Hi Doug, Thanks for your reply again. It's getting more and more clear now.
I've however one question remaining, which is regarding the correction for sex. What I did not tell (my fault ;-) ), is that 75% of the cohort is female. Comparing the sex-corrected results with male-only and female-only results, it appears to me that the relatively small male-group partly 'drives' the results in the sex-corrected results. I guess this is because the males and females are currently equally weighted in the contrast matrices. Shouldn't the differences in sex also be represented in the contrast matrices, like [.25 .75 -.25 -.75 0 0 0 0 0 0 0 0] [0 0 .25 .75 -.25 -.75 0 0 0 0 0 0] [ .25 .75 0 0 -.25 -.75 0 0 0 0 0 0] ? Or am I wrong? Best, Martijn On Wed, Dec 21, 2011 at 5:45 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > Hi Martijn, sorry for the delay. Your contrast matrices look correct. The > differences between demeaning and not demeaning is somewhat expected. When > you do not demean, you are testing whether there is a difference between > groups at age=0 (ie, birth). When you demean, you are testing for a > difference at age=MeanAge. If the slope of each group with respect to age > is the same, then this will yield the same result since the regression > lines will be parallel and the distance between parallel lines will always > be the same. If the slopes differ, then the distance will change with age. > For example, there will be an age where the lines cross. If you test at > this age, you are assured not to see a difference! For this reason, it is > better to test for a difference in the slopes, and, if there is no > difference, then reanalyze with DOSS which forces the lines to be parallel. > In your case, you found that there is some difference in insula. If this is > not the area that you are interested in, then I would not worry about it. > You should just keep in mind that you should not try to draw conclusions > from this area. > doug > > Martijn Steenwijk wrote: > >> Dear Doug, >> >> Thanks again for your reply. Based on that I did some further work. >> >> I first demeaned the age of all subjects. Actually, I have a third group >> which I would like to compare to, so my contrast matrices will be [.5 .5 >> -.5 -.5 0 0 0 0 0 0 0 0] >> [0 0 .5 .5 -.5 -.5 0 0 0 0 0 0] >> [.5 .5 0 0 -.5 -.5 0 0 0 0 0 0] >> to test for CT differences between all the groups while correcting for >> age and sex. Surprisingly, I'm observing a big difference in the results >> compared to the results without demeaning. Could you explain the reson for >> this? In the FSGD-examples (eg http://surfer.nmr.mgh.harvard.** >> edu/fswiki/FsgdFormat<http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat>), >> age is also not normalized. Does normalizing the variance to 1 also >> influence the results? >> Given this big difference, I started wondering whether it would maybe be >> better to analyze the data in pairs of two groups (and then demean by the >> mean of the two groups). Would this be a better approach? >> >> Concerning your second suggestion: if I test the data for differences in >> group slope, a number of small area's are significantly different. Regions >> popping up are especially in the neighborhood of the insula. Unfortunately >> this suggests that I cannot use the DOSS model, or am I wrong? >> >> Looking forward to your reply, >> With best regards, >> Martijn >> >> >> On Sat, Dec 10, 2011 at 7:16 PM, Douglas Greve >> <gr...@nmr.mgh.harvard.edu<mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> wrote: >> >> Yes, that is correct, though I think your matrix should be [.5 .5 >> -.5 -.5 0 0 0 0]. You should also remove the mean from the age >> (mean computed from all subjects). Or even better, first test >> whether there is a group difference in age slope with [0 0 0 0 .5 >> .5 -.5 -.5]. If there is nothing that is significant, then re-run >> your analysis using the Different Offset Same Slope (DOSS) model >> with this contrast [.5 .5 -.5 -.5 0]. >> >> doug >> >> >> On 12/10/11 4:15 AM, Martijn Steenwijk wrote: >> >>> >>> Dear all, >>> >>> >>> I’m relatively new with Freesurfer, but slowly getting more and >>> more used to it’s great possibilities. To be ‘sure’, I’ve a >>> question about the design of a GLM. >>> >>> >>> I want to compare CT in Healthy Controls vs Diseased, and control >>> for age and sex. It appears to me that factors (eg sex) cannot be >>> used as covariate/variable, which forces me to model them as a >>> separate class although I’m not interested in sex differences. >>> This brings me to the following FSGD file: >>> >>> >>> # HcDis.fsgd >>> >>> GroupDescriptorFile 1 >>> >>> Title HcDis >>> >>> Class Hc_Male >>> >>> Class Hc_Female >>> >>> Class Dis_Male >>> >>> Class Dis_Female >>> >>> Variables Age >>> >>> Input subjid1 Hc_Male 35 >>> >>> Input subjid2 Dis_Female 30 >>> >>> …. >>> >>> >>> Then the difference between Hc and Dis, corrected for age and sex >>> is given by the contrast matrix >>> >>> #Hc-vs-Dis.mtx >>> >>> 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 >>> >>> >>> Is this correct? >>> >>> >>> Best, >>> >>> Martijn >>> >>> >>> >>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >>> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >
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