Hi Freesurfer Experts,
I have some questions regarding mri_glmfit - some basic and some not so basic - that I hope you can help me with.
1.) I want to do a thickness analysis looking at the effect of a continuous variable on thickness while regressing out effects of both continuous and categorical variables. Let's just say I have one continuous variable of interest, one to regress out, and one categorical variable (with four groups) to regress out. From reading other posts, it seems that I should make my categorical variables into a class - if I do this will this contrast look at the effect of my continuous variable while regressing out effects from the other variables (including group)? This is assuming I am running a DOSS analysis
0 0 0 0 0 1
2.) In the cluster corrected significant image, I am a bit confused on what the positive and negative significance values represent. If I was looking at group differences - would red indicate that the first group > second group, and blue indicate first group < second group (that is, first group with increased or decreased thickness compared to second group)?
3.) Lastly, I see that you can use mris_preproc and glmfit to look at volume. Does this look at volume in a voxel-based way? That is, is it comparing volume on a voxel level? If so, would the correct commands be:
mris_preproc --fsgd FSGD FILE --target fsaverage --hemi lh --meas volume --out OUT.mgh