Hello Dorian,
Indeed, the whole volume is realigned. The idea is to correct for (rather) slow motion occuring across the whole scanning session. In case only a few slices are affected by motion (e.g. the last few slices acquired), this will inevitably lead to imperfect correction. This should be a minor problem though, except you have abrupt motion onset or heavy motion inside a TR. But then your data probably suffers of signal increases/decreases as well, not only of motion as such.
You might want to try out the SPM toolbox Artrepair http://cibsr.stanford.edu/tools/human-brain-project/artrepair-software.html which allows to detect and correct "bad" slices inside a volume.
Best,
Helmut
|