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.
