Hi Robin,

So the EPI localizer datasets are all in original, vr_base_min_outlier space.

Is this volume oblique, and is it the same obliquity as with the subsequent EPI runs? I would expect so. And if so, I do not see why the subsequent data would have the obliquity altered or removed, or was the same thing done to the localizer EPI? I would think no obliquity adjustment would be needed for this, just leave it oblique.

Otherwise, what you are doing looks okay.

If 3dvolreg is not succeeding, the volumes are starting too far apart. If that is because of altering the obliquity of the later EPI, maybe omit that step. I would expect that there is no reason to alter the obliquity of any of the EPI data. Either way, such datasets should be handled identically.

If they are far apart because the subject might have moved a lot between the runs (or did they even leave the scanner?), then it might be good to add the -twopass option to the 3dvolreg command.

Note that an external volume (like the localizer vr_base_min_outlier) can be given to afni's realtime plugin to be used for volume registration in real-time. Then any ROI averages other real-time afni output would be with respect to that registered data.

- rick