Dear Freesurfer experts,

I am comparing cortical thickness data of two patient groups (Group A; Group B) and one control group (Group C) without any covariates.

In a simple t-test I observe a significant difference in cortical thickness only between Group B and Group C in several clusters (corrected p!).

Now I am running an ANOVA ("Three Groups (One Factor/Three Levels), No Covariates") as documented in your FSGD examples.

In the output of the f-test (using the following matrix [1 -1 0; 1 0 -1]) the clusters from my t-test remain but do not survive the correction using "mri_glmfit sim" as below. 

Do I have to correct the results of my f-test using mri_glmfit-sim? If yes, why do I reveal a significant group-difference in the corrected t-test and not in the corrected f-test?

mri_glmfit-sim \
  --glmdir lh.gender_age.glmdir \
  --cache 4 neg \
  --cwp  0.05\
  --2spaces

Thank you very much in advance!

Sincerely,

Leon