Hi Freesurfer et al.,

Since no one has responded to my email below, I'll assume my question is poorly formed.

I'm trying to compose an appropriate contrast matrix (what I've called the "C.txt" file) for a regression of surface thickness categorical comparison (two categories) with two nuisance variables.

Can someone clarify what each column of the contrast file represents and how to set it up for this? I'm having trouble finding documentation of this. It is my hope that when I call:

mri_glmfit --fsgd fsgd.txt --y lh.TEMP.mgh --C C.txt --surf fsaverage lh --cortex --glmdir lh.TEMP.output I am prepping to run a regression looking at the relationship between Patient status (i.e. 1 or 0) and cortical thickness, partialing out age and gender.

Thanks in advance for any help you can offer, Justin

On Apr 23, 2014, at 3:40 PM, Justin Baker jtbaker@partners.org wrote:

Hi all,

I'm trying to run what should be a very simple cortical thickness regression analysis in mri_glmfit, but could use some help with putting together my "C.txt" and FSGD files. I have two classes (e.g. Patient, Control) and two nuisance variables (i.e. Age, Gender).

My FSGD file looks like this: GroupDescriptorFile 1 Title FS_Thickness Class Patient Class Control Variables Age Gender Input 130725_GB49NP Patient 18 1 Input 130620_HU64KP Patient 21 2 ...

And my "C.txt" file looks like: 1 -1 0 0 0 0 ...which I'm pretty sure is wrong, but I don't quite understand what the columns mean, so any light shed would be appreciated!

-Justin