Hi Justin,
I've found the problem - it is caused by the -Z option in bet (as used in your custom processing script) altering the sform information. It isn't very important and you can ignore the warning. However, when I looked at the brain extracted image that it created from your script it was very, very bad and I would use this. Also, I do not understand why you are running bet on the rad/s fieldmap image at all. I would delete this line. Just use the non-brain extracted fieldmap (rad/s) image and the brain extracted magnitude image in FEAT and everything should work much better and without warnings.
All the best,
Mark
On 21 Jan 2013, at 15:58, Justin Hulbert <[log in to unmask]> wrote:
> Thanks. I uploaded the fieldmap, EPI, structural, and flash, as well as an example .fsf file with our preprocessing parameters (upload reference 952076, fieldmapError.zip).
>
> Thanks you kindly for looking into the matter. Any insights would be most greatly appreciated.
>
> Cheers,
>
> Justin
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