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
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Habets P (SP)