Using Workbench Command

Workbench Command is a set of command-line tools that can be used to perform simple and complex operations within Connectome Workbench.

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RESAMPLE A CIFTI FILE TO A NEW CIFTI SPACE
   wb_command -cifti-resample
      <cifti-in> - the cifti file to resample
      <direction> - the direction of the input that should be resampled, ROW or
         COLUMN
      <cifti-template> - a cifti file containing the cifti space to resample to
      <template-direction> - the direction of the template to use as the
         resampling space, ROW or COLUMN
      <surface-method> - specify a surface resampling method
      <volume-method> - specify a volume interpolation method
      <cifti-out> - output - the output cifti file

      [-surface-largest] - use largest weight instead of weighted average or
         popularity when doing surface resampling

      [-volume-predilate] - dilate the volume components before resampling
         <dilate-mm> - distance, in mm, to dilate

         [-nearest] - use nearest value dilation

         [-weighted] - use weighted dilation (default)

            [-exponent] - specify exponent in weighting function
               <exponent> - exponent 'n' to use in (1 / (distance ^ n)) as the
                  weighting function (default 7)

            [-legacy-cutoff] - use v1.3.2 logic for the kernel cutoff

      [-surface-postdilate] - dilate the surface components after resampling
         <dilate-mm> - distance, in mm, to dilate

         [-nearest] - use nearest value dilation

         [-linear] - use linear dilation

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

            [-exponent] - specify exponent in weighting function
               <exponent> - exponent 'n' to use in (area / (distance ^ n)) as
                  the weighting function (default 6)

            [-legacy-cutoff] - use v1.3.2 logic for the kernel cutoff

      [-affine] - use an affine transformation on the volume components
         <affine-file> - the affine file to use

         [-flirt] - MUST be used if affine is a flirt affine
            <source-volume> - the source volume used when generating the affine
            <target-volume> - the target volume used when generating the affine

      [-warpfield] - use a warpfield on the volume components
         <warpfield> - the warpfield to use

         [-fnirt] - MUST be used if using a fnirt warpfield
            <source-volume> - the source volume used when generating the
               warpfield

      [-left-spheres] - specify spheres for left surface resampling
         <current-sphere> - a sphere with the same mesh as the current left
            surface
         <new-sphere> - a sphere with the new left mesh that is in register
            with the current sphere

         [-left-area-surfs] - specify left surfaces to do vertex area
            correction based on
            <current-area> - a relevant left anatomical surface with current
               mesh
            <new-area> - a relevant left anatomical surface with new mesh

         [-left-area-metrics] - specify left vertex area metrics to do area
            correction based on
            <current-area> - a metric file with vertex areas for the current
               mesh
            <new-area> - a metric file with vertex areas for the new mesh

      [-right-spheres] - specify spheres for right surface resampling
         <current-sphere> - a sphere with the same mesh as the current right
            surface
         <new-sphere> - a sphere with the new right mesh that is in register
            with the current sphere

         [-right-area-surfs] - specify right surfaces to do vertex area
            correction based on
            <current-area> - a relevant right anatomical surface with current
               mesh
            <new-area> - a relevant right anatomical surface with new mesh

         [-right-area-metrics] - specify right vertex area metrics to do area
            correction based on
            <current-area> - a metric file with vertex areas for the current
               mesh
            <new-area> - a metric file with vertex areas for the new mesh

      [-cerebellum-spheres] - specify spheres for cerebellum surface resampling
         <current-sphere> - a sphere with the same mesh as the current
            cerebellum surface
         <new-sphere> - a sphere with the new cerebellum mesh that is in
            register with the current sphere

         [-cerebellum-area-surfs] - specify cerebellum surfaces to do vertex
            area correction based on
            <current-area> - a relevant cerebellum anatomical surface with
               current mesh
            <new-area> - a relevant cerebellum anatomical surface with new mesh

         [-cerebellum-area-metrics] - specify cerebellum vertex area metrics to
            do area correction based on
            <current-area> - a metric file with vertex areas for the current
               mesh
            <new-area> - a metric file with vertex areas for the new mesh

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

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

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

      CUBIC
      ENCLOSING_VOXEL
      TRILINEAR

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

      ADAP_BARY_AREA
      BARYCENTRIC