Hi Anthony
yes, you can using the expert options to change the parameters of mri_normalize. Motion could mess it up, as it assumes a sharp enough gradient at the gray/white boundary to prevent the white matter region growing from crossing into the gray matter. Make sure that it's not just the window levels of the visualization though. Usually when the normalization fails you'll see regions of gray matter that have been set to 110, not just reduced contrast.
cheers Bruce
On Tue, 11 Sep 2012, Anthony Dick wrote:
I have a pretty terrible T1 from a child. The functional data, acquired first, are fine. But the T1, acquired last, has pretty serious movement artifact (attached image). While I would not use this particular scan for morpohological analysis, it seems like a reasonable surface reconstruction could be used to project functional data.
My problem is, the original T1 seems to have a better grey-white boundary than the intensity-normalized image. Is there a way to adjust the parameters for normalization to try to improve this? Would this be adjustments to only the autorecon1 series? That is, if I can improve the contrast, should autorecon2 and 3 run normally? Are control points the only way to improve this?
Anthony