Hi Freesurfer Experts,

I have used freesurfer smoothed images (lh.thickness.fsaverage.fwhm15.gii) to perform a cortical thickness analysis. I used qdec with a surface-based morphometric analysis to compare two groups. As my discrete fixed factor I used group membership. As Nuisance factors I used age (years), sex (0/1), site(1-10) and years of education(years). I used Threshold min=2, max=5 which I assume refers to a T-stat threshold. I see an FDR correction which and the Monte Carlo Null-Z simulation.

1) Do I run both monte carlo and fdr or just one after my figure apprears?
Is the monte-carlo with threshold = 1.3(0.5) similar to a clusterwise threshold with a fixed p value?
Are results valid when just setting the threshold min=2, max=5 but they are just uncorrected results?

2) When running Qdec with no nusiance factors and just a discrete fixed factor of group membership, my results look almost identical to AFNI's 3dttest++ output when the tmin=2. However, when I add the nuisance factors the results between the two softare packages are different.

When nuisances covariates are added does Qdec still use a ttest or switch to some other method?

How is centering assumed between groups for covariances? Is the mean from each covariate calculated and removed from each group separately based on group membership or calculated together with all subjects and removed?

Does the analysis assume to have pooled or unpooled variance across the two groups?

3) For the viewer it displaces a logarithmic scale from what I have read in other papers. Is there a way to switch this to displace tvalue?

4) There was a previous post I saw yesterday saying qdec only uses 2 nuisance covariates and so I wanted to see if this is the case or not so I can try to understand why my afni and freesurfer results match with no covariates added but are very different once covariates are added.

Thanks,

Ajay