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I'm sorry, I didn't realize I could use config files with fslvbm. I've used fnirt with config files before, and if there's a way to use them in fslvbm's template creation, that would be perfect. Could you point me to the documentation on how to pass config files to fslvbm_2_template ? On Wed, Jun 16, 2010 at 12:37 PM, Jesper Andersson <[log in to unmask]> wrote: > 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 > > >