Hi Marco, I'm copying the list on this because this is a good question about an aspect that is not well documented.

The answer to the question has to do with the sign of the test. By default, mri_glmfit produces p-values that are for unsigned tests. The p-value for a signed test if half that of the signed test (ie, it is more significant). When the p-value is expressed as -log10(p), then the signed test will be 0.301 higher than the unsigned test. Eg, if you have a p-value of .01, the value in the sig.mgh file will be 2.0, but for a signed test it would be .005, making the value in the sig.mgh file 2.3.

When you run mri_glmfit-sim and specify a signed test (ie, --sim-sign pos or --sim-sign neg), it lowers the threshold to account for this. So below you specified 1.3 as the threshold and --sim-sign pos, so it lowered the threshold to 1.0.

hope this is clear

doug

Marco Loggia, PhD wrote:

Sorry Doug,

Below are directory and command line. Also attached is a screenshot showing a vertex located on a significant cluster, but below threshold in the sig.mgh.

Thanks! Marco

dir=/autofs/cluster/randy/2/lbp/freesurfer/patients+controls/analyses/lh.lbp +ctrl.session1.asl2-asl1_30sept10_sm7_03mm_masked_projfrac-max_P=0.05.glmdir /lbp_only_24sept10

pbsubmit -c "mri_glmfit-sim --glmdir lh.lbp+ctrl.session1.asl2-asl1_30sept10_sm7_03mm_masked_projfrac-max_P=0.05. glmdir --sim perm 10000 1.30103 perm.positive --sim-sign pos --overwrite"

-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 18, 2010 10:34 AM To: Marco Loggia, PhD Subject: Re: montecarlo

Hi Marco, can you send the command-line and directory that you ran it from? In general, it is always a good idea to send this ...

doug

Marco Loggia, PhD wrote:

...

Hello Doug,

I have one question about the montecarlo simulation.

When I compare the mc-z.positive.sig.cluster.mgh and the mc-z.positive.sig.masked.mgh, I notice that the significant clusters include also some vertices that are below the cluster forming threshold. Is this normal? Why is that?

Thanks,

Marco

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Marco L. Loggia, PhD

Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital

Harvard Medical School

CNY Building 120, suite 101E

Charlestown, Massachusetts 02129

Phone: (617) 643-7267

Fax: (617) 643-7340 marco@nmr.mgh.harvard.edu

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