> I am having difficulty overlaying an spmT image on top of an anatomical image using spm5. The difference between this analysis and a standard analysis is I normalized all the functional images to the individual's anatomical image instead of using the standard EPI image in spm. Upon comparison between this analyis and prior analysis where the functional images were normalized to the standard EPI template, I have discrepancies between the two.
I'm not quite sure what you mean by "normalized all the images to the
individual's anatomical image." Once you've realigned all the
functional images for a subject, if you coregister their structural to
the mean functional, everything will be in the same space (i.e.
subject space). There's generally no 'normalization' step needed.
> For the current analysis, normalized to the individual's anatomical brain, the spmT image overlay appears to be too small in MRIcron, however, when slovered the overlay appears to fit. On the other hand, in the previous analysis with the images normalized to the standard EPI template, the spmTimage overlay seems to fit perfect in MRIcron, as well as once slvered. Based on comparing these results I am distrustful of the current results (images normalized to individual's anatomical image).
What image are you overlaying the t image on? If you've coregistered
your (realigned) functional images with a subject's structural image
(and verified this with checkReg), you should have good correspondence
between the t maps and that subject's structural image. [Since you
haven't normalized to a standard space, overlaying on a standard
template (like ch2bet, or any of the SPM templates) isn't going to
Hope this helps,