I have a couple of questions regarding settings of scanner sequences and how it affects subsequent data processing in SPM.
1. If we scan, say, coronally or saggitally during our T1-sequence and acquire our functional data with an axial EPI-sequence, will this create a problem later in SPM for example with the normalisation process? I.e. is it recommended to always acquire all the data in the same direction?
2. A follow-up question: If i scan during the same paradigm with the same EPI-sequence, but collecting the slices in different directions (i.e. coronally vs. axially) should I then expect any differences in the data acquired? (other than the slice gaps obviously appearing at different places)
3. We use an EPI-sequence at our lab with a TR=3, which collects all slices as fast as possible and then rests during the reminder of the TR. I guess this should be good for minimizing the time differences between slices, but could this create a problem for an event related paradigm? So far we have only used traditional block designs.
Thank you for any reply!
Best regards, Jonas