Hi, Have you tried fsl_anat for brain extraction? All the best, Mark On 23 Oct 2013, at 16:36, Rujing Zha <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Gwenaëlle, This -R cannot strip the bottom left of brain images.What else can I do? Any advice will be appreciated! Thanks! Rujing Zha 在 2013-10-15 19:34:14,"Gwenaëlle DOUAUD" <[log in to unmask]<mailto:[log in to unmask]>> 写道: Hi Rujing, thanks. Maybe try with: fslvbm_1_bet -N -R? and let us know if this helps. Cheers, Gwenaëlle ------------------------------------------------------------------------------------------------ Gwenaëlle Douaud, PhD MRC Career Development Fellow FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 <x-msg://2666/>www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud<x-msg://2666/> ----------------------------------------------------------------------------------------------- ________________________________ De : Rujing Zha <[log in to unmask]<mailto:[log in to unmask]>> À : [log in to unmask]<mailto:[log in to unmask]> Envoyé le : Mardi 15 octobre 2013 12h04 Objet : Re: [FSL] fslvbm_1_bet cannot strip skull and neck Hi, yes! two pictures were attached here. thanks. Best. rujing At 2013-10-15 18:26:48,"Gwenaëlle DOUAUD" <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi, so you have run the same command for all subjects? It would be useful if you could attach an example (low resolution snapshot) of one subject on which the process worked well and one on which it didn't. Cheers, Gwenaëlle ------------------------------------------------------------------------------------------------ Gwenaëlle Douaud, PhD MRC Career Development Fellow FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 <x-msg://2666/>www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud<x-msg://2666/> ----------------------------------------------------------------------------------------------- ________________________________ De : Rujing Zha <[log in to unmask]<mailto:[log in to unmask]>> À : [log in to unmask]<mailto:[log in to unmask]> Envoyé le : Mardi 15 octobre 2013 3h32 Objet : [FSL] fslvbm_1_bet cannot strip skull and neck Hi all, when i run fslvbm_1_bet -N, some subjects can extract brain volumn.however some subjects cannot strip neck and skull. what should i do? any reply will be appreciated. best. rujing zha