Hi,
I agree with this advice.
You could also try a weighting image that highlights the ventricles (contains 1 in all voxels except those in and around the ventricles where it contains a large number like 100, 1000 or 10000). Try both of these options and see how you get on.
All the best,
Mark
On 8 Feb 2012, at 17:07, Dixit, Sachin wrote:
> Hi Christiane,
> What you can do is may be manual edit the MPRAGE and take out part out of the brain which is redundant. We had similar problems likes this but when we edited our MPRAGE especially by taking out fat bone marrow signal around dura we indeed got better registratio.This all can be done in FSL.
>
> Regards
> Sachin
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Christiane Jockwitz
> Sent: Tuesday, February 07, 2012 10:41 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Linear vs. nonlinear registration
>
> Dear Mark,
>
>
> Unfortunately field maps were not acquired at the time of imaging. I tried to improve the brain extraction on the highres but I still have problems with the example_func to standard as well as the fMRI to standard space(see link). Is there any other possibility to better adjust the bold images to the structural images?
> Thank you very much.
>
>
> http://registrationchristianej.blogspot.com/2012/02/registration2.html
>
>
> Best regards,
> Christiane
>
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