It may take that long, depending on your smoothing level. I have actually run these simulations under a lot of conditions in order to generate tables used for correction. You can get them from here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz

To install them,

cd $FREESURFER_HOME/average tar xvfz mult-comp-cor.tar.gz

I also have a new version of the simulation script that can use these tables instead of running the simulation, so it will finish in seconds, not weeks

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim

You can copy this to $FREESURFER_HOME/bin/mri_glmfit-sim Make a backup first!

Then you should be able to run:

mri_glmfit-sim --glmdir /home/joana/subjects/qdec/results_2sample --cache 2 abs

This new functionality will be available in the new version of FS, coming out "soon"

doug

Joana Braga Pereira wrote:

Dear all,

I'm running the mri_glmfit script that has been automatically generated in qdec:

mri_glmfit-sim \

--glmdir /home/joana/subjects/qdec/results_2sample \ --sim mc-z 10000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite

Because i want to get the clusters, area size and hopefully z or p values of my results.

I made a comparison of cortical thickness between 2 groups, with 2 covariates and in qdec this analysis shows that there are some clusters corrected at FDR.

Is the script that i'm using correct? It has been running for a week now, which is the average time that it takes?

Many thanks for your help,

Joana

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