Hi Jess,
It certainly is a problem, from the snapshots though it looks like there is some visible contrast there, so control points should help. be sure to only place them in true WM regions, and avoid partial volumed voxels. A few spread out on each slice should do the trick - no need to overload them. Then you can run recon-all -autorecon2-cp, and see if it fixes your surfaces.
How does the aseg look? I'd imagine it's pretty bad as well.
Jenni
On Thu, 7 Jun 2007, Turner, Jessica wrote:
Hi experts-I have some very low-contrast images from an older dataset and the Freesurfer segmentation completely misses the lower and posterior bits of the occipital lobe on many of the subjects (see attached images from an example subject). What is the recommendation in this case? Can I fix this with control points? It's a much more extensive failure than I'm used to seeing fixed with control points.
Thanks,
Jess
Jessica Turner, Ph.D.
Project Scientist, FBIRN (www.nbirn.net)
Department of Psychiatry and Human Behavior
University of California, Irvine
Phone: (949) 824-3331
Fax: (949) 824-3324