Thanks Rick

I have been using align_epi_anat.py to do (or at least start) my co-registrations of anatomicals to the time-series functional scan.

Is there any way to use -blip_forward_dset xxx+orig and -blip_reverse_dset xxxrev+orig (I collect a forward and backward both) in align_epi_anat.py? Maybe field map info could be somehow incorporated as part of (just prior to) the co-localization of EPI and anat.

If ALL I wanted to do was the very initial reconstruction of the time-series dataset from slices (using the field-map values), or maybe work from an initially-reconstructed .nii 3d+time image to re-warp it using field-map values, how could I use afni_proc.py to do only this?

If you could simply respond with what the command line would look like, that would be keen.

Jim