Dear FreeSurfer experts...

Please be patient with a newbie's questions.

For the first time, I'm trying to analyze between-group differences in cortical thickness (controls vs. patients) by using FS 5.1.0 and QDEC.

I've read through the online manual and mailing lists; however, I cannot figure out the following queries.

1) I selected 'group' (con, pat) as a fixed factor (gender is not applicable because all are females), and demeaned age as a continuous covariate. After analyzing using DODS option, several questions are shown in the Display GUI panel. Does the question "Does the average thickness differ between con and pat?" mean between-group difference of cortical thickness after controlling for the effect of age?

2) Should I include average cortical thickness of the left or right cortex (calculated from the command, mris_anatomical_stats -l lh.cortex.label -f subid.txt subid lh) as a nuisance variable? I know this issue has been addressed many times before, and it is generally recommended not to include as a nuisance factor. However, in case of statistically significant difference in mean cortical thickness of one hemisphere (unpaired two sample t-test by SPSS), is it still not necessary to include it as a nuisance factor? From the similar points of view, how about volume and surface area analyses (include or not total cortical volume and total surface area as a nuisance factor, respectively) ?

3) I found several significant clusters that are corrected for multiple comparisons using Monte Carlo simulation (corrected P < 0.01) in the bottom of Display panel. I assume that this procedures take 10,000 permutations by default. Am I right?

4) Last question, how can I extract individual value (cortical thickness per subject) from the significant clusters? I want to do this 'all-at-once'. Please let me know the command.

Apology for bothering you.

Any comments would be greatly appreciated.

Thanks.

Kim