On Wed, Aug 24, 2011 at 9:57 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Martina
Can you send us one example dataset?
Bruce

On Aug 24, 2011, at 10:52 PM, Martina Ly <ly.martina@gmail.com> wrote:

> Hello freesurfers,
> Dura is being included in the pial surface of the superior section of the brain in about 80% of the subjects (about 200) that I'm processing in fs version 5.1 on Mac OS X 10.6.8. The T1s were acquired on a GE 3T scanner. It takes too much time to manually edit the dura and I would not like to do so much manual intervention on the other 2 time points. Adjusting the watershed parameters and the -gcut flag did not help. Would I be able to adjust nu_correct or mri_normalize (the intensity normalization steps prior to skull stripping)?
>
> I'm also thinking of using another intensity correction software (i.e. unicorr) to put back into the freesurfer pipeline but I would prefer a flag or parameter I can adjust within fs.
>
> Any suggestions would be appreciated!
>
> Best,
> Martina

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