Good morning AFNI folks,

Two fun things:
I'm looking through the script that afni proc script and I noticed something I think might be a small issue. I'm performing blip up and blip distortion correction, using single band reference images (created by the multiband sequence, very high contrast to noise). I also use the single band reference image from my functional run as the external_volreg_base (it the same as the functional data in all ways, except better contrast). This all works fantastically, and leads to what appears to be good anatomical alignment - however I think it could be improved.

Specifically, the align_epi_to_anat portion of the afni_proc output uses the original external_volreg_dataset, rather than the dataset that has been corrected for distortions by the blip up/down process. It seems that it would be better to use the undistorted, 'corrected data', to calculate the alignment with the anatomy, while continuing to use the original version as the volreg alignment target. Perhaps I have done something wrong, and that is why this is happening?

My second question also concerns blip up/down correction - is it possible to use different blip datasets per run? In one cases, I am doing a pre vs post comparison, and therefore want to include both runs of data in a single afni proc. Unfortunately, I can only use a single blip up/down dataset, even though there are likely differences in the head position and therefor distortions between runs. Is there any interest in adding the possibility of multiple blip datasets into a single afni proc run?

Thanks again for afni_proc - it has made my life so easy that I am finding new ways to make it difficult.