Dear Mar,
When reorienting files to better match orientation of the template you should reorient everything, e.g. structural AND functional data based on the structural volume (or possibly, if there's a rather large discrepancy between orientations of the structure and functional data, reorient them separately, e.g. structure based on itself and functional data based on a functional mean). Otherwise orientation of the structure might better match that of the template afterwards, but differ to a large extent from that of the functional data, resulting in a failure of the Coreg module.
In short, you want to have functional and structural data in a relatively good alignment (otherwise Coreg might fail), and you would want to have the structure to be aligned reasonably well with the templates / tissue probability maps, otherwise normalisation / segmentation might fail.
Best
Helmut
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