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