Hi Shahrokh,


Thank you for providing more details on your study design.
What SPHARM-PDM uses the first ellipsoid is for 1) a pose correction that is performed over the parameterization only (before even a pdm is generated) and 2) it is true that after that step there is a pdm ellipsoide-aligned. The three PDM families SPHARM-PDM provides are *surfSPHARM.vtk, *surfSPOHARM_ellalign.vtk and *surfSPHARM_procalign.vtk. All of those PDM collections have a pose corrected parameterization that uses the 1st order ellipsoid, but we do not call that a registration. 

In our OO 2014 paper, we choose to perform an initial registration to our binary images based in a semi automatic method based in anatomical landmarks of the TMJ neck (as many of the TMJ OA samples have huge dismorphologies in the condylar heads). Since we do not want our SPHARM generated PDM's  to override this expert registration, we use the *surfSPHARM.vtk files. The fact these files have a pose corrected parameterization has nothing do do with registration.
Have you selected the group column in the CSV file paramter tab? You will have to click in the text box that reads select input file column and then double click in a cell of the column named "SPHARM Surface in Original Space(*_pp_surfSPHARM.vtk)". A number should appear into your text box, before you go onto Test Parameters and group test column title in the "test column" foldable menu. Does this make sense?


I hope that helps,
Beatriz