For the visualization of the CBF alignment with the WM mask in the standard space, add two extra options:

x.bVisualQCCBFvsWMTemplate - if on, then produces an additional file that use the template WM instead of the individual WM - to be used when the WM segmentation is questionable.
x.bVisualQCCBFvsWMContour - if on, then produces the the WM as a contour, not a full ROI - 1 pixel thickness (contour calculated per slice basis).

These options work on top of the standard output and produce files with different names - so that it could be recognized. Once this functionality is done - we can discuss all the names and the exact logistics.

Release notes

Option to use template WM and contour for alignment QC