Sorry,

I was actually able to compile a FSGD file that has a single line for each subject (containing the fsid base) along with gender and age at baseline. I ran this through the mris_preproc command (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) in order to stack the spc files which were previously cached. 

I guess my question really is can I now simply continue on and use the mri_glmfit instructions on the group analysis tutorial page or is there a special procedure because I am dealing with longitudinal data? I was planning on simply using contrasts i had designed before for my cross-sectional analysis, controlling for age at baseline and gender. 

Thanks and my apologies for all the questions!

Arsenije