Hi, Clem-

If your EPI and anatomical truly overlap exactly/closely in the coordinates stored in the header, when the obliquity is applied then this set of steps should lead to close alignment (but probably not exact, due to different grids) between the "new" EPI and anatomical dsets.

If this leads to bad initial alignment between the new anat and EPI, then I would guess that the actual datasets probably don't line up well to start with.

You could check this assertion by running the following to apply the obliquity information to both the EPI and anatomical dsets:

3dWarp -deoblique -prefix ANAT_DEOB.nii.gz [anat dset]
3dWarp -deoblique -prefix EPI_DEOB.nii.gz [epi dset]

... and check the overlap of ANAT_DEOB.nii.gz and EPI_DEOB.nii.gz. If those don't line up well (as I suspect they won't), then the coordinate problem is inherent to your dsets from the get-go. If those *do* line up well, then, well, I'd like to see a pair of those to see what might be happening.

--pt