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 <tud...@gmail.com > <mailto:tud...@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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
