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
Try 1 -1 0 -1 1 0 ... 0 1 -1 0 -1 1 ...
The first row look for the interaction between dm and fm, the second for mh and fm, then using both will test for an interaction in either
On 1/16/2023 12:21 AM, 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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David -
Douglas N. Greve