2012/6/12 Douglas N Greve <greve@nmr.mgh.harvard.edu>

yes, though I would probably do it outside of qdec as it can take a while (hours or days)

On 06/12/2012 08:03 AM, Marie Schneider wrote:

Thank you very much for your answer.

Are 10 000 iterations also used when I am running a Monte Carlo simulation in qdec?

Thanks, Marie

2012/6/9 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

they are two different correction schemes. If they gave the same
answer,
then it would not make sense to have both. the monte carlo tries to
compute the probability of a cluster of the given size under the null
hypothesis. FDR controls for the number of false positives relative to
the total number of positives under the assumption that if any 5% of
your positives are false, then you would not change your conclusion.

For monte carlo, we generally use 10000 iterations. If you are
using the
whole hemisphere, then you can used the cached tables. See the
"command-line" tutorial.

doug

On 06/08/2012 08:03 AM, Marie Schneider wrote:
> Dear FreeSurfer experts,
>
> I have some questions about corrections for multiple comparisons in
> FreeSurfer. I have two samples, one consisting of two groups and one
> consisting of three groups.
>
> I do the comparison with the sample of two groups in qdec.
Correcting
> for multiple comparisons, I get a significant result using FDR,
but no
> significant result using Monte Carlo simulation. How can that be?
>
> I analyze the sample with the three groups by mri_glmfit. In your
> tutorial, I only found how to correct for multiple comparisons with
> the Monte Carlo simulation using the command line, but not how to
> correct with FDR using the command line. Is there a possibility
to do
> this? If not, how many iterations are usual to use within the Monte
> Carlo simulation?
>
> Any help is appreciated.
>
> Thank you very much,
>
> Marie
>
>
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MGH-NMR Center
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