afni.nimh.nih.gov

You would have to compute the transformation to align your data with the template. The tools to do this in AFNI are typically @auto_tlrc, auto_warp.py. Also align_epi_anat.py, 3dAllineate and 3dQwarp can also be useful. These tools are described in their own help and in the class presentation material here:

https://afni.nimh.nih.gov/pub/dist/edu/latest/afni10_volreg_talairach/