A colleague of mine is having trouble getting on the listserv and asked
me to post this question for him. He can be reached at
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Due to problems with field of view, the inferior slices of some
anatomical images in my data fall out (some portions of cerebellum for
example, cannot be detected well). This has been causing rotations in my
images after using FLIRT for registration and resulting in misalignments
between my stuctural and functional images.
What is the best way to treat this data in FLIRT so that I can account
for these missing structural data and keep my functionals from being
rotated to misalignment during linear registration?