Dear Martin,
Thanks for your prompt reply.
I think you are right, the outputs are correct.
Because I generated xxxxMagnitudePearson.txt and xxxMagnitudeSpearman.txt.
If I force it to test the second column, (i.e. testColumn 1) the result files looks the same, but the values in the files are different.

When I replied yesterday, I was confused by the log:
==========
data in group_type 0 has been relabeled: 1 --> group A = -1 ; 2 --> group B = 1
#(A)= 12; #(B)= 5
==========
Now I understand that is the permutation of gender, which is a GroupType factor.

I have two minor questions:
1) among the output file, I still find a xxx_diffMesh.txt.
This is the diff Mesh of gender difference, isn't it?
2) in the log, there are some extreme big/small number, what does this mean?
for example, 6.9136e-310, 2.122e-314 ... Bold in the log below.
===========
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 6.9136e-310
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_103.txt -1 6.9136e-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 8.76842e-317
/home/chaosuo/Desktop/Spharm/data/OUTPUT/OBJ1/Diffs/input/diff_121.txt -1 8.76914e-317
/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 8.7693e-317
/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

==============

Thanks a lot.

Chao