Using Workbench Command

TRANSFORM AND RESAMPLE A LABEL VOLUME FILE
   wb_command -volume-label-resample
      <volume-in> - volume to resample
      <volume-space> - a volume file in the volume space you want for the
         output
      <volume-out> - output - the output volume

      [-smooth-edges] - apply smoothing to the ROIs between resampling and
         indexmax operations, increases boundary smoothness at the cost of
         fidelity
         <kernel-size> - smoothing amount to use, gaussian sigma in mm

         [-fwhm] - use specified kernel size as full width at half maximum,
            rather than sigma

      [-unlabeled-mask] - instead of treating the 'unlabeled' voxels as just
         another label, treat them as a mask

      [-affine] - repeatable - add an affine transform
         <affine> - 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

      [-affine-series] - repeatable - add an independent affine per-frame
         <affine-series> - text file containing 12 or 16 numbers per line, each
            being a row-major flattened affine

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

      [-warp] - repeatable - add a nonlinear warpfield transform
         <warpfield> - the warpfield file

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

      Resample a label volume file with an arbitrary list of transformations.
      You may specify -affine, -warp, and -affine-series multiple times each,
      and they will be used in the order specified.  For instance, for rigid
      motion correction followed by nonlinear atlas registration, specify
      -affine-series first, then -warp.

      Internally, this command makes an ROI for each label, resamples them with
      TRILINEAR, and then takes the label from the ROI with the largest value
      at each voxel.  By default, unlabeled voxels are treated as if they were
      a label, use -unlabeled-mask to instead treat them as a separate mask.
      Using mask behavior can reduce an effect where a junction between labels
      that is next to unlabeled voxels will 'pinch inwards', particularly when
      using -smooth-edges.