On 07/07/2013 01:36 PM, jh kim wrote:
> 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*?
Yes, it controls for all your other factors.

>
> 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) ?

I don't have a strong opinion about removing the global mean thickness,
but I think others (Mike Harms?) recommend to do so. For volume and
surface area, you probably want to normalize by the ICV.

>
> 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?

It is 10k iterations of generating white noise (not a permutation test
unless you specified that explicitly).

>
> 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.

There should already be a file in the output folder called
something.y.ocn.dat that has a row for each input subject and a column
for each cluster.
doug

>
> Apology for bothering you.
> Any comments would be greatly appreciated.
>
> Thanks.
> Kim
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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