I am getting back up to speed with SPM after almost a decade doing other things, AFNI, EEG, etc. I completed the process all the way up to the stats. When I tried to overlay the functional activity onto the anatomical image, there is clear activity outside the occipital lobe. The image realignment revealed no greater than 1.1 mm maximal out of all three planes. What I found strange was the coregistration step. In my memory, I thought that we coregistered the functional images to the anatomical image. The anatomical image was a template. However, following the SPM manual and example, it was suggested to use the mean functional image was to be used as a template to which the anatomical image was to be aligned. This is what I did. Could this be the problem? Should I have coregistered the functional images to the anatomical (as a template)? Thus, the functional activation would be forced into the anatomical space and when overlain, would be inside the brain.
Please let me know what to do. The normalised images show the AC/PC line clearly intersected in the same place with the mean functional on the bottom left plot and the anatomical on the bottom right plot. So, it appears that the "Normalised Mutual Information Coregistration" did work well. Again, this makes me think I should have aligned all the functional images to the anatomical image (as a template).
Thanks in advance for your advice!
Edward Justin Modestino, Ph.D.
Postdoctoral Research Associate
Ray Westphal Neuroimaging Laboratory
Division of Perceptual Studies
Department of Psychiatry and Neurobehavioral Sciences
University of Virginia
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