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Hi, Use the epi_reg script ( http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide#epi_reg ) , as this is what it is designed for. All the best, Mark On 8 Aug 2014, at 11:14, Hiroki Kurashige <[log in to unmask]> wrote: > Dear FSL experts, > > I would like to use bbr in flirt. > So, I read the help of flirt and found the options related to bbr, -wmseg, -wmcoords and -wmnorms. > However, I don't know that how I should set these options. > Could you mind let me know the example of the setting of these options? > > I guess that -wmseg is the white matter nifti file separated from the others. > But I don't know how I can make it using FSL tool. > > Thanks, > Hiroki