Hi Marie, On 9/20/13 4:30 PM, Marie Schaer wrote: > Hi Doug, > > I'm jumping in the discussion because I was a bit scared with your previous > email mentioning that this DOSS bug affects all FreeSurfer's versions. Does > that also affect statistical analyses computed with mri_glmfit using the > command line? Do you have an insight whether the bias introduced by the bug > is important or not? (as others may also be, I'm becoming a bit anxious about > previously published results…) It does not affect the command-line version, only in QDEC. It was basically not creating a contrast matrix that matched the hypothesis question under some circumstances. > > Finally, to get back to Elisa's question: do you have some suggestion in the > mean time to assess the relationship between cortical thickness and a > clinical measure correcting for age and gender? Using DODS? With or without demeaning the covariates and nuisance? Sorry for the abundance of questions, and, as always, thanks a lot for your answer! Marie
I would probably do it with DODS and just test the mean across the two groups, eg, Class M Class F Variables ClinicalVar Age [0 0 .5 .5 0 0] This would account for possible differences in slope between M and F. In the end, I think it will give you about the same as if use DOSS. If you have a small sample size, you could use DOSS because DODS will cost you 2 more DOF doug On Sep 20, 2013, at 6:13 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: >> Hi Elisa, don't use the DOSS feature in QDEC. Sorry, I sent out an email >> about 6mo ago on this, but it is not easy to let people know about a bug >> once the bug is out there. >> doug >> >> >> On 09/19/2013 11:30 AM, E. Scariati wrote: >>> Dear Freesurfer experts, >>> >>> I would like to study the relationship between cortical thickness and >>> one clinical variable with qdec, but correcting for age and gender. >>> >>> Given that I have only one group and 2 covariates (one continuous, one >>> dichotomic) I don't know how I should set the design of my analysis in >>> qdec, especially for the gender variable. >>> >>> I have tried two different ways (both DOSS design): >>> >>> 1) selecting Discrete = gender; Continuous = clinical measure; >>> Nuisance factor = age >>> and looking at the contrast called : "Does the correlation between >>> thickness and clinical measure accounting for gender differ from 0? >>> nuisance factor : age" >>> >>> 2) selecting : continuous = clinical measure; Nuisance Factor = age, >>> gender (coded as 1 and 2) >>> and looking at the contrast called : "Does the correlation >>> between thickness and clinical measure differ from 0, nuisance factor >>> : age, gender" >>> >>> But the two contrasts give very different results, which I find very >>> surprising. I exported cortical thickness at the peak significance of >>> the clusters and tried to run a GLM myself in SPSS and it seems that >>> coding gender as a continuous variable with two values (1 and 2) >>> provides the most realistic results. However, I saw many times on the >>> mailing list that you recommend to use gender as a discrete variable, >>> so I am very confused. >>> Could you explain me the difference between these contrasts and help >>> me to identify which one will accurately identify the correlation >>> between cortical thickness and my clinical variable correcting for the >>> effect of age and gender. >>> >>> Thank you in advance for your answer, >>> Best regards >>> Elisa >>> >>> >>> _______________________________________________ >>> 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. >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
