"Is it possible to tell from the fmri data (structural/functional) if it has been captured in the axial-oblique (parallel to AC-PC plane) or axial-orthogonal format?"
If I understand you correctly, it should be easy. The way I would do it would be to view it in SPM using the "Display" button. One of the blue crosshairs should be parallel to the plane of acquisition in the sagittal view. It should be clear from that.
"Also is there any difference between the normalisation procedure for these two kinds of data?"
I wouldn't think so, but John Ashburner would be the best person to ask.
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