Hi Josh

it might if the white matter is very dim, as it appears in your images. You might also try 5.2, which I think is better about this kind of thing. If you try control points, make sure that they get applied in the mri_ca_normalize step and not just to cortical normalizaation in mri_normlaize (in some versions they were applied to both, but that made people unhappy so we backed off on it)

cheers Bruce On Tue, 26 Mar 2013, Joshua Lee wrote:

A subcortical segmentation error sometimes get Freesurfer (v 5.1) is cortical areas coming over into the hippocampus, ignoring the wm inferior and lateral to the hippocmapus (coronal). See attached png. Will adding wm control points help, or do they not inform the aseg segmentation. What is the best way to (non-manually) fix this kind of issue?

Josh