Dear Freesurfer experts,
I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :)
1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast "Does the avg thickness, accounting for gender, differ between group1 and group2?" and not also "..acounting for gender and age,.."?
2) In QDEC, if I am left with a cluster after setting the FDR rate to 0.1, does that qualify as a "trend towads significance" in the same way as when obtaining a p value <.1 for a behavioural effect?
3) From the group tutorial, I see that mris_preproc has to be called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh
4) When comparing two healthy groups, is there anything to gain from using a fsaverage built from the sample (with make_average_subject) as opposed to using the default fsaverage?
5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage?
6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions!
Thanks! Tudor