Particular alignment dilemma...advice appreciated

Hi all,

I’m no stranger to troubleshooting alignment woes, but this is a particularly frustrating case, and I welcome any tips.

I have a dataset with about 15 T1w structural images and ~80 resting state EPIs (same brain). The T1w image is more or less AC-PC, whereas the EPIs are extremely oblique. Long story short, the segment of my pipeline is not having a great time. I have typically managed this across a dataset by figuring out the general shifts and rotations necessary to get things reasonably close to alignment with the T1w structural, and then apply 3dZeropad and 3drotate across all of the EPIs. The trouble is that the EPIs vary pretty widely in how far off they are, and in what ways. Thus, if I figure out a ballpark set of parameters to use for one scan, it will work on a dozen or so and fail on all the rest. (For the record, I did not acquire these data…)

Is there some way I can: A) prepare my EPIs such as to minimize the probability of an alignment error, and/or B) loop through and figure out the approximate shifts/angles I need to apply to each dataset…
…or am I: C) basically stuck nudging each dataset manually before running


have you tried @Align_Centers on the problematic subject’s T1W and EPI images before trying to coregister them?

Thanks for the reply! I actually have not tried that - thank you for the suggestion. Will report back in a day or so.

[Edit - this helped, and what finally worked was computing an average EPI image across all of the runs and applying the starting rotations and displacements that got this volume into anatomical space to each individual scan. Thanks!]