Dear Mark,
For some subjects , the EPI image is not contain the top slices of the brain and when I do registration, FNIRT stretches the brain (in EPI data) to fill the the top of the brain and even beyond that. But registration from T1 to Atlas look good and I donot know what should I do.
I think it doesn't make sense. If the non-linear transform that get in transforming the T1 to Atlas is directly apply to transform the EPI (which is now registered in T1) to Atlas, we shouldn't have this much stretch in the EPI (when we transform the EPI_registered_T1 to atlas)
Bests,
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