On 05/14/2013 10:05 AM, Tudor Popescu wrote:
Not sure whether anyone'd seen my last email (below). Again apologies for the multitude of questions, I hope this is the last batch for this analysis..
On 12 May 2013 16:45, Tudor Popescu <tudor3@gmail.com mailto:tudor3@gmail.com> wrote:
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,.."?
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.
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?
It is hard to related FDR to traditional FPR. FDR does not give clusters and there is no FDR associated with the cluster you found. It just gives a list of vertices that meet the FDR criteria. You form the clusters with your eyes. The 0.1 means that 10% of the vertices are falsely activated. If those 10% are all in your cluster, then that is a problem.
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?
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?
Probably not. make_average_subject really just gives you a folding pattern to display your results on. If you want to analyze your data on the actual new average subject, you will need to register to that average subject (takes about 2 hours per subject), then specify the new registration with --surfreg.
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.
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 doug
Thanks! Tudor
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