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Hi Gabor,
	       Using the eroded fieldmap magnitude will still give different results due to registration differences ( and why non-eroded version is fine ). I just mentioned the masking to make it clear that the fsl_prepare_fieldmap processing with the eroded image wasn’t being ignored.

Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

> On 24 Aug 2017, at 15:00, Gabor Perlaki <[log in to unmask]> wrote:
> 
> 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.