Thanks, Martin.
I am now understand how to process the group wise tests.

Can I ask a further question about regression analysis.
For example the design matrix is :

reg, gender, cov1, cov2, infile
21,  1    ,  30,  1538,  xx/xx/xx/xx1.vtk
18,  1    ,  45,  1300,  xx/xx/xx/xx2.vtk
19,  1    ,  38,  1431,  xx/xx/xx/xx3.vtk
25,  1    ,  42,  1212,  xx/xx/xx/xx4.vtk
...

I'd like to do the regression analysis on the first column (reg), while controlling for gender, cov1 and cov2.
I tried the command as below, but not working very well
====================================================
shapeAnalysisMANCOVA ./design.csv --infileColumn 4 --numGroupTypes 1 --columnGroupTypes 1 --numIndependent 3 --columnIndependent 0,2,3 --interactionTest --KWMinput --testColumn 0
====================================================

The output indicated it is still a group-wise test, attached below:
--------------------------------------------------------------------------------------------------------
input file specified: ./design.csv
vect indecol 0 0
vect indecol 1 2
vect indecol 2 3
filename: ./age_onset_obj1_csv.csv numIndependent: 3
Num Subjects: 17

data in group_type 0 has been relabeled: 1 --> group A = -1 ; 2 --> group B = 1
#(A)= 12; #(B)= 5
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_101.txt -1 6.9135e-310
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_103.txt -1 6.9135e-310
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_104.txt 1 2.122e-314
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_108.txt -1 9.07231e+223
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_109.txt -1 1.19465e-70
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_116.txt 1 3.81554e+262
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_117.txt -1 0
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_118.txt 1 6.37345e-322
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_119.txt -1 1.8729e-316
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_121.txt -1 1.87298e-316
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_122.txt -1 1.58101e-322
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_124.txt -1 2.37152e-322
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_125.txt 1 1.87299e-316
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_127.txt -1 7.41098e-323
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_130.txt -1 2.122e-314
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_132.txt -1 6.92834e+228
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_133.txt 1 1.72632e-306
KWM Files Readed...
No statistic type selected, defaulting to Hotelling.
Now running nonparametric tests:
Performing MANCOVA permutation testing.
Using 10000 permutations.
---------------------------------------------------------------------------------------------------------------------------

I have tried to added --simpleCorrs as well, but no luck.

Could you please help to check whehter I made the command wrong?

Thanks,

Chao