I’ve been tasked with analyzing some older data that were never written up, that involve a scan procedure wherein for physiological monitoring and other procedures, the participant was removed from the scanner then re-entered and re-localized THREE times amid the single scan session. The three task runs were distributed in two (and sometimes three(!) different localizations, as was the MP-RAGE anatomical. Moreover, the scan montage did not cover the whole brain in some individual runs.
I have tried a whole different set of align_anat_epi.py and 3dAllineate scripts with different parameters, including -big_move, and including @align_centers as a preparatory step. However, it’s not working out. I’m not getting three aligned task runs, either with themselves, or with an anatomical base.
Could someone response with a suggested script language to cover this, especially when one task run EPI might have the top or the bottom of the brain cut off due to head positioning at the extremes of the collection space?