Dear Douglas and Trisanna, Thank you very much for your explanations.
I just would like to be sure of what I am doing since there is no example on the wiki as complex as mine. If I have the following classes : Diagnosis : Patient or Control Gender : Male or Female Site : Site1 or Site2 or Site3 NregressorsDODS = Nclasses*(Nvariables+1) = 6*(0+1) = 2*2*3*(1+1) = 24 Regressor1: ones for PatientMaleSite1 subjects, 0 otherwise. Codes intercept for Group 1 Regressor2: ones for PatientMaleSite2 subjects, 0 otherwise. Codes intercept for Group 2 Regressor2: ones for PatientMaleSite3 subjects, 0 otherwise. Codes intercept for Group 3 .... Regressor12: ones for ControlFemaleSite3 subjects, 0 otherwise. Codes intercept for Group 12 Regressor13: age for PatientMaleSite1 subjects, 0 otherwise. Codes age slope for Group 1 Regressor14: age for PatientMaleSite2 subjects, 0 otherwise. Codes age slope for Group 2 ... Regressor24: age for ControlFemaleSite3 subjects, 0 otherwise. Codes age slope for Group 12 *I assume my FSGDF file should look like : * GroupDescriptorFile 1 Title analysis Class PatientMaleSite1 Class PatientMaleSite2 Class PatientMaleSite3 Class PatientFemaleSite1 Class PatientFemaleSite2 Class PatientFemaleSite3 Class ControlMaleSite1 Class ControlMaleSite2 Class ControlMaleSite3 Class ControlFemaleSite1 Class ControlFemaleSite2 Class ControlFemaleSite3 Variables Age Input subject1 PatientMaleSite1 30 Input subject2 PatientFemaleSite2 45 Input subject3 PatientFemaleSite3 85 Input subject4 PatientFemaleSite4 75 ... As for the contrast analysis : If my question is : *is there a difference between Patient and Controls age slope regressing out the effects of gender and site? * *Contrast1 patient-control.slope.mtx* 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 with all regressor1 to regressor12 equal to *0* with regressor13 to 18 equal to *0.5 *(regressor with Patient in it) with regressor19 to 24 equal to *- 0.5* (regressor with Controls in it) If my question is :* is there a difference between cortical thickness in patients and controls, regressing out the effects of age, gender and site ? * *Contrast2 patient-controls.mtx* 0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 with all regressor1 to regressor6 equal to *0.5*with all regressor7 to regressor12 equal to -*0.5* with all regressor13 to regressor24 equal to *0* Thank you very much in advance for your help and sorry for taking your time. Best, Charles 2016-10-05 17:44 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > This is a straightforward extension to the FSGD examples. You have 3 > discrete factors (2 diagnosis, 2 gender, 6 centers), this yields > 2*2*6=24 classes. With one covariate, you would have 24 covariate > regressors (one for each class) for a total of 48. You would then need > to create a contrast matrix that tests for an interaction between > diagnosis and age which is also a straight-forward extension to the > examples. > > Having said that, I think that 48 regressors is a lot unless you have > about 500 subjects. It is also possible to have a less agressive model > and just have two regressors, one for each diagnosis. But you'd have to > create the design matrix yourself as this is outside of the FSGD > specification. > > > On 10/05/2016 09:22 AM, charles laidi wrote: > > Dear FreeSurfers, > > > > I would like to study the interaction between age and cortical > > thickness in patients and controls. > > My hypothesis is that there is an interaction and that cortical > > thickness is decreasing faster with age in patients than in controls. > > I have both Male and Female included in 6 different centers. > > I would like to consider also Gender and Site (6 centers) as confounds. > > > > My understanding is that I should perform a surface based group > > analysis with freesurfer. > > > > I am not able to find an example for my problem in the documentation > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V > > > > Would anyone had some tips to build the Fsgd file and the contrast file ? > > > > Thank you very much in advance. > > > > Best, > > > > Charles > > > > > > > > _______________________________________________ > > 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. > >
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