Hi Vinod

One more thing, the amygdala is a structure that's fairly blobby/ellipsoidal and SPHARM usually has problems with such structures (in general structures that possess any rotational symmetry). Can you display your structures with the phi-coloring in ShapePopulationViewer (I think the procrustes aligned vtk surfaces have both phi and theta coloring attributed to the meshes) and check the correspondence? Maybe make a screenshot and post it here.

Btw, for that purpose simply load the output csv in the folder OutputGroupFile into ShapePopulationViewer and select the column with the procrustes aligned surfaces

Martin