Hi Mark,
I took your advice and I've been perusing the lower level reports to see if I could find any problems. The registration did not throw any errors and it seems as though the registration matrix created at the lower level was applied and the brains resampled using the standard algorithms.
However, what concerns me is that, in the example_func2standard.png image from the report_reg.html file, it seems like the red outline shown in the two rows is applied to the wrong hemisphere. The red traces exactly match the images from line above or below, respectively.
I then took a closer look at the registration set-up in the feat gui and the report_log.html file and it appears that I set the registration to proceed with a normal search with 12 degrees of freedom instead of a full search and, in addition, the searchrx, searchry and searchrz are all set to -90 90 instead of -180 180. The pop-up help window suggests that full search be used in case there is a difference in orientation between any of the images. I'm going to try to make these changes to see if this will rectify this registration discrepancy. What do you think?
Thanks for your advice so far.
Best,
Craig.
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