Hello Doug, Hello Marie, thank you very much for your answers, I'm sorry I had missed your previous mail about QDEC!
I will use mri_glmfit then to confirm my results, Best, Elisa 2013/9/20 Douglas Greve <gr...@nmr.mgh.harvard.edu> > > 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 >
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