Dear Yoni,
Can you specify which modules you want to use? Keep in mind that within SPM12, the normalise module means a segmentation, which in your case, could be based on the EPI means. This might or might not be what you want. Possibly you would prefer the Old normalise then, in which the EPI means are low-dimensionally registered onto an EPI template.
The bounding box as such is no issue, you can adjust its size and the voxel resolution depending on needs. The coordinates would still reflect MNI coordinates as long as you rely on some MNI template during normalisation.
Best regards
Helmut
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