Hello,
Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top of the cortex, even when set at an extremely low threshold.
When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present.
After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view.
We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever.
Please let me know if you have an answer to how this could have happened.
Dave Brohawn