You need much more than 5 iterations! If you are doing whole hemisphere
analysis, then you can use the precomputed tables.

doug

On 09/24/2013 01:46 PM, ye tian wrote:
> Dear Freesurfers,
> Sorry for having posted an incorrect question. I basically ran

> *mri_glmfit-sim *on both hemispheres and tried both *--sim-sign neg
> *and *--sim-sign pos*. Although I only had 5 iterations, I found no

> significant clusters on any case. Does that mean that I accept the
> null hypothesis?
> PS: I found in
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23324.html
> that 10,000 iterations are commonly used.
> Thank you very much!
>
>
> On Mon, Sep 23, 2013 at 9:47 PM, ye tian <tianye730@gmail.com

> <mailto:tianye730@gmail.com>> wrote:
>
>     Dear Freesurfers,
>     I used the following command line to find significant clusters
>     after glm analysis (before MC clusters attached)
>     mri_glmfit-sim \
>       --glmdir lh.meditation_age.glmdir \
>       --sim mc-z 5 4 mc-z.negative \
>       --sim-sign neg --cwpvalthresh 0.05\
>       --overwrite
>     I didn't find any, i.e., there are no clusters listed in file
>     mc-z.negative.sig.cluster.summary. Does this mean that I should
>     accept the null hypothesis for the whole cortex?
>     Also, how many iterations of mc do people typically perform? I
>     guess it doesn't make a difference if I do 1000 iterations instead
>     of 5 anyways.
>     Thank you very much!
>     Sincerely,
>     Ye
>
>
>
>

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

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