Hi Dear Beatriz,

This study includes CBCT data acquired from 20 patients with TMJ OA and 40 healthy controls. Left and right condyles were cropped and segmented with MATLAB, itksnap and Slicer for generating 3D-binary images (mat files) and then convert to gipl format by SPHARM in MATLAB. In the first phase of it, I want to study shape differences and morphological changes between two groups. For determination these differences, I get the following models and volumes in spharm module in Slicer:

Post Processed Segmentation(none), Parameterization of Original Surface(*_pp_para.vtk), SPHARM Surface in Original Space(*_pp_surfSPHARM.vtk), SPHARM Coefficient in Original Space(*_pp_surfSPHARM.coef), SPHARM Surface in Ellipsoid Aligned Space(*_pp_surfSPHARM_ellalign.vtk), SPHARM Coefficient in Ellipsoid Aligned Space(*_pp_surfSPHARM_ellalign.coef), SPHARM Surface in Procaligned Space(*_pp_surfSPHARM_procalign.vtk), Euler Number(2), Spherical topology(1)

I do all steps mentioned in SPHARM-MAT Documentation (Release 1.0.0). According with chapter 5 in this documentation (SURFACE ALIGNMENT), I think that SPHARM-PDM do the registration automatically for example with first order ellipsoid for alignment. Is it true? If so, why do you point out to do pre-registration in your last reply and also you mentioned in your paper (Osteoarthritis and Cartilage 22 (2014))? If it is wrong and I must do pre-registration, is there an automatic way for the registration?

Please we suppose that my data (you mentioned *surfSHARM.vtk) are registered. I want to do the steps mentioned in the pdf manual file of shapeAnalysisMANCOVA_Wizard (NA-MIC Tutorial Contest: Summer 2011, ShapeAnalysisMANCOVA_Wizard-Tutorial.pdf). I do following steps precisely:
Step 1: Run shapeAnalysisMANCOVA_Wizard in bash terminal
Step 2: In first tab (CSV File), I click on "Load File" and load csv output file of Slicer (ShapeAnalysisModule_OutputFile.csv, attached in my last message)
Step 3: According with the manual of ShapeAnalysisMANCOVA_Wizard-Tutorial.pdf, I got to the second tab (Test Parameters), I check the box "Group test". At this moment, unfortunately, I can not see the list of headers of the group test columns to chose the desired parameters, for example SPHARM Surface in Original Space!? Why? Where I'm wrong?

Please guide me,
Thanks a lot,
Shahrokh