I would like some clarification on the preprocessing steps, particularly
Realign, Coreg and Normalization. Thus far, I've been doing preprocessing
blindly. The order in which I do it is: Slice timing -> Realign (not
'Realign & Unwarp') -> Coregister -> Normalize -> Smooth.
I have EPI functional scans, 35 slices, and I have a T1 weighted anatomical
scan for each subject.
My understanding of coregistration is that it is a within subject
registration using a rigid-body model. But so is the 'Realign' step. If
'Realign' does the motion correction, what is the purpose of Coreg? If coreg
is based on a 'rigid body' model, how can the EPI scans that are not in the
same voxel-to-voxel correspondence with the hi-res T1-weighted scans, be
registered with the same?
I actually tried the estimate&reslice option of coreg with the hi-res
anatomical as the reference image, the 1st volume EPI as the source and the
remaining volumes as other images. The joint histogram it generated was very
bad. My question is, what am I misunderstanding? Thanks.