Hi Sungjin,
Sorry for being slow. We have finished a bootcamp and are still in middle of a subsequent hackathon, and I am losing track of the details here...
Ooooh! Going back I just noticed you have a comment about using 3dresample to change the orientation and grid size, but now you are not doing that.
Have you re-run afni_proc.py using the original 3mm data? The 3dNwarpApply command should not be using "-dxyz 1" anymore. But to be sure, what is the output of:
3dinfo -d3 -n4 -prefix pb00.265001.r01.tcat+orig
Getting to your alignment question, what is the output of:
3dinfo -extents -prefix DATASET
run on the anat and EPI DATASETs?
And to be sure, have you run 3dWarp or 3dresample on anything before running afni_proc.py?
Thanks,
- rick