Deer Freesurfer Experts,

We are trying to perform 3 group comaprison analysis in Freesurfer (mri_glmfit). 

Our fixed factors are "group (Case1, Case2, Healthy)" and our dependent variables are "thickness variables".

We want to control "CPZ" continuous variable but CPZs of healthy group are all zero.

So, it makes following errors in Freesurfer 

1. ill-conditioned problem, Freesurfer design matrix maybe be linearly-dependent

2. Badly scaled problem, CPZ variables are higly different between groups (Case1, Case2 have big CPZ variables, but Healthy have all zero)

To solve this problem, we are going to make own design matrix using only two indicator varibles for three groups.

(Freesurfer's design matrix seems to use three indicators, which may make error in this analysis)

And we are going to change the contrast to suit my design matrix with two indicators.

Is it possible to use two indicator design matrix in Freesurfer to perform 3 group comparison analysis(mri_glmfit)?

mri_glmfit help page said that the design matrix can be specified in matlab4 format, can't in excel?, Shoud it be version 4 in the matlab?

Finally, to solve badly scaled problem, can i use z-score calculated on all group samples?

Best regards,

Yonggab Kim