Sorry - my mistake - you are right that the mask needs to be a binary
image for applywarp. So you would need to insert an fslmaths command
in before to create an appropriate binary mask from this image.
All the best,
Mark
On 29 Jul 2011, at 11:58, Torsten Ruest wrote:
> Hi Mark,
>
> thanks! I tried this and it looks alright, except that the intensity inhomogeneities within the brain are more pronounced compared to the original as well as to your earlier suggestion where you would use masking as without fieldmap. I am not entirely sure, but does the image you use with the --mask option need to be binary?
>
> Thanks,
>
> Torsten
>
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