For technical reasons regarding the MRI scanner used, the contrast between grey and white matter on the right hemisphere of a few of my subjects is very different from the contrast on the left hemisphere. This leads FreeSurfer to erroneously estimate the white matter (and subsequently pial) boundary (see attached image).

To attempt to solve this issue, I am thinking of using the Livewire voxel draw on Freeview to manually obtain the white and grey matter boundaries.

However, I was wondering what you would advise in such a situation, and if it is possible to solve this issue not having to rely on a 100% manual intervention.