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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   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.