Hi FSL experts:
I met problems when I conducted comparison analysis among three groups in TBSS.
I have three groups, named HC (23 subjects), RP (17 subjects), LP (13 subjects). Now the null hypothesis is that are there any differences of FA skeleton between the three groups. The results were expected to be corrected for multi-comparison using Cluster-based thresholding. Then I called randomise as follow:
randomise -i all_FA_skeleton -o tbss -d design.mat -t design.con -f design.fts -m mean_FA_skeleton_mask -e design.grp -F 5
In this command, design files are set up as follows:
In design.mat file: the last two colums are nuisance variables, which would be regressed out in the analysis.
Ev1 Ev2 Ev3 Ev4(gender) Ev5(age)
1 0 0 2 26
1 0 0 2 20
1 0 0 1 19
1 0 0 2 27
1 0 0 1 24
1 0 0 2 25
1 0 0 1 23
1 0 0 2 19
1 0 0 2 18
1 0 0 1 29
1 0 0 1 25
1 0 0 2 35
1 0 0 2 49
1 0 0 1 31
1 0 0 1 30
1 0 0 1 19
1 0 0 1 21
1 0 0 1 18
1 0 0 2 27
1 0 0 2 26
1 0 0 2 25
1 0 0 1 24
1 0 0 1 24
0 1 0 1 16
0 1 0 2 23
0 1 0 1 27
0 1 0 2 24
0 1 0 1 28
0 1 0 1 20
0 1 0 2 30
0 1 0 2 15
0 1 0 2 29
0 0 1 1 18
0 0 1 1 17
0 0 1 2 25
0 0 1 2 38
0 0 1 1 15
0 0 1 1 19
0 0 1 1 18
0 0 1 1 22
0 0 1 2 35
0 0 1 1 25
0 0 1 2 22
0 1 0 2 24
0 0 1 1 36
0 0 1 2 18
0 1 0 2 25
0 1 0 2 20
0 1 0 1 23
0 1 0 2 28
0 1 0 1 53
0 1 0 1 26
0 1 0 2 21
In the design.con file, the contrast matrix is :
1 -1 0 0 0
1 0 -1 0 0
0 1 -1 0 0
And the F contrast file (design.fts) is :
1 1 0
The design.grp file is :
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
3
2
3
3
2
2
2
2
2
2
2
Now, i have some questions about the process.
1. are these design files correct?
2. In the randomise command above, should I use -n option to set the numbers of permutation or does the command do it automatically?
