Hi Rito,

To correlate cortical thickness with cognitive score at baseline, that would presumably be done were the correlation is across subjects for each ROI, does that seem correct? So using 3dttest++ as Gang suggets, the input files would be one list of ROI values (baseline) per subject. Then the cognitive scores would be applied as a covariate.

<Gang, please correct me if this does not seem correct.>

Comparison of the two groups would then be a 2-sample t-test. So A command would look similar to the class demo with a covariate file, AFNI_data6/group_results/s6.ttest.covary .

In this case it might read something like:

3dttest++ -prefix cognitive_100_vs_105    \
          -AminusB                              \
          -setA group_100                       \
               s0000 s0000_ROIs.1D              \
               s0001 s0001_ROIs.1D              \
               ...                              \
               s0099 s0099_ROIs.1D              \
          -setB group_105                       \
               s1000 s1000_ROIs.1D              \
               s1001 s1001_ROIs.1D              \
               ...                              \
               s1104 s1104_ROIs.1D              \
          -covariates cognitive_scores_covary.txt

Where s0000_ROIs.1D would have the 187 ROI averages, one value per row.
And where cognitive_scores_covary.txt would be a text file with one row per subject, and might look like:

subject cog_score
s0000  43.7
s0001  86.0
...
s1104  56.2

Does that seem reasonable?

- rick