[Freesurfer] T1-weighted quality

Hello, We are starting to use FreeSurfer v4.5.0 for segmentation purposes and after running freesurfer and correcting the wm surfaces following the online instructions we still get abnormal surfaces (wm looks better after corrections, but gray matter still the same). We are suspecting the problem to be due to intensity problem in the original T1-weighted volumes and thus we would like to consult with you the T1 sequence we use to know if there is what we could fix/change about that.

T1-weighted scans were imaged using 3D FSPGR BRAVO sequence (TR 12.1ms, TE 5.2 ms, slice thickness 1.0 mm, FOV 24.0 cm, matrix 256 x 256, and flip angle 20 º, parallel imaging factor 2, NEX 1).

Thanks a lot in advance, Ahmed