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
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