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Perhaps its estimation is not optimal for your brains and you can do better. You might attempt some sort of registration with the skull on to get all the brains oriented the same way and in about the same coordinate space prior to BET. You could pick a random subject, register all of your others to that one, average all the images to make a rough template and then reregister all of your images to that template. You could then figure out what setting of -c gives you optimal results and then run the same setting on all your subjects (the point of all this is to avoid having to manually set -c independently for every subject, something that I have found to be very annoying ;)). If you aren't scripting all this, then making this rough template might be more trouble than it is worth and you might as well set -c manually. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Xue, Feng Sent: Monday, March 22, 2010 11:53 PM To: [log in to unmask] Subject: Re: [FSL] BET in infants Hi Matt, Should -R do that automatically? On Tue, Mar 23, 2010 at 11:39 AM, Matt Glasser <[log in to unmask]> wrote: > Moving the center of the initial sphere ( -c X Y Z ) closer to the front of > the brain might help. > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf > Of Xue, Feng > Sent: Monday, March 22, 2010 10:32 PM > To: [log in to unmask] > Subject: Re: [FSL] BET in infants > > Hi, > > Many be you could try draw a mask on the T1 image in fslview then mask > out those regions. But this may means a lot of labor as I did before:( > I wonder if anyone have other good idea? > > On Tue, Mar 23, 2010 at 12:21 AM, Michael Yoong <[log in to unmask]> > wrote: >> Does anyone have any tips on using BET to skull strip T1 weighted scans in >> very young children (under 6 months)? >> >> I have been adjusting the intensity settings and got a reasonable result >> with -R -f 0.7, but there is a persistent small patch of skull remaining > in >> the occipital region of every child under 6 months. I would like to > improve >> on this, as it messes up any co-registration I then go on to do (I also >> would like to get measurements for brain volume). >> >> Are there any other settings that people have found useful to tweak in > this >> situation? >> >> I am also having trouble getting a satisfactory brain extraction on some >> other scans with more severe abnormalities - is there any way to mask out > a >> region so that it is ignored by BET? (A couple of the children have had >> previous neurosurgery for VP shunt insertion and the edges of the surgical >> lesion are not dealt with very well by BET. >> >> Many thanks, >> >> Michael >> > > > > -- > Best Regards > > Xue, Feng Phd. candidate > Major in Developmental Cognitive Neuroscience > > National Key Laboratory of Cognitive Neuroscience and Learning > Beijing Normal University > Beijing, China. 100875 > Tel: +86-13810154455 > web: http://psychbrain.bnu.edu.cn > ============================================== > Welcome to MuDuo JinSheng BBS @ Beijing Normal University > telnet://bbs.mdjs.org > http://bbs.mdjs.org > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org