You have to pass the label to mri_glmfit. The mask is created there. --cache-label to mri_glmfit-sim assumes that you are using pre-computed results with the given label, eg, the cortex label pre-computed results are be found here $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex. It is possible to generate your own precomputed values, see here

http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

This can often be done faster than running the simulation in mri_glmfit-sim, and you can reuse the results

doug

On 05/06/2014 10:22 AM, Garikoitz Lerma-Usabiaga wrote:

Hi, we are trying to run glmfit restricted to a label, with the following commands:

mri_glmfit --y lh.p.thickness.10.mgh --label lh.l.label --fsgd f.fsgd --C C.mtx --surf fsaverage lh --cortex --glmdir lh.p.thickness.10.glmdir

mri_glmfit-sim --glmdir lh.p.thickness.10.glmdir --sim mc-z 10000 1.3 mc-z.abs --sim-sign abs --cache-label lh.l.label --cwpvalthresh .999 --overwrite

but if we check mc-z.abs.sig.masked.mgh and mc-z.abs.sig.cluster.mgh, we found clusters outside the label (see image below).

Are we doing it properly? How can we be sure that both the analysis and the correction are done inside the label?

thanks! Gari

Inline image 1

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