Hi,
This worked just fine for me.
Did you specify the _brain image in the GUI and name the non-brain-extracted version with the same name except for the _brain at the end? Did FEAT give you a warning about using only brain-extracted images?
If you specified the names correctly and did not get a warning (which should pop-up if you got the names wrong) then I don't know what could have happened, as I just ran the standard FSL version 4.1.9 of FEAT with default settings (except that I turned on the non-linear registration) and got a perfectly good registration (see attached).
All the best,
Mark
On 8 Aug 2012, at 20:55, Marina Shpaner wrote:
> Hello Mark,
>
> I uploaded the files to 923145.
> I'm concerned that highres2standard looks distorted in several directions, certainly not the way it was prior to the transformation.
>
> Thank you for looking into it.
>
> -Marina
>
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