If I understand, you run two analyses, one with an FSGD file with only two classes and one where the FSGD file has the same two classes but you include two variables. You are doing the same test (group1-group2) and  are wondering why the results are different.

They are different because you have different models. Eg, if age is a covariate, then it will remove effects of age that are in the first analysis. You will also have fewer degrees of freedom in the 2nd analysis. The differences may be large or small depending on how the covariates interact.

On 5/20/2020 5:37 AM, John wrote:

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Hi friends, (1) I have two groups, I set '1 -1' in .mtx file. (2) I add two variables in the .fsgd file, and set '1 -1 0 0 0 0' in the corresponding .mtx file. While, after run mris_preproc, mri_glmfit, I found the result of (1)  and (2) are different. [e.g. freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh]

I think the result of '1 -1' and '1 -1 0 0 0 0' will be same, right?

Thanks John

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