I've been pushing people to use this method when running monte carlo sims

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

To correct for two hemis, just add --2spaces to the command line. All this does is to bonferroni correct the final clusterwise p-values across two measurements

On 08/24/2016 10:25 AM, Gold, Andrea (NIH/NIMH) [F] wrote:

Hi,

I have a question about correcting for 2 hemispheres in a thickness analysis using a PFC mask. Here are the steps I ran:

1. I ran the analysis in qdec without a mask.

2. I found the mri_glmfit.log file from step 1 and cut out the mri_glmfit

command that runs the analysis and replaced ³label² option with path to our mask: cmdline mri_glmfit --y /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/y.mgh --fsgd /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/qdec.fsgd dods --glmdir /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151 --surf fsaverage lh --label /gpfs/gsfs3/users/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/lab el/labels/PFC_mask_8ROIs_LH --C /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/contrasts/lh-Avg-Intercept- thickness.mat --C /gpfs/gsfs3/users/EDAN/freesurfer/subjects/readyForGroupAnalysis/healthy_vs _anxious/qdec/Thickness_LH_sm10_Dichtomous_n151/contrasts/lh-Diff-anxiousyo uth-healthyyouth-Intercept-thickness.mat

3. I then ran mri_glmfit-sim:

mri_glmfit-sim --glmdir ./Thickness_LH_sm10_Dichtomous_n151 --sim mc-z 10000 1.3 mc-z.1p3.abs --sim-sign abs

Question: I am 99% the mri_glmfit-sim command does not correct for both hemispheres. Is it possible to figure out if the cluster survives correction for 2 hemis based on the cluster summary file (attached) from steps 1-3 above?: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 2.480 124922 479.68 -7.2 29.0 -16.8 0.00440 0.00360 0.00530 887 medialorbitofrontal

Thanks! Andrea

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