2013/7/11 Douglas N Greve <greve@nmr.mgh.harvard.edu>

On 07/09/2013 10:07 PM, jh kim wrote:

Dear Prof. Greve

I have additional (and probably silly) questions.

1) Is there much difference between result of monte-carlo null-z simulation (QDEC GUI) analysis and that of clusterwise correction for multiple comparisons using 10000 permutations? I'm guessing similar results between both methods; however I'm wondering whether significant clusters from the former processing might disappeared when using the latter process, or vice versa?

When you say permutation, do you mean the permutation method where you permute your own data? It is hard to say whether they will give the same result. I usually find permutation to give less significant results (which may just be more accurate).

2) Does QDEC analysis automatically produce *.glmdir files for each contrast? If not, how can I make *.glmdir from the QDEC (not using the mri_glmfit command)?

It creates a glmdir for the whole analysis. Within the glmdir, it creates a folder for each contrast
doug

Thank you for your kindness
Kim

2013/7/9 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

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

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