Dear Martin,

It works!!! Thanks !!!

Can I ask two further questions:
1) if the first covariance is binary (e.g., gender) rather than continues variable. 
i still want to test the simple group effect and controlling for these 6 continues covariance + 1 binary covariance.
For example the design file is:
group, gender, cov1, cov2, cov3, cov4, cov5, cov6, input file path,
My understanding is to do:
shapeAnalysisMANCOVA ./designfile.csv --infileColumn 8 --numGroupTypes 2 --numIndependent 6 --columnGroupTypes 0 --columnIndependent 2,3,4,5,6,7

Am I right?

2) in the pre-processing stage, I have quite a few cases 20% failed to generate a correct surface (i.e., xxx_surfSPHARM_procalign.vtk) for MANCOVA analysis.
The good case and bad cases are attached. The input binary masks (nifti forma) are manual traced hippocampi using software called Analyze. 
I am using the Spharm-PDM plug-in on Slicer4.3.1, with the default setting. The command line after hitting the "Apply" button is 

ShapeAnalysisModule --RescaleSegPostProcess --sx 0.5 --sy 0.5 --sz 0.5 --label 1 --NumberofIterations 1000 --SubdivLevelValue 10 --SPHARMDegreeValue 15 --thetaIterationValue 100 --phiIterationValue 100 --columVolumeFile 0 --varX 10 --varY 10 --varZ 10 --regTemplate None --flipTemplate None --paraOutTemplate --noFlip --HorizontalGridPara 5 --VerticalGridPara 5 --UseProcalign --startRegularization 10 --endRegularization 0.01 --optimizationIt 200 --RelativeWeight 1 /home/.../filelist.csv /home/outputdir

So based on my description, is this type of error shape normal? Can i fix it by changing some parameters above?

Thanks a lot!
Chao