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 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.
