Hi Bruce, 

The -gcut does not appear to make any difference on our skull stripping. I also saw that you can change flags for watershed option. Do you recommend this? If so, how would you implement this on freesurfer output that was already run? 

We achieve fairly good skull stripping with this dataset using afni's skullstrip function. Would it be possible to enter the already-skull stripped data into freesurfer? if so, how would you set this up? Right now, I am entering the original dicom files as input to freesurfer -- is it possible to use other file formats as input? 

Thanks!
Michelle 

On Mon, Jun 12, 2017 at 4:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
-gcut should do the trick


cheers
Bruce
On Mon, 12 Jun 2017, Michelle VanTieghem wrote:

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


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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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.




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