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 -- Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health Room 201, Bldg. 15K, MSC 2670 Bethesda, MD 20892-2670 Phone: 301-827-9804 Fax: 301-402-2010 Email: andrea.g...@nih.gov <applewebdata://D38F487B-BA2B-4BF6-A9C4-96248AB2BE51/andrea.g...@nih.gov>
mc-z.1p3.abs.sig.cluster.summary
Description: mc-z.1p3.abs.sig.cluster.summary
_______________________________________________ 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.
