Just to add to MJ's reply.
In your case you will want to use the --inmask option for the stroke
masking. You will need to manually draw a ROI in the subjects scan,
delineating the stroke with a little bit of margin. You will then need
to invert it so that you have a mask with zeros where the stroke is
and ones everywhere else. The resulting file should be used as input
to the --inmask argument.
Good luck Jesper
On 21 Aug 2009, at 17:25, Mark Jenkinson wrote:
> 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