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