afni.nimh.nih.gov

Also auto_warp.py includes an affine alignment step by default, which may be something you want; it's often a good starting point. It call @auto_tlrc to do that step. 3dQwarp has a -allineate option that can do something similar. The transformations are concatenated together in that script. Another difference is auto_warp.py puts all its output into a separate directory. It's probably just easier to let auto_warp.py worry about the details unless you need to do some more tweaking of the options.