Hi Doug,
Thank you for your reply.
My command was:
mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh --cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir
My FSGD file is attached. It contains 2 classes and two covariates (Age and Sex).
My design matrix is:
1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects of age and sex)