[Freesurfer] error in WM segmentation?

Hello there,

I am testing out various standard SPGR protocols and am having trouble with one in particular in that FS fails to recognise the GM/WM boundary accurately.

I have attached some screen dumps of brainmask.mgz, T1.mgz and WM.mgz. The image on the left is much better than the one on the right (although it still requires some correcting, but I have just used it for comparison) - the one on the right has most of the GM classified as WM in fact.

Is there some way of adjusting input parameters so as to get around this or do I need to manually edit the WM.mgz?

I am getting to grips with the program and am still a little hazy on the background.

Thanks,

Rysia