Dear Andy,
Yes, but during the 2nd coreg you must apply the reorientation parameters to the T1 as well, otherwise the T2 is in alignment with the EPI mean, but not the T1. Thus:
1st coreg:
reference: T2 volume
source: T1 volume (this file is reoriented)
followed by 2nd coreg:
reference: EPI mean
source: T2 volume (this file is reoriented)
other: T1 volume (this file is reoriented accordingly once the reorientation parameters have been calculated)
Of course one can think of other (combinations of) coreg steps, it's just important that you apply the reorientation parameters in a meaningful manner. E.g. when reorienting the EPI mean (defined as a source) you very likely have to specify the whole EPI series as "other images" in that coreg step.
Best,
Helmut
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