Did you compare the number of slices to that of your sequence? I have had issues when overzealously pulling data off of bourget (that is before the files have completed being sent). A simple re-conversion to mgz (or whatever format you prefer) has fixed this when waiting a bit longer till bourget has finished (depending on the sequence you can check this by just counting the number of dicom files (usually should correspond to # of slices).
HTH, D
On Thu, Apr 4, 2013 at 2:46 PM, qtnguyen@nmr.mgh.harvard.edu wrote:
Dear Freesurfer experts,
After I ran the functional to structural registration using the bbregister command, it looks like the dorsal part of the brain for this participant is cut off in the BOLD images. When we ran the scan, we made sure that the slice prescription covered the entire brain. We also looked at the functional scan in the control room right after the scan and it looked ok.
We aren't sure what went wrong and why the bold data is cut off. Is there any way I can look at the raw dicom files to check if it includes the entire brain?
Thank you,
Trang
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