Dear Matthew,
Thank you for your quick answer. However, I'm a little bit confused based on the answer.
I calculated the FMAP_RADS using the eroded version of brain extracted fieldmap magnitude (FMAP_MAG_brain_ero) in fsl_prepare_fieldmap and tried two different setups for the "Fieldmap mag" in FEAT’s prestats. In the first case the eroded version of brain extracted fieldmap magnitude (FMAP_MAG_brain_ero) was used as "Fieldmap mag" in FEAT’s prestats, while in the second case the non-eroded version (FMAP_MAG_brain) was used. However, the final results were not the same especially at the edges of the brain. You said that "FEAT’s prestats unwarping generates a mask which effectively takes into account the masking performed in fsl_prepare_fieldmap". Since my FMAP_RADS is more tight than FMAP_MAG_brain I think the final mask (which effectively takes into account the masking performed in fsl_prepare_fieldmap) and the results should be the same in both cases. Do I miss something?
Thank you in advance for your help.
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