Hi Matthieu
well, first, I see you are using meta files (and not vtk files) for shapeAnalysisMANCOVA. I think it should still work but the vtk files are probably better in order to add the p-value maps etc to the meshes.

Regarding the question: I know it is counterintuitive (and maybe bad design on our part), but exchanging the group number in the file does not matter. It actually does not matter at all what you choose as group number, i.e.  you could use 2 and 5 for the two groups. The program will always read in the group information and relabel them to 0 and 1 (as that is the only valid input). The first group that is listed in the file is assigned "0" and the second "1".  Thus the direction should be from the first listed group in the file to the second listed group. If you look at the terminal output of shapeAnalysisMANCOVA, it will tell you which group has been reassigned which label (i.e. 0 or 1).


Martin