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
> 1 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 MNIZCWP
> CWPLowCWPHi NVtxs Annot
> 12.480 124922479.68 -7.2 29.0 -16.8 0.00440
> 0.00360 0.00530 887 medialorbitofrontal
>
> Thanks!
> Andrea
>
>
>
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