afni.nimh.nih.gov

Hi-

The auto_warp.py function is a wrapper for 3dQwarp, but it does a bit of pre-processing on the input volume before aligning it using 3dSkullstrip and 3dUnifize. So, in that sense, it might be preferable to use auto_warp.py to start with (I find it's often helpful to 'polish' up images for helping alignment, so single spikes in values in CSF or edges don't ruin everything). In the history of your output from auto_warp.py, you will see the full set of 3d* commands, including 3dQwarp.

--pt