Hi Gabor,
The non-eroded version is fine - note that FEAT’s prestats unwarping generates a mask which effectively takes into account the masking performed in fsl_prepare_fieldmap.
Hope this helps,
Matthew
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Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 24 Aug 2017, at 11:03, Gabor Perlaki <[log in to unmask]> wrote:
>
> Sorry for posting it again, but I'm in a hurry. Which version of the brain extracted fieldmap magnitude image should be used as "Fieldmap mag" in FEAT/Pre-stats/B0 unwarping? The eroded version (FMAP_MAG_brain_ero), which was also used when processing the "fieldmap phase" using fsl_prepare_fieldmap, or the non-eroded one (FMAP_MAG_brain)?
>
> I'd really appreciate any help regarding the above issue.
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