ENH: modifications to allow choice of 2- vs 3-parameter model

Something is wrong with this code, produces garbage maps for Ktrans/ve, and
crashes randomly.
BUG: added missing initialization of the model for cost function
BUG: Two parameter model is more stable if the time resolution is limited
BUG: Tissue bolus arrival time needs to be aligned with AIF before estimation
BUG: Evaluating RMS of parametric model to decide whether to keep parameter estimates
Switched to R-squared goodness of fit instead of RMS.

We may want R-squared to be an output and then allow the user to mask the
parameter files interactively by thresholding R-squared.
Merge remote-tracking branch 'origin/master' into TwoParameter_BATAlignment_GoodnessOfFit
Merge remote-tracking branch 'fedorov/fpv-selection-parameter' into TwoParameter_BATAlignment_GoodnessOfFit (after conflict resolution)
Initialize outputs that may not be used
Removing unused code
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()
Commentary on using R-squared as a mask for a nonlinear fit.

R-squared is not a good metric to evaluate a nonlinear fit. The
values are not constrained to be in [0,1].  In practice, we get
negative R-squared values when the fit is really bad.