Hi Matt

yes, we have done this a number of times but of course it depends a lot
on the details of the abnormality so it is hard to give generic advice

cheers
Bruce

On Fri, 28 Dec 2018, Michael Sughrue
wrote:

>
>         External Email - Use Caution        
>
> Has anyone had success extracting surfaces of brains with obviously abnormal
> surfaces....post-surgical or very distorted cortices from tumor etc....even if the extraction is
> imperfect, is it possible to do with freesurfer and get something imperfect but useable.
> ....typically this gets hung up at the fix tesselation step.....
> if this isnt possible presently, any suggestions about how to create modify the source code to
> create such a tool?
>
> On Fri, Dec 28, 2018 at 8:49 PM Matthieu Vanhoutte <matthieuvanhoutte@gmail.com> wrote:
>               External Email - Use Caution       
>
>       Dear Freesurfer’s experts,
>
>       I used mri_coreg command to coregister PET image onto T1 volume. Basically, this command
>       coregister PET image onto orig.mgz volume (default target). However, I wonder if T1.mgz
>       wouldn’t be a better target since it has been corrected for inhomogeneities and
>       intensity normalized ?
>
>       Thanks for helping !
>
>       Best,
>       Matt
>
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