Hi,
Right, if there is some masking then this makes sense.
If you really wanted to try and use your masks then you could replace the
--mask image with EF_UD_fmap_mag_brain and see if that worked better
for you (that is have --mask=EF_UD_fmap_mag_brain at the end of those
applywarp lines). I think that should do what you are hoping for.
All the best,
Mark
On 26 Jul 2011, at 16:26, Torsten Ruest wrote:
> Hi Mark,
>
> yes there is some degree of masking, and brain/background threshold is set to 10%, also bet is switched on. I only spent some time to extract the magnitude images nicely and since the masks to mask non-brain tissue have been derived from those I hoped...
>
> Thanks again,
>
> Torsten
>
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