didn't I answer this last week?
On 1/27/2023 8:52 PM, David wrote:
External Email - Use Caution
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
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