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<http://www.ccf.fiu.edu/>, an FIU Preeminent 
Program<https://beyondpossible.fiu.edu/preeminent-programs/>
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu<mailto:ad...@fiu.edu>; Webpage: 
http://dcn.fiu.edu<http://dcn.fiu.edu/>; Join the 
SSHD<http://www.sshdonline.org/>
#####
Check out the new book<http://www.routledge.com/9781138960039>:
Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, 
Theory, and Method. Taylor & Francis.


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jason Tourville 
<jayt...@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 <bobbiegholl...@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
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