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Dear Benjamin, > I've recently started working with fslvbm for use with patient data > with large stroke lesions. In generating a template it uses FNIRT to > register the subjects, and I'm wondering if there's any way to > integrate options from FNIRT. Specifically, I'd like to be able to > mask out lesions from registration (and potentially analysis) since > I've seen that this helps the registration tremendously for these > patients. I am not sure what you mean by "integrate options", but if you mean collecting a set of options so you don't have to specify them all every time, then yes there is. Have a look at http://www.fmrib.ox.ac.uk/fsl/fnirt/index.html#fnirt_config_files For masking out lesions have a look at http://www.fmrib.ox.ac.uk/fsl/fnirt/index.html#fnirt_inmask Good luck Jesper