Hi Shady, Try assembling the design as this:
EV1: Group 1 (coded as 0/1) EV2: Group 2 (coded as 0/1) EV3: Group 3 (coded as 0/1) EV4: Sex (coded as +1/-1) EV5: Site (coded as +1/-1) The contrasts to compare the three groups are then: C1: [1 -1 0 0 0] C2: [1 0 -1 0 0] C3: [0 1 -1 0 0] C4: [-1 1 0 0 0] C5: [-1 0 1 0 0] C6: [0 -1 1 0 0] >From the description it seems site and group are confounded, although not completely, such that it should be possible to still draw some inferences, although without much power. The above does not include terms for interactions. If it's something you could be interested in, then extra EVs can be added. All the best, Anderson On 30 August 2016 at 11:40, Shady Rahayel <shady.raha...@gmail.com> wrote: > Greetings, > > I want to design a matrix that contains 3 fixed factors. The first is > diagnosis (3 levels), the second is gender (2 levels), and the last is > imaging site (2 levels). However, the thing is that the imaging site factor > only applies to only one level of the diagnosis factor (i.e. patients from > the first level of the diagnosis factor were seen in 2 different imaging > sites, whereas for the two other groups of patients the same imaging site > was used). > > I have followed the tutorials but I still be am confused concerning how I > should go about creating the design matrix with 3 fixed factors. Would it > be: > > GroupDescriptorFile 1 > Title xx > Class Diagnosis1-Male-Site1 > Class Diagnosis1-Female-Site1 > Class Diagnosis1-Male-Site2 > Class Diagnosis1-Female-Site2 > Class Diagnosis2-Male-Site1 > Class Diagnosis2-Female-Site1 > Class Diagnosis3-Male-Site1 > Class Diagnosis3-Female-Site1 > Input etc etc... > > Afterwards, if I'm looking for a difference between Diagnosis1 and > Diagnosis2, what would be the contrast? > 0.25 0.25 0.25 0.25 -0.5 0.5 0 0 ? > > Thank you very much for your help, > > Shady > > -- > *Shady Rahayel* > Étudiant au Ph.D. en neuropsychologie R/I > Université du Québec à Montréal > > Centre d'Études Avancées en Médecine du Sommeil > Hôpital du Sacré-Coeur de Montréal > > _______________________________________________ > 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. > >
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