Dear Mahiko,
check the following:
1) Is the structural volume roughly aligned to the functional series before the automatic coregistration? Subjects might have moved between the two parts to a large extent / the structure might have been acquired on a different day, leading to a very different orientation. In that case coreg might fail.
2) Are structure and functional series roughly aligned to the MNI template / is their origin near the anterior commissure? Otherwise segment might fail.
In both cases try to manually reorient the volumes with "Display" before you forward them into your preprocessing pipeline.
Best,
Helmut
|