Hi Martijn, yes, that is a good thing to do! doug Martijn Steenwijk wrote: > 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 <mailto: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), 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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel: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> > >
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
