Dear Experts:

I apologize about these basic questions, but I wish to analyze the data of 30 subjects (15controls, 15patients) all of the subjects also underwent T1scanning. My goal is to examine group differences in BOLD activation. 

In regard to the first level fMRI preprocessing steps:

1) I am not exactly sure if I should go for a “direct normalization approach” or an ‘indirect normalization approach”. Could you explain to me the advantages/disadvantages either way?

I used the ‘direct normalization approach  (skipping the coregistration step), so my preprocessing steps included:

Realign: Estimate & Reslice

Normalize: Estimate &Write

Smooth

 

During the Normalise step:

 2) I chose the Realign:Estimate &Reslice:Mean image as my “Source Image”. Is that correct?

3) I chose the EPI.nii (from the spm8/templates) as my Template Image. Is that correct?

Should I also select the  /templates/ T1.nii image? Would the selection of the T1 image yield better spatial resolution for my functional data, especially when I am interested in group analysis of the BOLD signal?

4) I have read that during the ‘direct normalization”, it is not necessary to coregister, is this correct? Is it advisable to coregister to the MNI template ( or each person’s own T1 scan) and then normalize and skipping segmentation?

Very best Regards,

Catherine