Sorry for the following onslaught of naive newbie q's...I'm closely following and adapting Rik Henson's Matlab batch_spm5_preproc.m script, which is available on the MRC CBU Wiki http://imaging.mrc-cbu.cam.ac.uk/imaging/SpmBatch5, to analyze my event-related fMRI data in SPM8. This script has an option of a 2-stage normalization approach, which I'm reading is supposed to be a more robust normalization approach.
I'd like to make sure that I am understanding this normalization approach properly.
From what I understand, there is a first pass to correct for intensity variation across the structural images which uses affine registration to match size and position of images (?). Then the second pass, which does segmentation, uses nonlinear warping to match the overall brain shape and creates a matrix. Then there is coregistration of the mean functional to the structural (and here the results of the coregistration are written into the header of the structural image??? If I slice-time corrected my data, can I take the coregistration orientation matrix from the mean EPI -> structural coregistration call to reorient my slice-time corrected functional images as I'd like to smooth those files instead of the mean EPI?? Or would it not be better to move structural to mean EPI?).
So up to now in the normalization process, no new data files are written until the call to
but I don't see at any point where the MNI templates are called? How is it normalized to MNI space then? (The templates are only specified in the classic normalization option where the normalization parameters are derived from the templates?)? I guess I'm missing something conceptually?
With the script, the usual SPM.ps file doesn't get saved either -- what do I need to do in the script to make sure these are generated?
Any help and corrected explanations are very very appreciated!!
Thx in advance,