Dear Bruce, I needed the label maps for other registration purposes to run other software. So I was thinking if freesurfers outputs one I can use the same one instead of creating new ones.
Thanks for the suggestion and time, I will try to binarize the brainmask. Thanks again Best Regards, Sarina ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, October 19, 2016 10:53 AM To: Freesurfer support list Subject: Re: [Freesurfer] Question regarding: Binary label map to skull strip brains sure, internally at times but most of the volumes we save have a bit more info than that. Is there some reason you need something to actually be binary? You could binarize the brainmask if you wanted cheers Bruce On Wed, 19 Oct 2016, Karmacharya, Sarina wrote: > Thank you Bruce. > > Does freesurfer use any binary label map during any processing steps? > > Best Regards, > Sarina > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, October 19, 2016 10:48 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Question regarding: Binary label map to skull strip > brains > > Hi Sarina > > the skull stripping is done by combining a deformable surface with a > watershed algorithm not with a label mask. The volume brainmask.mgz can > be used to specify what is in brain (voxels >5) and what is not in brain > (voxels < 5) > > cheers > Bruce > > > On Wed, 19 Oct 2016, Karmacharya, Sarina wrote: > >> Dear Freesurfer team, >> >> I have a questions for you regarding the binary masks (labels maps) that >> freesufer uses to skull strip the brain in the first >> part of recon-all. >> >> I was wondering if freesurfer stores/saves this label mask that it uses to >> skullstrip? If so what would be the naming convention >> of this label map/mask and the location of the label map/mask in the >> freesurfer folder. >> >> I will be waiting to hear back from you. >> >> Best Regards, >> Sarina >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
