Make optional outputs truly optional.

All the output volumes are optional and should only be written if
requested by the user.
Moved the switch between 2 parameter and 3 parameter to the parameter section
Added ability to output a volume of R-squared goodness of fit values.

For the CLI:

If the user requests the volume of R-squared goodness of fit values
for each voxel, then the other parameter volumes are not masked by
a threshold on the R-squared value.

If the user does not request the volume of R-squared goodness of fit
values, then the other parameter volumes are masked by a threshold
on the R-squared value.

For the filter:

This behavior is controlled by a variable MaskByRSquared()