> > > 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. > > 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) > > 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? > > 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! > > > Look for C.dat in the contrast folders > I have no C.dat under /contrasts, only files such as lh-Avg-Intercept-thickness.mat. Don't the different clickable "questions" that appear in QDEC's Display screen each correspond to a contrast, with each contrast sitting in its own file? _____ And a couple more.. A) Why does mris_preproc need to be pointed to a .FSGD, when its output should just be a concatenation of registered structurals, and thus independent from the design of any particular analysis? 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... 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.. Thanks again Doug!
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