help > PALM output have all value of 0
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Nov 1, 2019  04:11 PM | Thomas Tan
PALM output have all value of 0
Hi team,

I have run the following command for my analysis on a single group of subjects, and the result was fine.
palm -i ${fname}_L.func.gii -o results_L_cort -T -tfce2D -s $surfL L_area.func.gii -logp -n 1000 -precision "double"
palm -i ${fname}_R.func.gii -o results_R_cort -T -tfce2D -s $surfR R_area.func.gii -logp -n 1000 -precision "double"
palm -i ${fname}_sub.nii -o results_sub -T -logp -n 1000
However, when I tried to run the same analysis with two additional co-variate. According to the contrast matrix, should 1 0 0 contrast give me the similar main group effect to the analysis in step 1, however the result was 0.
Contrast Matrix:
1,0,0
0,1,0
0,0,1

Design Matrix:
1,-1.5550455745,-1.5869822383
1,-0.6060939462,0.5747289652
1,0.5671516524,-0.212503622
1,0.766699016,0.6808586817
1,0.5731274014,0.4002300862
1,-0.9216698471,-1.3244732811
1,-0.2244986315,-0.2076533774
1,-0.0954910795,0.3697971434
1,0.1976012883,0.1861681819
1,-0.1871925939,0.1848973159
1,-0.0551979981,0.1959462064
1,0.9763852303,0.9574098386
1,0.1521081491,-0.4181632128

palm -i ${fname}_L.func.gii -d $desmat -t $conmat -o results_L_cort -T -tfce2D -s $surfL L_area.func.gii -logp -n 1000 -precision "double"
palm -i ${fname}_R.func.gii -d $desmat -t $conmat -o results_R_cort -T -tfce2D -s $surfR R_area.func.gii -logp -n 1000 -precision "double"
palm -i ${fname}_sub.nii -d $desmat -t $conmat -o results_sub -T -logp -n 1000


Thank you,

Thomas
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