Like Donna says, caret and freesurfer are not really for that. however, I think you'd get a great 3d rendering of a skull from a t1 MRI, a CT or whtever else using mango (google mango mri).
you may wish to perform intensity adustments and/or segmentation using FAST from FSL. What I'd do is is use fast (or nu_correct from MNI) to make the intensities normalized. then open in mango, and the skull, being bone, should be easy to make an roi with in mango. then you make a new vol from the roi and click "make surface". basically, messing with mango, and maybe something to normalize the intensity of what is skull from what isn't, will work fine. just play with that software. it's gloriously easy to use. you'll feel no desire to extract your own skull via banging. some patience and exploration obviously. On 24 April 2012 18:00, <[email protected]> wrote: > Send caret-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Re: 3d image of the skull (Donna Dierker) > > > ---------- Forwarded message ---------- > From: Donna Dierker <[email protected]> > To: "Caret, SureFit, and SuMS software users" < > [email protected]> > Cc: > Date: Mon, 23 Apr 2012 13:03:17 -0500 > Subject: Re: [caret-users] 3d image of the skull > Not really. Caret (and SureFit, from which the segmentation stuff came) > just wasn't designed to segment the skull. You can toggle on keep > intermediate files and look at the various intermediate volumes to see if > you can use one of them as a starting point, but I don't think any of them > will work without substantial processing. > > There will be many intermediate volumes, so to help narrow your focus, the > ones listed at the tail end of SegmentCerebralWhiteMatter are your best > bets: > > > http://surefit.cvs.sourceforge.net/viewvc/surefit/SureFitSrc/SureFitPython/Scripts.py?revision=1.13&view=markup > > I would think something like FSL's bet would be a better bet: > > http://fsl.fmrib.ox.ac.uk/analysis/research/siena/siena/node4.html > > It also seems like something in Brian Avants' orbit, but I don't see it > here: > > http://www.picsl.upenn.edu/ANTS/ > > Above all, don't extract the skull by banging your head on your desk. > > > On Apr 23, 2012, at 11:17 AM, Maestri, Matthew wrote: > > > Hi Donna, > > > > Is it at all possible to map a 3d image of the skull using Caret? If so, > how might I go about doing that? Looking forward to your reply. > > > > Thanks, > > Matthew > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
_______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
