You can use the --refmask and --inmask options to specify a
mask of the valid voxels (hence excluding the lesion region).
All the best,
On 21 Aug 2009, at 15:57, Anastasia Ford wrote:
> I would like to register FA maps of patients with stroke to the MNI
> Fa template using FNIRT.
> Is there an option to use some sort of deweighting factor so that
> the lesion region would not
> create significant registration warping of the surrounding intact
> Thank you