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Hi, Under Windows You can get the bet.exe from MRIconand use this dos command 'bet.exe %1.img s_%1.img -f 0.5'%1 being the image name and -f is a threshold parameteryou can play with. Hope this helps Brahim > Date: Fri, 10 Jun 2011 01:00:28 -0700 > From: [log in to unmask] > Subject: [SPM] Using bet in spm/matlab > To: [log in to unmask] > > Hi all, > > Could anyone please tell if we could run brain extraction tool in matlab/spm? If yes, could you please send me the relevant files for running. > > Thank you for your time, > Aaryani