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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
