I also use FS to identify subcortical atrophy with affected HD patients; have you checked the aseg, as well as white & pial surfaces for accuracy? I have found in some of my older data at lower resolution (1.5 T) that the intensities do not differ much in subcortical regions and FS has problems differentiating structures. If this is the issue, you can give FS intensity priors to go on ... Have to ask list re: exact procedure/command lines for this, as I have not experimented with this in my own data set as of yet.

Hop this helps,

Julie

Julie E. McEntee, MA, CCRP
Senior Research Program Coordinator
Department of Psychiatry- Neuroimaging
Johns Hopkins University School of Medicine
600 N. Wolfe St./Phipps 300
Baltimore, MD 21287
Phone: 410-502-0468
Fax: 410-614-3676


On 3/30/10 8:32 AM, "Diego Herrera" <herrera.diego@gmail.com> wrote:

Hello
I tried recon-all in a patient with Huntington´s disease with severe atrophy of caudate nucleus (visually). It seems that freesurfer subcortical segmentation failed because the volume reported is within normal limits. How can I correct this?

Thanks