Dear experts,
Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from misbehaving, and so after running a first whole-brain group cortical thickness analysis on my structural data, I have some questions:
1. After running recon-all with the –qcache flag (i.e. presmoothing), files of the type lh.thickness.*.mgh were created for all 38 subjects (19 in each group), however files of the type *rh*.thickness.*.mgh were not created for 5 out of the 19 subjects of the first group. Log files *recon-all-status.log * and *recon-all.log* (attached, for one of those 5 subjects) both mention that the process ran on Mar22nd ended with errors, although I can't quite see what that was
2. When I take age as a continuous factor (covariate), the list of clusters in my results look dramatically different from the clusters that I get for the same contrast ran without the covariate. Why is that, given that normally adding a covariate very rarely changes the results by a great deal? Also in my case, I had quite a narrow (and well-balanced between the groups) age range!
3. I know that discrete factors cannot be taken as nuisance factors, but it seems they also can't be taken as covariates. How does one, then, control for the effects of e.g. gender in a group comparison?
4. When should values other than 10 be used for the FWHM parameter of the smoothing?
5. How come QDEC allows you to set the FWHM parameter, when in fact it is also set in the qcache stage of recon-all, which precedes QDEC?
Many thanks in advance!!
Tudor