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Hi Susana, Generally, the whole purpose of brain extraction is to register brain to brain. While you may be missing some brain information, this is not detrimental to the registration. Having skull included, can, and will, lead to inaccurate registration. This is explained further within the FSL course material. I do not consider myself an expert, so take what I say with a grain of salt. Bryson On Tue, Mar 24, 2015 at 10:31 AM, Susana Santos Maia <[log in to unmask]> wrote: > Thank you Bryson. Can I ask what do you mean that I should not care if I > miss some brain parts. I thought the idea was to get rid of the skull but > making sure the whole brain was there! Can you explain? > > Susana Maia > PhD student, Psychology department > Room A105, Heslington, York, YO10 5DD, UK > Email: [log in to unmask] <[log in to unmask]> > Tel: +44 7456555876 > > EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm > > > *------------------------------Please consider the environment before > printing this e-mail.* > > > On 24 March 2015 at 14:04, Bryson Dietz <[log in to unmask]> wrote: > >> Hi Susana, >> >> This is a common issue, I am sure if you try a threshold of (lets say) >> 0.2, you will avoid the skull. Note, generally BET is used for registration >> purposes, and therefore, you do not *really *care if your missing some >> brain. Perhaps others have more robust methods, but generally I have always >> been able to correct this issue by changing the -f option. Also, I find >> using the -R option helps a ton. >> >> Bryson >> >> On Tue, Mar 24, 2015 at 9:42 AM, Susana Santos Maia <[log in to unmask]> >> wrote: >> >>> Hi everyone, >>> I am fairly new to fMRI data analyses. I am having some problems >>> regarding performing BET extraction in the structural images. I have played >>> around with the several options BET offers, and also by changing the >>> threshold level from the default 0.5, but I can not get a good extraction >>> for one participant. I get an extracted image with a lot of non-brain >>> (please see file attached). I would be very thankful if someone could give >>> any advice on how to sort this. >>> >>> Best regards, >>> >>> Susana Maia >>> PhD student, Psychology department >>> Room A105, Heslington, York, YO10 5DD, UK >>> Email: [log in to unmask] <[log in to unmask]> >>> Tel: +44 7456555876 >>> >>> EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm >>> >>> >>> *------------------------------Please consider the environment before >>> printing this e-mail.* >>> >>> >> >