Hi Michelle

you can try using the graph cuts skull stripping. It is more aggressive and more likely to remove more skull/dura (and also to remove some brain)

cheers
Bruce

On Mon, 12 Jun 2017, Michelle VanTieghem wrote:

Hello, 
We have assessed freesurfer output for 160+ brains, and about 50% have poor
segmentation of pial matter that includes too much skull.  Manual edits and
re-running does work to improve the problem, but is very time/labor
intensive for so many scans.

I saw on the freesurfer wiki that you can include T2 or Flair images to
improve the segmentation for this problem. However, we do not have these
extra scans. What do you recommend to do otherwise? 

Thank you!


--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2115@columbia.edu

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.