Hi Freesurfer experts,

    I'm very sorry to bother you, but I am very confused with the
    following questions:

    My experimental design includes two discrete factors:
    with three levels (d,m,h); gender (f, m), and two Nvariables

    So I can get 6 classes: df, dm,mf, mm,hf,hm.

     I want to perform the difference between any of the classes
    leves analysis with regressing out the effect of gender and two
    Nvariables, but I don't know the rules for setting the contrasts for
    the F-test. The contrast matrix I used is:

    1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
    1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0

My orders are as follows：

mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi lh --meas thickness --out lh_teach3.mgh

mris_preproc --fsgd glmteach3.fsgd --target fsaverage --hemi rh --meas thickness --out rh_teach3.mgh

mri_glmfit --y lh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir group3.testA1_10sm.lh --fwhm 10 --surface fsaverage lh --eres-save

mri_glmfit --y rh_teach3.mgh --fsgd glmteach3.fsgd --C glmteach3.mtx --glmdir group3.testA1_10sm.rh --fwhm 10 --surface fsaverage rh --eres-save

mri_glmfit-sim --glmdir group3.testA1_10sm.lh --cache 3 abs --cwp .05 --2spaces

mri_glmfit-sim --glmdir group3.testA1_10sm.rh --cache 3 abs --cwp .05 --2spaces

We obtained five differential brain regions and extracted their cortical thickness. And then put the extracted cortical thickness into SPSS for general linear model analysis, but two of the brain regions were not statistically significant.

Why? Is the contrast matrix I used wrong? Or other errors?

Any help will be very appreciated.

Best wishes