Hi Onur,


The differences between the two alignment methods have been very well described by your post: Whereas the ellalign (1st order ellipsoid) alignment is object inherent, the procalign (rigid body Procrustes) alignment uses a template as target, which can optionally be supplied. If not indicated, uses the object contained in the Template folder.

The questions you should consider for choosing an alignment method template are: 
- Is my data registered before SPHARM-PDM computation? i.e. do I register my images/segmentations beforehand via Atlas based registration or other methods? Do I want to keep that registration? Then you should use *surfSPHARM.vtk files, which are PDMs in the original space.
- Am I interested in displacements, shape morphology changes, both? If you are interested in displacements also keep the original space provided to SPHARM. If you are interested in morphology changes, i'd recommend using *surfSPHARM_procalign.vtk.



I hope that helps.

BEATRIZ