Yes, that all looks correct. The only other thing you may want to do is to demean (ie, remove the mean from) your continuous variables. When you test for a difference in thickness (as opposed to slope), you are implicitly testing at your variables=0. Eg, if age is one of your variables, then you are testing at age=0 (birth). If there is not an interaction between age and group, then this is not a problem. If there is an interaction, then the difference will depend on what age you compute the difference. So, it's a good idea to test for an interaction between group and your continuous variables. The contrasts would basically look the same (ie, four 0.25s, four -0.25s, and 24 zeros), they will just be rearranged differently.
doug Habets P (SP) wrote: > Hi Doug, > > Just a final check that my fsgd and contrasts are properly defined. > This is now my fsgd file > > GroupDescriptorFile 1 > Title fsgd_pat_con.txt > MeasurementName CorticalThickness > > Class controls_male_mdeft > Class controls_female_mdeft > Class controls_male_adni > Class controls_female_adni > Class patients_male_mdeft > Class patients_female_mdeft > Class patients_male_adni > Class patients_female_adni > > Variables Age Education Handedness > > Input C001 controls_female_mdeft 25 6 100 > Input C002 controls_female_mdeft 27 6 100 > Input C003 controls_male_mdeft 46 5 -89.47368622 > Input C004 controls_female_mdeft 43 4 100 > Input C005 controls_male_mdeft 25 8 100 > Input C006 controls_male_mdeft 19 7 100 > Input P001 patients_male_mdeft 32 7 -100 > Input P002 patients_female_mdeft 46 3 -23.07691956 > Input P003 patients_male_mdeft 26 6 100 > Input P004 patients_female_mdeft 19 6 60 > Input P005 patients_male_mdeft 23 5 100 > Input P006 patients_male_mdeft 21 3 100 > > My hypothesis is than patients differ from controls with regard to cortical > thickness, regressing out the effects for gender scantype age educational > level and handedness. > So my contrast is: > 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 and 24 zero's (together 32 > regressors) > > Is this properly defined? > Thx! > Bw Petra > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Friday, February 11, 2011 5:10 PM > To: Habets P (SP) > Cc: freesurfer@nmr.mgh.harvard.edu; Gronenschild Ed (NP) > Subject: Re: [Freesurfer] Contrasts for GLM DODS with both discrete as > continues covariates > > Hi Petra, you have mixed up a class with the level of a factor (an easy > thing to do). From your FSGD, it looks like you would need 8 classes, > each class would be a combination of a level from each factor. So one > class would be control-male-adni, etc. Once you have a proper FSGD file, > FreeSurfer will create the proper design matrix. After you looked at the > FSGD examples on the wiki? Do a search for FSGD, and they will pop up. > > doug > > Habets P (SP) wrote: > >> I want to run a GLM DODS in Freesurfer to test whether patients differ >> from controls with regard to cortical thickness, meanwhile I want to >> control for several variables, both discrete as continues. >> >> This is my manually made fsgd file >> >> GroupDescriptorFile 1 >> >> Title fsgd pat con.txt >> >> MeasurementName Cortical Thickness >> >> Class controls >> >> Class patients >> >> Class female >> >> Class male >> >> Class mdeft >> >> Class adni >> >> Variables Age Education Handedness >> >> input C002 controls female mdeft 27 6 100 >> >> input C003 controls male mdeft 46 5 -89.47368622 >> >> input C004 controls female mdeft 43 4 100 >> >> input P001 patients male mdeft 32 7 -100 >> >> input P003 patients male mdeft 26 6 100 >> >> input P004 patients female mdeft 19 6 60 >> >> The problem I have is how to specify contrasts, on the Freesurfer >> website I found that : >> >> For DODS, the number of regressors is Nc*(Nv+1) >> >> In my case that would be 6* (3+1) = 24 >> >> Would the contrast than be: >> >> 1 -1 and 22 zero's >> >> Does Freesurfer automatically create the correct design matrix using >> the fsgd file? Because it is not clear to me how I should create the >> design matrix with some discrete variables as confounders. >> >> Bw Petra Habets >> >> * * >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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: 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 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.
