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