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