Hello Jason,

The freesurfer folks may have some suggestions for adjusting certain parameters, but you can also try some denoising approaches before going into the freesurfer pipeline. There are a number of flavors. The link below is a good place to start I think.

https://www.sciencedirect.com/science/article/pii/S1361841515000171

Anthony

Anthony Steven Dick, Ph.D.

Associate Professor

Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience

Florida International University MM Campus AHC4 454

Department of Psychology and Center for Children and Families, an FIU Preeminent Program

11200 S.W. 8th Street

Miami, FL 33199

Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879

Email: adick@fiu.edu; Webpage: http://dcn.fiu.edu; Join the SSHD

#####

Check out the new book:

Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, Theory, and Method. Taylor & Francis.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jason Tourville <jaytour@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, February 1, 2018 at 11:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Barbara Holland <bobbiegholland@gmail.com>
Subject: [Freesurfer] options for a poor T1

We have a few scans from kids that look like the image shown in the attached pic. We see a falloff in signal intensity in the gray matter that results in lots of cortex being excluded from the pial surface (e.g., along the dorsal surface and lateral temporal areas in the image). Typically, we would toss out this data and try to require from the subject or drop the subject from our analyses. But because of the age and clinical diagnosis of this subject we'd like to try to salvage this scan.

Can you offer any suggestions for how to improve the reconstruction? Is there a parameter that we can change that will allow the pial surface to fall farther from the white matter surface in terms of voxel intensity and distance? We would trade the need for more manual edits to get greater inclusion of cortex within the pial surface.

Do you have any tools or suggestions for a better intensity normalization of the original T1?

Thanks for any help that you can provide.

Best,

Jason

Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755