[Freesurfer] GLM question

Hello group,

I am a new user of Freesurfer and just learning to process data through the pipeline. Sorry if this is an amateur question. I was just trying to look at cortical thickness differences between a patient group and a control group. So, my fsgd file would just list the input files and the corresponding diagnosis. Now, if I were to design a contrast matrix to look at cortical thickness differences between the 2 groups, I understand that I would have only 2 regressors . So, my contrast matrix would just be [-1 1]? I tried doing that and I got a matrix read error for the contrast file. Thanks in advance for your help.

Regards Koushik