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 _______________________________________________ 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.
