Hi,
Thanks for your response. Maybe I am missing something, but I haven't been able to find any documentation about how to use graph cuts skull stripping in the freesurfer pipeline. can you please advise?
Thanks, Michelle
On Mon, Jun 12, 2017 at 2:48 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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
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