Hi Doug, I'm trying to skull strip in order to do something outside of freesurfer. Thanks - I will try running mri_watershed.
Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lris...@uw.edu P Please consider the environment before printing this e-mail. On Tue, Nov 30, 2010 at 9:51 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Hi Lisa, are you trying to skull strip in order to do something outside of > freesurfer or are you trying to troubleshoot a freesurfer failure? If you > want to run the skull stripping by itself, you can run the mri_watershed > program. > > doug > > Lisa F. Akiyama wrote: > >> Hello FreeSurfers, >> >> By reading through the wiki, it seems like the skullstrip command uses >> nu.mgz and T1.mgz, >> but is there a way to just run the skullstrip command without >> nuintensitycor or normalization? >> I have MRIs of a few subjects in which the intensity normalization seems >> to not have beneficial for preparing the MRIs for skullstripping. >> I've attached the snapshot of brainmask.mgz to this email. >> >> Thanks in advance. >> >> >> Best, >> Lisa >> ______________________________ >> Lisa F. Akiyama >> Research Study Assistant >> Institute for Learning & Brain Sciences (I-LABS) >> University of Washington >> >> P Please consider the environment before printing this e-mail. >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. >
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