Dear Varina,
This image does look extremely difficult to brain extract due to the highly
variable nature of the non-brain tissue. In this case I would recommend
trying to run a 6 DOF registration to your T1w structural image (non-brain
extracted) and if you can get this to work well, which I think you should be
able to, then do brain extraction on the T1w image and transform the
brain mask from the T1w image space into the fieldmap image space and
apply it. I suspect that this will be the most successful strategy for this
kind of image.
All the best,
Mark
On 10 May 2012, at 04:02, Varina Wolf wrote:
> Hello Experts,
>
> I am trying to skull strip my Field Map Magnitude image for improved registration of my functional MRI. I have tried many different settings (both from the command line and gui) and variations of BET, including eye clean up, etc, and have tried FAST as well, but these either output a near exact version of the input file or grossly take chunks out of the brain. I think this is due to the near isointensity of the image. Below is a screen clip of the image.
>
> What do you suggest?
>
> Thank you for your help!
> Varina
>
>
> https://skydrive.live.com/embed?cid=DC678833E6FA9962&resid=DC678833E6FA9962%21292&authkey=ADm9dmlsu_zTCME
>
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