors, then while there are any extrema within <distance> of each  other,  take
              the two extrema closest to each other and merge them into one by a weighted average
              based on how many original extrema have been merged into each.

              By default, all input subvolumes are used with  no  smoothing,  use  -subvolume  to
              specify  a  single  subvolume  to  use,  and  -presmooth to smooth the input before
              finding the extrema.

       -volume-fill-holes FILL HOLES IN AN ROI VOLUME

              wb_command -volume-fill-holes

              <volume-in> - the input ROI volume <volume-out> - output - the output ROI volume

              Finds all face-connected parts that are not included in the ROI, and fills all  but
              the largest one with ones.

       -volume-find-clusters FILTER CLUSTERS BY VOLUME

              wb_command -volume-find-clusters

              <volume-in>  -  the  input  volume  <value-threshold>  -  threshold for data values
              <minimum-volume> - threshold for cluster volume, in mm^3 <volume-out>  -  output  -
              the output volume

              [-less-than] - find values less than <value-threshold>, rather than

              greater

              [-roi] - select a region of interest

              <roi-volume> - the roi, as a volume file

              [-subvolume] - select a single subvolume

              <subvol> - the subvolume number or name

              [-size-ratio] - ignore clusters smaller than a given fraction of the

              largest cluster in map <ratio> - fraction of the largest cluster's volume

              [-distance] - ignore clusters further than a given distance from the

              largest  cluster  <distance>  -  how far from the largest cluster a cluster can be,
              edge

              to edge, in mm

              [-start] - start labeling clusters from a value other than 1

              <startval> - the value to give the first cluster found

              Outputs a volume with nonzero  integers  for  all  voxels  within  a  large  enough
              cluster,  and zeros elsewhere.  The integers denote cluster membership (by default,
              first cluster found will use value 1, second cluster 2, etc).  By  default,  values
              greater than <value-threshold> are considered to be in a cluster, use -less-than to
              test for values less than the threshold.  To apply this as a mask to the  data,  or
              to do more complicated thresholding, see -volume-math.

       -volume-gradient GRADIENT OF A VOLUME FILE

              wb_command -volume-gradient

              <volume-in>  -  the  input  volume  <volume-out>  -  output  -  the output gradient
              magnitude volume

              [-presmooth] - smooth the volume before computing the gradient

              <kernel> - sigma for gaussian weighting function, in mm

              [-roi] - select a region of interest to take the gradient of

              <roi-volume> - the region to take the gradient within

              [-vectors] - output vectors

              <vector-volume-out> - output - the vectors as a volume file

              [-subvolume] - select a single subvolume to take the gradient of

              <subvol> - the subvolume number or name

              Computes the gradient of the volume by doing linear  regressions  for  each  voxel,
              considering  only  its  face  neighbors  unless  too few face neighbors exist.  The
              gradient vector is constructed from the partial derivatives of the resulting linear
              function, and the magnitude of this vector is the output.  If specified, the volume
              vector output is arranged with the x, y, and  z  components  from  a  subvolume  as
              consecutive subvolumes.

       -volume-label-export-table EXPORT LABEL TABLE FROM VOLUME AS TEXT

              wb_command -volume-label-export-table

              <label-in>  -  the  input volume label file <map> - the number or name of the label
              map to use <table-out> - output - the output text file

              Takes the label table from the volume label map, and writes it  to  a  text  format
              matching what is expected by -volume-label-import.

       -volume-label-import IMPORT A LABEL VOLUME TO CARET FORMAT

              wb_command -volume-label-import

              <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

              [-discard-others] - set any voxels with values not mentioned in the label

              list to the ??? label

              [-unlabeled-value] - set the value that will be interpreted as unlabeled

              <value> - the numeric value for unlabeled (default 0)

              [-subvolume] - select a single subvolume to import

              <subvol> - the subvolume number or name

              [-drop-unused-labels] - remove any unused label values from the label

              table

              Creates a new 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:

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

              Do  not  specify  the  "unlabeled"  key in the file, it is assumed that 0 means not
              labeled unless -unlabeled-value is specified.  Label names must be  on  a  separate
              line,  but  may  contain  spaces  or  other  unusual  characters (but not newline).
              Whitespace is trimmed from both ends of the label name, but is kept if it is in the
              middle  of a label.  The values of red, green, blue and alpha must be integers from
              0 to 255, and will specify the color the label is drawn  as  (alpha  of  255  means
              opaque,  which is probably what you want).  By default, it will set new label names
              with names of LABEL_# for any values encountered that are not mentioned in the list
              file, specify -discard-others to instead set these voxels to the "unlabeled" key.

       -volume-label-probability FIND FREQUENCY OF VOLUME LABELS

              wb_command -volume-label-probability

              <label-maps> - volume label file containing individual label maps from

              many subjects

              <probability-out> - output - the relative frequencies of each label at

              each voxel

              [-exclude-unlabeled] - don't make a probability map of the unlabeled key

              This command outputs a set of soft ROIs, one for each label in the input, where the
              value is how many of the input maps had that label at that voxel,  divided  by  the
              number of input maps.

       -volume-label-to-roi MAKE A VOLUME LABEL INTO AN ROI VOLUME

              wb_command -volume-label-to-roi

              <label-in>  - the input volume label file <volume-out> - output - the output volume
              file

              [-name] - select label by name

              <label-name> - the label name that you want an roi of

              [-key] - select label by key

              <label-key> - the label key that you want an roi of

              [-map] - select a single label map to use

              <map> - the map number or name

              For each map in <label-in>, a map is created in <volume-out>  where  all  locations
              labeled  with <label-name> or with a key of <label-key> are given a value of 1, and
              all other locations are given 0.  Exactly one of -name and -key must be  specified.
              Specify -map to use only one map from <label-in>.

       -volume-label-to-surface-mapping MAP A LABEL VOLUME TO A SURFACE LABEL FILE

              wb_command -volume-label-to-surface-mapping

              <volume> - the volume to map data from <surface> - the surface to map the data onto
              <label-out> - output - the output gifti label file

              [-ribbon-constrained] - use ribbon constrained mapping algorithm

              <inner-surf> - the inner surface of the ribbon <outer-surf> - the outer surface  of
              the ribbon

              [-volume-roi] - use a volume roi

              <roi-volume> - the volume file

              [-voxel-subdiv] - voxel divisions while estimating voxel weights

              <subdiv-num> - number of subdivisions, default 3

              [-thin-columns] - use non-overlapping polyhedra

              [-subvol-select] - select a single subvolume to map

              <subvol> - the subvolume number or name

       Map label volume data to a surface.
              If -ribbon-constrained is not

       specified, uses the enclosing voxel method.
              The ribbon mapping method

              constructs  a polyhedron from the vertex's neighbors on each surface, and estimates
              the amount of this polyhedron's volume that falls inside any nearby voxels, to  use
              as  the  weights  for  a popularity comparison.  If -thin-columns is specified, the
              polyhedron uses the edge midpoints and  triangle  centroids,  so  that  neighboring
              vertices   do   not  have  overlapping  polyhedra.   This  may  require  increasing
              -voxel-subdiv to get enough samples in each voxel to  reliably  land  inside  these
              smaller  polyhedra.   The volume ROI is useful to exclude partial volume effects of
              voxels the surfaces pass through, and will cause the mapping to ignore voxels  that
              don't  have  a positive value in the mask.  The subdivision number specifies how it
              approximates the amount of the volume the polyhedron intersects, by splitting  each
              voxel  into  NxNxN  pieces, and checking whether the center of each piece is inside
              the polyhedron.  If you have very large voxels, consider increasing this if you get
              unexpected unlabeled vertices in your output.

       -volume-math EVALUATE EXPRESSION ON VOLUME FILES

              wb_command -volume-math

              <expression>  -  the  expression to evaluate, in quotes <volume-out> - output - the
              output volume

              [-fixnan] - replace NaN results with a value

              <replace> - value to replace NaN with

              [-var] - repeatable - a volume file to use as a variable

              <name> - the name of the variable, as used in the expression <volume> - the  volume
              file to use as this variable

              [-subvolume] - select a single subvolume

              <subvol> - the subvolume number or name

              [-repeat] - reuse a single subvolume for each subvolume of calculation

       This command evaluates <expression> at each voxel independently.
              There

              must be at least one -var option (to get the volume space from), even if the <name>
              specified in it isn't used in <expression>.  All volumes must have the same  volume
              space.   Filenames  are  not  valid in <expression>, use a variable name and a -var
              option with matching <name> to specify an input file.  If the -subvolume option  is
              given to any -var option, only one subvolume is used from that file.  If -repeat is
              specified, the file must either have only one subvolume,  or  have  the  -subvolume
              option  specified.   All  files that don't use -repeat must have the same number of
              subvolumes requested to be used.  The format of <expression> is as follows:

              Expressions consist of constants, variables, operators, parentheses, and functions,
              in  infix  notation,  such  as 'exp(-x + 3) * scale'.  Variables are strings of any
              length, using the characters a-z, A-Z, 0-9, and _, but may not take the name  of  a
              named  constant.   Currently,  there is only one named constant, PI.  The operators
              are +, -, *, /, ^, >, <, >=, <=, ==, !=, !, &&, ||.  These behave as in  C,  except
              that  ^  is  exponentiation, i.e. pow(x, y), and takes higher precedence than other
              binary operators (also, '-3^-4^-5' means '-(3^(-(4^-5)))').  The <=, >=, ==, and !=
              operators  are  given  a small amount of wiggle room, equal to one millionth of the
              smaller of the absolute values of the values being compared.

              Comparison and logical operators return 0 or 1, you can do masking with expressions
              like  'x * (mask > 0)'.  For all logical operators, an input is considered true iff
              it is greater than 0.  The expression '0 < x < 5' is not syntactically  wrong,  but
              it  will NOT do what is desired, because it is evaluated left to right, i.e. '((0 <
              x) < 5)', which will always return 1, as both possible results of a comparison  are
              less  than  5.   A  warning is generated if an expression of this type is detected.
              Use something like 'x > 0 && x < 5' to get the desired behavior.

              Whitespace between elements is ignored, ' sin  (  2  *  x  )  '  is  equivalent  to
              'sin(2*x)',  but  's  in(2*x)' is an error.  Implied multiplication is not allowed,
              the expression '2x' will be parsed as a variable.  Parentheses are (), do  not  use
              [] or {}.  Functions require parentheses, the expression 'sin x' is an error.

              The following functions are supported:

              sin:  1 argument, the sine of the argument (units are radians) cos: 1 argument, the
              cosine of the argument (units are radians) tan: 1  argument,  the  tangent  of  the
              argument (units are radians) asin: 1 argument, the inverse of sine of the argument,
              in radians acos: 1 argument, the inverse of cosine  of  the  argument,  in  radians
              atan:  1  argument,  the  inverse  of  tangent of the argument, in radians atan2: 2
              arguments, atan2(y, x) returns the inverse of tangent of

              (y/x), in radians, determining quadrant by the sign of both arguments

              sinh: 1 argument, the hyperbolic  sine  of  the  argument  cosh:  1  argument,  the
              hyperbolic  cosine  of the argument tanh: 1 argument, the hyperboloc tangent of the
              argument asinh: 1 argument, the inverse hyperbolic sine of the  argument  acosh:  1
              argument,  the  inverse  hyperbolic  cosine  of the argument atanh: 1 argument, the
              inverse hyperboloc tangent of the argument ln: 1 argument, the natural logarithm of
              the  argument  exp:  1 argument, the constant e raised to the power of the argument
              log: 1 argument, the base 10 logarithm of the argument sqrt: 1 argument, the square
              root  of  the argument abs: 1 argument, the absolute value of the argument floor: 1
              argument, the largest integer not greater than the argument round: 1 argument,  the
              nearest integer, with ties rounded away from

              zero

              ceil: 1 argument, the smallest integer not less than the argument min: 2 arguments,
              min(x, y) returns y if (x > y), x otherwise max: 2 arguments, max(x, y)  returns  y
              if (x < y), x otherwise mod: 2 arguments, mod(x, y) = x - y * floor(x / y), or 0 if
              y == 0 clamp: 3 arguments, clamp(x, low, high) = min(max(x, low), high)

       -volume-merge MERGE VOLUME FILES INTO A NEW FILE

              wb_command -volume-merge

              <volume-out> - output - the output volume file

              [-volume] - repeatable - specify an input volume file

              <volume-in> - a volume file to use subvolumes from

              [-subvolume] - repeatable - select a single subvolume to use

              <subvol> - the subvolume number or name

              [-up-to] - use an inclusive range of subvolumes

              <last-subvol> - the number or name of the last subvolume to

              include

              [-reverse] - use the range in reverse order

              Takes one or more volume files and constructs a new volume  file  by  concatenating
              subvolumes from them.  The input volume files must have the same volume space.

              Example:  wb_command  -volume-merge  out.nii -volume first.nii -subvolume 1 -volume
              second.nii

              This example would take  the  first  subvolume  from  first.nii,  followed  by  all
              subvolumes from second.nii, and write these to out.nii.

       -volume-palette SET THE PALETTE OF A VOLUME FILE

              wb_command -volume-palette

              <volume> - the volume file to modify <mode> - the mapping mode

              [-subvolume] - select a single subvolume

              <subvolume> - the subvolume number or name

              [-pos-percent] - percentage min/max for positive data coloring

              <pos-min-%>  -  the  percentile  for  the  least  positive  data  <pos-max-%> - the
              percentile for the most positive data

              [-neg-percent] - percentage min/max for negative data coloring

              <neg-min-%> - the  percentile  for  the  least  negative  data  <neg-max-%>  -  the
              percentile for the most negative data

              [-pos-user] - user min/max values for positive data coloring

              <pos-min-user>  -  the value for the least positive data <pos-max-user> - the value
              for the most positive data

              [-neg-user] - user min/max values for negative data coloring

              <neg-min-user> - the value for the least negative data <neg-max-user> -  the  value
              for the most negative data

              [-interpolate] - interpolate colors

              <interpolate> - boolean, whether to interpolate

              [-disp-pos] - display positive data

              <display> - boolean, whether to display

              [-disp-neg] - display positive data

              <display> - boolean, whether to display

              [-disp-zero] - display data closer to zero than the min cutoff

              <display> - boolean, whether to display

              [-palette-name] - set the palette used

              <name> - the name of the palette

              [-thresholding] - set the thresholding

              <type>  -  thresholding  setting  <test> - show values inside or outside thresholds
              <min> - lower threshold <max> - upper threshold

              [-inversion] - specify palette inversion

              <type> - the type of inversion

       The original volume file is overwritten with the modified version.
              By

              default, all columns of the volume file are adjusted to the new settings,  use  the
              -subvolume  option to change only one subvolume.  Mapping settings not specified in
              options will be taken from the first subvolume.  The <mode> argument must be one of
              the following:

              MODE_AUTO_SCALE    MODE_AUTO_SCALE_ABSOLUTE_PERCENTAGE   MODE_AUTO_SCALE_PERCENTAGE
              MODE_USER_SCALE

              The <name> argument to -palette-name must be one of the following:

              ROY-BIG-BL  videen_style  Gray_Interp_Positive  Gray_Interp   PSYCH-FIXED   RBGYR20
              RBGYR20P  RYGBR4_positive  RGRBR_mirror90_pos Orange-Yellow POS_NEG_ZERO red-yellow
              blue-lightblue FSL power_surf fsl_red fsl_green  fsl_blue  fsl_yellow  RedWhiteBlue
              cool-warm  spectral  RY-BC-BL  magma JET256 PSYCH PSYCH-NO-NONE ROY-BIG clear_brain
              fidl raich4_clrmid raich6_clrmid HSB8_clrmid POS_NEG

              The <type> argument to -thresholding must be one of the following:

              THRESHOLD_TYPE_OFF THRESHOLD_TYPE_NORMAL THRESHOLD_TYPE_FILE

              The <test> argument to -thresholding must be one of the following:

              THRESHOLD_TEST_SHOW_OUTSIDE THRESHOLD_TEST_SHOW_INSIDE

              The <type> argument to -inversion must be one of the following:

              OFF POSITIVE_WITH_NEGATIVE POSITIVE_NEGATIVE_SEPARATE

       -volume-parcel-resampling SMOOTH AND RESAMPLE VOLUME PARCELS

              wb_command -volume-parcel-resampling

              <volume-in> - the input data volume <cur-parcels>  -  label  volume  of  where  the
              parcels  currently  are <new-parcels> - label volume of where the parcels should be
              <kernel> - gaussian kernel sigma to smooth  by  during  resampling  <volume-out>  -
              output - output volume

              [-fix-zeros] - treat zero values as not being data

              [-subvolume] - select a single subvolume as input

              <subvol> - the subvolume number or name

              Smooths  and resamples the region inside each label in cur-parcels to the region of
              the same label name in new-parcels.  Any voxels in  the  output  label  region  but
              outside  the  input  label  region  will  be  extrapolated  from  nearby data.  The
              -fix-zeros option causes the smoothing to not use an input value if it is zero, but
              still write a smoothed value to the voxel, and after smoothing is complete, it will
              check for any remaining values of zero, and fill them in with extrapolated values.

       Note: all volumes must have the same dimensions and spacing.
              To use a

              different output space, see -volume-parcel-resampling-generic.

       -volume-parcel-resampling-generic SMOOTH AND RESAMPLE VOLUME PARCELS FROM DIFFERENT VOLUME
       SPACE

              wb_command -volume-parcel-resampling-generic

              <volume-in>  -  the  input  data  volume  <cur-parcels> - label volume of where the
              parcels currently are <new-parcels> - label volume of where the parcels  should  be
              <kernel>  -  gaussian  kernel  sigma  to smooth by during resampling <volume-out> -
              output - output volume

              [-fix-zeros] - treat zero values as not being data

              [-subvolume] - select a single subvolume as input

              <subvol> - the subvolume number or name

              Smooths and resamples the region inside each label in cur-parcels to the region  of
              the  same  label  name  in  new-parcels.  Any voxels in the output label region but
              outside the input  label  region  will  be  extrapolated  from  nearby  data.   The
              -fix-zeros option causes the smoothing to not use an input value if it is zero, but
              still write a smoothed value to the voxel, and after smoothing is complete, it will
              check  for any remaining values of zero, and fill them in with extrapolated values.
              The output volume will use the volume space of new-parcels, which does not need  to
              be in the same volume space as the input.

       -volume-parcel-smoothing SMOOTH PARCELS IN A VOLUME SEPARATELY

              wb_command -volume-parcel-smoothing

              <data-volume> - the volume to smooth <label-volume> - a label volume containing the
              parcels  to  smooth  <kernel>  -  the  gaussian  smoothing  kernel  sigma,  in   mm
              <volume-out> - output - the output volume

              [-fix-zeros] - treat zero values as not being data

              [-subvolume] - select a single subvolume to smooth

              <subvol> - the subvolume number or name

              The  volume  is smoothed within each label in the label volume using data only from
              within the label.  Equivalent to running volume smoothing with ROIs  matching  each
              label separately, then adding the resulting volumes, but faster.

       -volume-reduce PERFORM REDUCTION OPERATION ACROSS SUBVOLUMES

              wb_command -volume-reduce

              <volume-in> - the volume file to reduce <operation> - the reduction operator to use
              <volume-out> - output - the output volume

              [-exclude-outliers] - exclude non-numeric values and outliers by standard

              deviation <sigma-below> - number of standard deviations below the mean to

              include

              <sigma-above> - number of standard deviations above the mean to

              include

              [-only-numeric] - exclude non-numeric values

              For each voxel, takes the data across subvolumes as  a  vector,  and  performs  the
              specified reduction on it, putting the result into the single output volume at that
              voxel.  The reduction operators are as follows:

              MAX: the maximum value MIN: the minimum value INDEXMAX: the 1-based  index  of  the
              maximum  value INDEXMIN: the 1-based index of the minimum value SUM: add all values
              PRODUCT: multiply all values MEAN:  the  mean  of  the  data  STDEV:  the  standard
              deviation   (N   denominator)   SAMPSTDEV:   the  sample  standard  deviation  (N-1
              denominator) VARIANCE: the variance of  the  data  TSNR:  mean  divided  by  sample
              standard   deviation   (N-1   denominator)  COV:  sample  standard  deviation  (N-1
              denominator) divided by mean MEDIAN: the median of the data MODE: the mode  of  the
              data COUNT_NONZERO: the number of nonzero elements in the data

       -volume-remove-islands REMOVE ISLANDS FROM AN ROI VOLUME

              wb_command -volume-remove-islands

              <volume-in> - the input ROI volume <volume-out> - output - the output ROI volume

              Finds all face-connected parts of the ROI, and zeros out all but the largest one.

       -volume-reorient CHANGE VOXEL ORDER OF A VOLUME FILE

              wb_command -volume-reorient

              <volume>  -  the  volume  to  reorient  <orient-string>  -  the desired orientation
              <volume-out> - out - the reoriented volume

              Changes the voxel order and the header spacing/origin  information  such  that  the
              value  of  any  spatial  point  is unchanged.  Orientation strings look like 'LPI',
              which means first index is left to right, second  is  posterior  to  anterior,  and
              third is inferior to superior.  The valid characters are:

       L      left to right

       R      right to left

       P      posterior to anterior

       A      anterior to posterior

       I      inferior to superior

       S      superior to inferior

       -volume-rois-from-extrema CREATE VOLUME ROI MAPS FROM EXTREMA MAPS

              wb_command -volume-rois-from-extrema

              <volume-in>  -  the  input volume <limit> - distance limit from voxel center, in mm
              <volume-out> - output - the output volume

              [-gaussian] - generate a gaussian kernel instead of a flat ROI

              <sigma> - the sigma for the gaussian kernel, in mm

              [-roi] - select a region of interest to use

              <roi-volume> - the region to use

              [-overlap-logic] - how to handle overlapping ROIs, default ALLOW

              <method> - the method of resolving overlaps

              [-subvolume] - select a single subvolume to take the gradient of

              <subvol> - the subvolume number or name

              For each nonzero value in each map, make a map with an ROI  around  that  location.
              If  the  -gaussian option is specified, then normalized gaussian kernels are output
              instead of ROIs.  The <method> argument to -overlap-logic must  be  one  of  ALLOW,
              CLOSEST,  or  EXCLUDE.   ALLOW  is  the  default,  and  means that ROIs are treated
              independently and may overlap.  CLOSEST means that ROIs may not overlap,  and  that
              no ROI contains vertices that are closer to a different seed vertex.  EXCLUDE means
              that ROIs may not overlap, and that any vertex within range of more  than  one  ROI
              does not belong to any ROI.

       -volume-set-space CHANGE VOLUME SPACE INFORMATION

              wb_command -volume-set-space

              <volume-in> - the input volume <volume-out> - output - the output volume

              [-plumb] - set via axis order and spacing/offset

              <axis-order> - a string like 'XYZ' that specifies which index is along

              which spatial dimension

              <x-spacing> - change in x-coordinate from incrementing the relevant

              index

              <y-spacing> - change in y-coordinate from incrementing the relevant

              index

              <z-spacing> - change in z-coordinate from incrementing the relevant

              index

              <x-offset>  -  the x-coordinate of the first voxel <y-offset> - the y-coordinate of
              the first voxel <z-offset> - the z-coordinate of the first voxel

              [-sform] - set via a nifti sform

              <xi-spacing> - increase in x coordinate from incrementing the i index  <xj-spacing>
              - increase in x coordinate from incrementing the j index <xk-spacing> - increase in
              x coordinate from incrementing the k index <x-offset> - x coordinate of first voxel
              <yi-spacing>  - increase in y coordinate from incrementing the i index <yj-spacing>
              - increase in y coordinate from incrementing the j index <yk-spacing> - increase in
              y coordinate from incrementing the k index <y-offset> - y coordinate of first voxel
              <zi-spacing> - increase in z coordinate from incrementing the i index  <zj-spacing>
              - increase in z coordinate from incrementing the j index <zk-spacing> - increase in
              z coordinate from incrementing the k index <z-offset> - z coordinate of first voxel

              [-file] - copy spacing info from volume file with matching dimensions

              <volume-ref> - volume file to use for reference space

              [-ignore-dims] - copy the spacing info even if the dimensions don't

              match

              Writes a copy  of  the  volume  file,  with  the  spacing  information  changed  as
              specified.   No reordering of the voxel data occurs, see -volume-reorient to change
              the volume indexing order and reorder the voxels to match.  Exactly one of  -plumb,
              -sform, or -file must be specified.

       -volume-smoothing SMOOTH A VOLUME FILE

              wb_command -volume-smoothing

              <volume-in>  - the volume to smooth <kernel> - the gaussian smoothing kernel sigma,
              in mm <volume-out> - output - the output volume

              [-roi] - smooth only from data within an ROI

              <roivol> - the volume to use as an ROI

              [-fix-zeros] - treat zero values as not being data

              [-subvolume] - select a single subvolume to smooth

              <subvol> - the subvolume number or name

       Gaussian smoothing for volumes.
              By default, smooths all subvolumes with

              no ROI, if ROI is given, only positive voxels in the ROI volume have  their  values
              used, and all other voxels are set to zero.  Smoothing a non-orthogonal volume will
              be  significantly  slower,  because  the  operation  cannot   be   separated   into
              1-dimensional smoothings without distorting the kernel shape.

              The -fix-zeros option causes the smoothing to not use an input value if it is zero,
              but still write a smoothed value to the voxel.   This  is  useful  for  zeros  that
              indicate  lack  of  information, preventing them from pulling down the intensity of
              nearby voxels, while giving the zero an extrapolated value.

       -volume-stats SPATIAL STATISTICS ON A VOLUME FILE

              wb_command -volume-stats

              <volume-in> - the input volume

              [-reduce] - use a reduction operation

              <operation> - the reduction operation

              [-percentile] - give the value at a percentile

              <percent> - the percentile to find

              [-subvolume] - only display output for one subvolume

              <subvolume> - the subvolume number or name

              [-roi] - only consider data inside an roi

              <roi-volume> - the roi, as a volume file

              [-match-maps] - each subvolume of input uses the corresponding

              subvolume from the roi file

              [-show-map-name] - print map index and name before each output

              For each subvolume of the input, a single number is  printed,  resulting  from  the
              specified  reduction  or  percentile operation.  Use -subvolume to only give output
              for a single subvolume.  Use -roi to  consider  only  the  data  within  a  region.
              Exactly one of -reduce or -percentile must be specified.

              The argument to the -reduce option must be one of the following:

              MAX:  the  maximum  value MIN: the minimum value INDEXMAX: the 1-based index of the
              maximum value INDEXMIN: the 1-based index of the minimum value SUM: add all  values
              PRODUCT:  multiply  all  values  MEAN:  the  mean  of  the data STDEV: the standard
              deviation  (N  denominator)  SAMPSTDEV:  the   sample   standard   deviation   (N-1
              denominator)  VARIANCE:  the  variance  of  the  data  TSNR: mean divided by sample
              standard  deviation  (N-1  denominator)  COV:  sample   standard   deviation   (N-1
              denominator)  divided  by mean MEDIAN: the median of the data MODE: the mode of the
              data COUNT_NONZERO: the number of nonzero elements in the data

       -volume-tfce DO TFCE ON A VOLUME FILE

              wb_command -volume-tfce

              <volume-in> - the volume to run TFCE on <volume-out> - output - the output volume

              [-presmooth] - smooth the volume before running TFCE

              <kernel> - the sigma for the gaussian smoothing kernel, in mm

              [-roi] - select a region of interest to run TFCE on

              <roi-volume> - the area to run TFCE on, as a volume

              [-parameters] - set parameters for TFCE integral

              <E> - exponent for cluster volume (default 0.5) <H> - exponent for threshold  value
              (default 2.0)

              [-subvolume] - select a single subvolume

              <subvolume> - the subvolume number or name

              Threshold-free  cluster  enhancement  is a method to increase the relative value of
              regions that would  form  clusters  in  a  standard  thresholding  test.   This  is
              accomplished by evaluating the integral of:

              e(h, p)^E * h^H * dh

              at  each vertex p, where h ranges from 0 to the maximum value in the data, and e(h,
              p) is the extent of the cluster containing  vertex  p  at  threshold  h.   Negative
              values  are  similarly enhanced by negating the data, running the same process, and
              negating the result.

              This method is  explained  in:  Smith  SM,  Nichols  TE.,  "Threshold-free  cluster
              enhancement:   addressing   problems   of   smoothing,   threshold  dependence  and
              localisation in cluster  inference."  Neuroimage.  2009  Jan  1;44(1):83-98.  PMID:
              18501637

       -volume-to-surface-mapping MAP VOLUME TO SURFACE

              wb_command -volume-to-surface-mapping

              <volume> - the volume to map data from <surface> - the surface to map the data onto
              <metric-out> - output - the output metric file

              [-trilinear] - use trilinear volume interpolation

              [-enclosing] - use value of the enclosing voxel

              [-cubic] - use cubic splines

              [-ribbon-constrained] - use ribbon constrained mapping algorithm

              <inner-surf> - the inner surface of the ribbon <outer-surf> - the outer surface  of
              the ribbon

              [-volume-roi] - use a volume roi

              <roi-volume> - the volume file

              [-voxel-subdiv] - voxel divisions while estimating voxel weights

              <subdiv-num> - number of subdivisions, default 3

              [-thin-columns] - use non-overlapping polyhedra

              [-gaussian] - reduce weight to voxels that aren't near <surface>

              <scale> - value to multiply the local thickness by, to get the

              gaussian sigma

              [-output-weights] - write the voxel weights for a vertex to a volume

              file  <vertex>  -  the  vertex  number  to  get  the  voxel  weights  for,  0-based
              <weights-out> - output - volume to write the weights to

              [-output-weights-text] - write the voxel weights for all vertices to a

              text file <text-out> - output - the output text filename

              [-myelin-style] - use the method from myelin mapping

              <ribbon-roi> - an roi volume of the cortical ribbon for this

              hemisphere

              <thickness> - a metric file of cortical thickness <sigma> - gaussian kernel  in  mm
              for weighting voxels within range

              [-legacy-bug] - emulate old v1.2.3 and earlier code that didn't follow

              a cylinder cutoff

              [-subvol-select] - select a single subvolume to map

              <subvol> - the subvolume number or name

       You must specify exactly one mapping method.
              Enclosing voxel uses the

              value  from  the  voxel  the  vertex  lies inside, while trilinear does a 3D linear
              interpolation based on  the  voxels  immediately  on  each  side  of  the  vertex's
              position.

              The  ribbon  mapping  method constructs a polyhedron from the vertex's neighbors on
              each surface, and estimates the amount  of  this  polyhedron's  volume  that  falls
              inside  any nearby voxels, to use as the weights for sampling.  If -thin-columns is
              specified, the polyhedron uses the edge midpoints and triangle centroids,  so  that
              neighboring   vertices  do  not  have  overlapping  polyhedra.   This  may  require
              increasing -voxel-subdiv to get enough samples  in  each  voxel  to  reliably  land
              inside these smaller polyhedra.  The volume ROI is useful to exclude partial volume
              effects of voxels the surfaces pass through, and will cause the mapping  to  ignore
              voxels  that  don't  have  a  positive  value  in the mask.  The subdivision number
              specifies how it approximates the amount of the volume the  polyhedron  intersects,
              by  splitting each voxel into NxNxN pieces, and checking whether the center of each
              piece is inside the polyhedron.  If you have very large voxels, consider increasing
              this  if you get zeros in your output.  The -gaussian option makes it act more like
              the myelin method, where the  distance  of  a  voxel  from  <surface>  is  used  to
              downweight the voxel.

              The  myelin  style  method uses part of the caret5 myelin mapping command to do the
              mapping: for each surface vertex, take all voxels that are in a cylinder with width
              and height equal to cortical thickness, centered on the vertex and aligned with the
              surface normal, and that are also within the  ribbon  ROI,  and  apply  a  gaussian
              kernel with the specified sigma to them to get the weights to use.  The -legacy-bug
              flag reverts to the unintended behavior present from the initial implementation  up
              to  and  including  v1.2.3, which had only the tangential cutoff and a bounding box
              intended to be larger than where the cylinder cutoff should have been.

       -volume-vector-operation DO A VECTOR OPERATION ON VOLUME FILES

              wb_command -volume-vector-operation

              <vectors-a> - first vector input  file  <vectors-b>  -  second  vector  input  file
              <operation> - what vector operation to do <volume-out> - output - the output file

              [-normalize-a] - normalize vectors of first input

              [-normalize-b] - normalize vectors of second input

              [-normalize-output] - normalize output vectors (not valid for dot

              product)

              [-magnitude] - output the magnitude of the result (not valid for dot

              product)

              Does  a  vector  operation  on  two  volume  files  (that must have a multiple of 3
              subvolumes).  Either  of  the  inputs  may  have  multiple  vectors  (more  than  3
              subvolumes),  but  not  both  (at  least  one must have exactly 3 subvolumes).  The
              -magnitude and -normalize-output options may not be specified together, or with the
              DOT operation.  The <operation> parameter must be one of the following:

              DOT CROSS ADD SUBTRACT

       -volume-warpfield-affine-regression REGRESS AFFINE FROM WARPFIELD

              wb_command -volume-warpfield-affine-regression

              <warpfield> - the input warpfield <affine-out> - output - the output affine file

              [-roi] - only consider voxels within a mask (e.g., a brain mask)

              <roi-vol> - the mask volume

              [-fnirt] - input is a fnirt warpfield

              <source-volume> - the source volume used when generating the fnirt

              warpfield

              [-flirt-out] - write output as a flirt matrix rather than a world

              coordinate  transform  <source-volume> - the volume you want to apply the transform
              to <target-volume> - the target space you want the transformed volume to

              match

              For all voxels in the warpfield,  do  a  regression  that  predicts  the  post-warp
              coordinate  from  the  source  coordinate.   When  -roi is specified, only consider
              voxels with a value greater than 0 in <roi-vol>.

              The default is to expect the warpfield to be  in  relative  world  coordinates  (mm
              space),  and  to write the output as a world affine (mm space to mm space).  If you
              are using FSL-created files and utilities, specify -fnirt and -flirt as needed,  as
              their coordinate conventions are different.

       -volume-warpfield-resample RESAMPLE VOLUME USING WARPFIELD

              wb_command -volume-warpfield-resample

              <volume-in>   -   volume   to   resample  <warpfield>  -  the  warpfield  to  apply
              <volume-space> - a volume file in the volume space you want for the

              output

              <method> - the resampling method <volume-out> - output - the output volume

              [-fnirt] - MUST be used if using a fnirt warpfield

              <source-volume> - the source volume used when generating the warpfield

       Resample a volume file with a warpfield.
              The recommended methods are

              CUBIC (cubic spline) for most  data,  and  ENCLOSING_VOXEL  for  label  data.   The
              parameter <method> must be one of:

              CUBIC ENCLOSING_VOXEL TRILINEAR

       -volume-weighted-stats WEIGHTED SPATIAL STATISTICS ON A VOLUME FILE

              wb_command -volume-weighted-stats

              <volume-in> - the input volume

              [-weight-volume] - use weights from a volume file

              <weight-volume> - volume file containing the weights

              [-match-maps] - each subvolume of input uses the corresponding

              subvolume from the weights file

              [-subvolume] - only display output for one subvolume

              <subvolume> - the subvolume number or name

              [-roi] - only consider data inside an roi

              <roi-volume> - the roi, as a volume file

              [-match-maps] - each subvolume of input uses the corresponding

              subvolume from the roi file

              [-mean] - compute weighted mean

              [-stdev] - compute weighted standard deviation

              [-sample] - estimate population stdev from the sample

              [-percentile] - compute weighted percentile

              <percent> - the percentile to find

              [-sum] - compute weighted sum

              [-show-map-name] - print map index and name before each output

              For  each  subvolume  of  the input, a single number is printed, resulting from the
              specified operation.  If -weight-volume is not specified, each  voxel's  volume  is
              used.   Use  -subvolume  to  only  give output for a single subvolume.  Use -roi to
              consider only the data within a region.  Exactly one of -mean, -stdev,  -percentile
              or -sum must be specified.

              Using  -sum  without  -weight-volume  is  equivalent to integrating with respect to
              volume.

       -wbsparse-merge-dense MERGE WBSPARSE FILES ALONG DENSE DIMENSION

              wb_command -wbsparse-merge-dense

              <direction> - which dimension to merge along, ROW or COLUMN <wbsparse-out> - output
              - the output wbsparse file

              [-wbsparse] - repeatable - specify an input wbsparse file

              <wbsparse-in> - a wbsparse file to merge

              The  input  wbsparse  files  must  have  matching  mappings along the direction not
              specified, and the mapping along the specified direction must be brain models.

       -zip-scene-file ZIP A SCENE FILE AND ITS DATA FILES

              wb_command -zip-scene-file

              <scene-file> - the scene file to make the zip file from <extract-folder> - the name
              of the folder created when the zip file is

              unzipped

              <zip-file> - out - the zip file that will be created

              [-base-dir] - specify a directory that all data files are somewhere

              within,  this will become the root of the zipfile's directory structure <directory>
              - the directory

       If zip-file already exists, it will be overwritten.
              If -base-dir is not

              specified, the base directory  will  be  automatically  set  to  the  lowest  level
              directory  containing  all files.  The scene file must contain only relative paths,
              and no data files may be outside the base directory.

       -zip-spec-file ZIP A SPEC FILE AND ITS DATA FILES

              wb_command -zip-spec-file

              <spec-file> - the specification file to add to zip file <extract-folder> - the name
              of the folder created when the zip file is

              unzipped

              <zip-file> - out - the zip file that will be created

              [-base-dir] - specify a directory that all data files are somewhere

              within,  this will become the root of the zipfile's directory structure <directory>
              - the directory

       If zip-file already exists, it will be overwritten.
              If -base-dir is not

              specified, the directory containing the spec file is used for the  base  directory.
              The  spec  file  must contain only relative paths, and no data files may be outside
              the base directory.  Scene files inside spec files are not checked for  what  files
              they  reference,  ensure that all data files referenced by the scene files are also
              referenced by the spec file.