For #2, it is hard to say without seeing the design. I would not say that covariates should not change the results (otherwise one would not add them), especially age. If you have a balanced design, then one would hope that adding age would reduce the residual noise and show more of an effect. But if you have a very narrow age range, then "age" can look like a constant which would be colinear with the actual group designations and so reduce activation. doug
On 4/15/13 5:52 PM, Nick Schmansky wrote: > Tudor, > > In the recon-all.log, it has this line: > ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh > > but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh > correctly, so this indicates to me that it might have run out of disk > space. is that the case? > > to answer the others: > 2. not sure > 3. you can select discrete can a regular variate along with your main > variate. 'nuisance' variates are like any other. > 4. depends on the expected 'blob' size > 5. the selection of fwhm in qdec corresponds directly with the values > selected by qcache (they are one-to-one related, ie the 10mm fwhm values > created by qcache are used by the 10mm fwhm selection in qdec). > > Nick > > > > On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote: >> 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 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
