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Hi Frank. I had this problem.I manually deleted the remaining non brain tissue in fslview. BW Fatemeh Dr Fatemeh Geranmayeh Wellcome Trust Clinical Research Fellow The Computational, Cognitive and Clinical Neuroimaging Laboratory Imperial College London Telephone : 020 7594 7994 On 03/08/2012 03:20, "SUBSCRIBE FSL Frank" <[log in to unmask]> wrote: >Hi, > >To follow along the question about phase map correction, I looked into >the information on this FSL webpage and it says that when betting >magnitude images, it is important that the brain extracted image does not >include non-brain tissue. >However, I tried betting my magnitude images couple times but still got >some chunks of non-brain tissues... >Anyone has any suggestions on how I can proceed? > >Thanks! >Frank