Thanks Mohammad, that makes sense. 

Regarding your question: Yes, you can use the shapeAnalysisMANCOVA, but not from within Slicer, i.e. you would need to use the command line interface. The software can be downloaded in the download section. You can also use Matlab or R, though that is not trivial if you want to do a template free, multi-variate analysis such as in shapeAnalysisMANCOVA. Alternatively, you can also use the vertex wise analysis in FSL to do the analysis, though you need to do a few extra steps and it renders the analysis template-specific.

Best regards
Martin