instead of normalization and normalization2 I tried to do mri_normalize -gentle which helps a bit but when I run autorecon2-wm it just makes it very bright again. There seems to be a threshold adjusting problem.

This of course messes up the segmentation of the white matter.

Is there any way I can change the normalization part of recon-all? How can I change normalization parameters? The scans that go into the SUBJ have the white matter already close to 110 and the normalization part makes it too bright.

Thanks for your help,

Daiana