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