You can mirror the surface data or the volumetric data by flipping the data from one side to another. For volumetric data, use 3dLRflip. For surface data, flip the surfaces with this kind of script.
The xmat input for ConvertSurface can do shifts and mirroring of surfaces.
ConvertSurface -o shift_left_pial.gii -i original_left_pial.gii -overwrite -xmat_1D shiftorigin.1D
ConvertSurface -o shift_right_pial.gii -i shift_left_pial.gii -overwrite -xmat_1D mirror.1D
where shiftorigin.1D is this:
1 0 0 dx
0 1 0 dy
0 0 1 dz
and mirror.1D is this:
-1 0 0 0
0 1 0 0
0 0 1 0
You could even concatenate the two transformations. In this case, I've kept it as two separate operations to make it clear what is going on.
