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Dear Mark, Thank you for the speedy reply! I will give this a try. Just to make sure I understand, the commands would look something like this? robustfov -r 245016_RFOV -i 245016_Structural bet 245016_RFOV 245016_Structural_brain -f .45 -c 78 130 110 -R or, do I no longer need to specify the -f and -c options? Laura --- Laura Banu Research Assistant Cardiac Neuroscience Laboratory Center of Alcohol Studies Rutgers University Work: (848) 445-3577 Cell: (646) 643-6917 On Thu, Aug 6, 2015 at 12:20 PM, Mark Jenkinson < [log in to unmask]> wrote: > Hi, > > We have found that the following prescription works quite well: > > - run robustfov to save out an ROI (-r option) without any neck > - run bet with the -R option > > Depending on your subjects and alignment the first stage may be too tight > in the z-direction, in which case you should alter the size of brain in z > (the -b option) but in general it works well. > > Give it a try and let us know how you get on. > > All the best, > Mark > > > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > Laura Banu <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Thursday, 6 August 2015 16:24 > To: "[log in to unmask]" <[log in to unmask]> > Subject: [FSL] Problematic Brain Extraction > > Dear experts, > > I have been working on a particular brain extraction for quite some time > and can't seem to get a good result. The most recent parameters I tried are > as follows: > > bet 245016_Structural 245016_Structural_brain -f 0.45 -c 78 130 110 -B > > No matter what I try, there seems to be a fair amount of frontal lobe > missing and a fair amount of non-brain at the top. Any advice is greatly > appreciated. > > Thanks, > Laura > > ps. Sorry if this message posted twice. I tried to attach the files, but > they were too large > >