> 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,.."?
>
I thought that it would have. Are you coding age as a nuisance
variable?
Also, are you coding gender as a continuous variable? That is
something
you should not do.

I was not coding age as a nuisance variable but as a continuous variable (co-variate). Gender was a discrete/fixed factor but I'm not sure whether this means 'continuous' in the sense discussed in your exchange with Arman. Anyway, in this configuration, it seems gender and age are not accounted (controlled) for at the same time.

It should be. Can you send your qdec table?

See attached

> 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
>
Where does it say to use ess.fwhm10thickn.fsaverage?

Sorry, typo. The flag is actually "--cache-in thickness.fwhm10.fsaverage", I file that I do not have after having run recon-all (including with the --qcache option)

Try running recon-all again with just the --qcache flag.

This is what I had done previously; the command was:
recon-all -s C${i} -qcache
where the ${i} was a counter in a script, to run the command on all my subjects

> 5) What is the difference between running
make_average_subject and
> running mris_preproc with --target fsaverage?
>
make average subject makes the average subject. mris_preproc
samples the
data into a common space defined by the registration surface and
concatenates the input subjects into a single stack.

But should the registration surface used by mris_preproc (i.e. its "--target" flag) come from the 'average' subject or from 'fsaverage'? In other words, which one of these becomes the study-specific template?

You have to tell mris_preproc both the target and the surface registration to use if you want to use a different average subject.

The command I used is:

mris_preproc --fsgd group_gender__age.fsgd --target average --hemi rh --meas thickness --out rh.thickness.mgh

So if I understand correctly, the fact that I didn't indicate a surface registration means that the surface from the "average" subject will be used, rather than the one from "fsaverage"? I still don't understand the difference between those two, and which, if any, can be referred to as the study-specific template.

B) All concatenated volumes from mris_preproc's output files (?h.thickness.mgh) appear blank in freeview, even though the individual structurals all look fine. Also, lh.thickness.mgh and rh.thickness.mgh have, surprisingly, *exactly* the same file size, which is also a bit small (~25MB) to be able to contain 38 registered structurals, which suggests something went wrong...
These are surface overlay files, not volumes. You can't load surfaces as volumes in freeview.

So assuming I don't visually inspect the surface overlays, can I assume that mris_preproc ran fine if lh.thickness.mgh and rh.thickness.mgh have exactly the same file size?

C) When running mri_surf2surf, I get an error saying that file /surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors..

It's extremely helpful to have command lines ...