Hi Ziad,
Is it necessary to redo the talairach transformation of the anatomy? Because the location of the markers will not change relative to each other, even though the orig anat needs to be moved around a little? Would it be enough to run the 3drefit output of 3dAnatnudge on the talairached anatomy? and then re-adwarp the functional bricks? As in can the nudge results be incorporated into the tlrc.HEAD in some way?
Further, is 3dTagalign a better way to do the anat to epi alignment?
-thanks,
shruti