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# $Id: mri_surfcluster.c,v 1.56 2012/05/31 22:08:59 greve Exp $ # $Id: mrisurf.c,v 1.751 2013/05/17 18:25:08 fischl Exp $ # CreationTime 2013/11/01-19:31:28-GMT # cmdline mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd lh.gender_age.glmdir/csd/mc-z.negative.j001-lh- Avg-thickness-age-Cor.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.clu ster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age -Cor/mc-z.negative.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.mgh --oannot lh.gender_ag e.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.ne gative.pdf.dat --cwpvalthresh 0.4 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.masked.mgh --no-fixmni --surf white # cwd /autofs/space/birn_045/users/BWH/buckner_data/group_study_fs5.3.0_unedited/glm |
# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2014/04/28-17:24:41-GMT # cmdline mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /mnt/macmini/apps/centos4_x86_64/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white # cwd /mnt/macmini/RW_tutorial_data/nmrclass22/buckner_data/tutorial_subjs/group_analysis_tutorial/glm |
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# hostname sangwoo | # hostname nmrclass22 |
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# group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 |
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# SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/group_study_fs5.3.0_unedited | # SUBJECTS_DIR /mnt/macmini/RW_tutorial_data/nmrclass22/buckner_data/tutorial_subjs/group_analysis_tutorial |
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# Bonferroni 0 | # Bonferroni 2 |
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# CW PValue Threshold: 0.4 | # CW PValue Threshold: 0.05 |
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# CSD nreps 5 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-age-Cor |
# CSD nreps 10000 # CSD simtype null-z # CSD contrast NA |
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# Overall max 4.09919 at vertex 139021 | # Overall max 4.09918 at vertex 139021 |
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# NClusters 35 | # NClusters 27 |
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# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -13.256 41081 7674.37 -32.9 -32.4 17.6 0.20000 0.00000 0.40000 16861 -95949.80 insula 2 -13.251 134037 4478.93 -11.6 34.2 26.8 0.20000 0.00000 0.40000 8528 -46277.49 superiorfrontal 3 -10.087 33898 853.18 -11.2 -56.5 29.8 0.20000 0.00000 0.40000 1970 -10142.74 precuneus 4 -8.756 8836 909.75 -31.7 -45.5 38.6 0.20000 0.00000 0.40000 2500 -12241.05 superiorparietal 5 -8.310 90999 990.06 -21.0 -69.8 1.1 0.20000 0.00000 0.40000 2010 -10842.06 lingual 6 -8.039 135316 1059.05 -43.2 -51.4 10.2 0.20000 0.00000 0.40000 2151 -10446.74 bankssts 7 -8.026 117530 719.04 -57.0 -37.9 41.0 0.20000 0.00000 0.40000 1622 -8230.07 supramarginal 8 -7.902 105523 912.75 -43.1 -10.3 51.6 0.20000 0.00000 0.40000 2095 -10364.25 precentral 9 -7.508 127827 675.17 -45.4 -66.3 -4.3 0.20000 0.00000 0.40000 1076 -5174.55 lateraloccipital 10 -7.155 52076 920.09 -28.5 -80.5 12.7 0.20000 0.00000 0.40000 1653 -8418.20 inferiorparietal 11 -7.112 120332 166.83 -20.3 -69.0 23.1 0.20000 0.00000 0.40000 330 -1660.40 precuneus 12 -6.113 81547 194.03 -28.6 -40.6 51.2 0.20000 0.00000 0.40000 410 -1858.02 superiorparietal 13 -5.981 101953 361.51 -45.3 -44.5 -14.5 0.20000 0.00000 0.40000 536 -2401.60 inferiortemporal 14 -5.980 157254 105.36 -46.6 -31.1 -5.3 0.20000 0.00000 0.40000 304 -1409.52 superiortemporal 15 -5.824 96719 145.57 -42.9 -71.1 11.9 0.20000 0.00000 0.40000 284 -1302.16 inferiorparietal 16 -5.703 120950 292.32 -30.3 -70.6 -9.4 0.20000 0.00000 0.40000 443 -1992.66 fusiform 17 -5.556 108035 114.50 -54.5 -5.1 41.0 0.20000 0.00000 0.40000 271 -1227.01 precentral 18 -5.482 81929 93.78 -9.2 -21.4 58.6 0.20000 0.00000 0.40000 215 -950.76 paracentral 19 -5.469 176 111.52 -23.4 53.7 11.1 0.20000 0.00000 0.40000 140 -615.04 rostralmiddlefrontal 20 -5.335 56417 98.52 -49.8 -53.9 43.8 0.20000 0.00000 0.40000 237 -1006.24 supramarginal 21 -4.976 16136 82.28 -12.4 -59.2 56.6 0.20000 0.00000 0.40000 186 -795.54 superiorparietal 22 -4.712 136899 96.51 -46.7 -7.3 -31.8 0.20000 0.00000 0.40000 134 -557.32 inferiortemporal 23 -4.677 78263 331.41 -43.6 -55.3 37.9 0.20000 0.00000 0.40000 744 -3084.92 supramarginal 24 -4.619 114728 83.28 -27.9 -51.9 -5.2 0.20000 0.00000 0.40000 183 -751.00 lingual 25 -4.524 22812 67.62 -34.2 -43.9 -14.9 0.20000 0.00000 0.40000 125 -512.20 fusiform 26 -4.522 60548 104.20 -37.6 36.7 -10.4 0.20000 0.00000 0.40000 183 -746.15 parsorbitalis 27 -4.348 36314 167.21 -33.4 34.9 28.1 0.20000 0.00000 0.40000 273 -1102.02 rostralmiddlefrontal 28 -4.188 65567 110.20 -32.0 49.5 5.2 0.20000 0.00000 0.40000 157 -622.60 rostralmiddlefrontal 29 -4.179 122382 59.05 -5.9 -69.5 42.6 0.20000 0.00000 0.40000 123 -483.22 precuneus 30 -3.933 158511 24.28 -11.9 -95.6 4.7 0.20000 0.00000 0.40000 29 -110.58 pericalcarine 31 -3.933 6360 12.26 -64.2 -24.9 -15.7 0.20000 0.00000 0.40000 22 -84.10 middletemporal 32 -3.883 91288 21.32 -9.6 -76.8 -5.4 0.20000 0.00000 0.40000 23 -87.21 lingual 33 -3.860 102161 0.43 -16.3 -40.2 3.0 0.20000 0.00000 0.40000 2 -7.72 unknown 34 -3.826 3247 7.22 -32.5 22.2 -20.2 0.20000 0.00000 0.40000 18 -67.73 lateralorbitofrontal 35 -3.798 87233 16.31 -30.0 -90.0 8.4 0.20000 0.00000 0.40000 22 -82.46 lateraloccipital |
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -13.256 41081 7674.37 -32.9 -32.4 17.6 0.00020 0.00000 0.00040 16861 insula 2 -13.251 134037 4478.93 -11.6 34.2 26.8 0.00020 0.00000 0.00040 8528 superiorfrontal 3 -10.087 33898 853.18 -11.2 -56.5 29.8 0.00020 0.00000 0.00040 1970 precuneus 4 -8.756 8836 909.75 -31.7 -45.5 38.6 0.00020 0.00000 0.00040 2500 superiorparietal 5 -8.310 90999 990.06 -21.0 -69.8 1.1 0.00020 0.00000 0.00040 2010 lingual 6 -8.039 135316 1059.05 -43.2 -51.4 10.2 0.00020 0.00000 0.00040 2151 bankssts 7 -8.026 117530 719.04 -57.0 -37.9 41.0 0.00020 0.00000 0.00040 1622 supramarginal 8 -7.902 105523 912.75 -43.1 -10.3 51.6 0.00020 0.00000 0.00040 2095 precentral 9 -7.508 127827 675.17 -45.4 -66.3 -4.3 0.00020 0.00000 0.00040 1076 lateraloccipital 10 -7.155 52076 920.09 -28.5 -80.5 12.7 0.00020 0.00000 0.00040 1653 inferiorparietal 11 -7.112 120332 166.83 -20.3 -69.0 23.1 0.00180 0.00100 0.00260 330 precuneus 12 -6.113 81547 194.03 -28.6 -40.6 51.2 0.00040 0.00000 0.00080 410 superiorparietal 13 -5.981 101953 361.51 -45.3 -44.5 -14.5 0.00020 0.00000 0.00040 536 inferiortemporal 14 -5.980 157254 105.36 -46.6 -31.1 -5.3 0.01554 0.01336 0.01772 304 superiortemporal 15 -5.824 96719 145.57 -42.9 -71.1 11.9 0.00300 0.00200 0.00400 284 inferiorparietal 16 -5.703 120950 292.32 -30.3 -70.6 -9.4 0.00020 0.00000 0.00040 443 fusiform 17 -5.556 108035 114.50 -54.5 -5.1 41.0 0.01236 0.01037 0.01435 271 precentral 18 -5.482 81929 93.78 -9.2 -21.4 58.6 0.02287 0.02010 0.02563 215 paracentral 19 -5.469 176 111.52 -23.4 53.7 11.1 0.01375 0.01177 0.01594 140 rostralmiddlefrontal 20 -5.335 56417 98.52 -49.8 -53.9 43.8 0.02049 0.01792 0.02307 237 supramarginal 21 -4.976 16136 82.28 -12.4 -59.2 56.6 0.03233 0.02918 0.03548 186 superiorparietal 22 -4.712 136899 96.51 -46.7 -7.3 -31.8 0.02109 0.01851 0.02366 134 inferiortemporal 23 -4.677 78263 331.41 -43.6 -55.3 37.9 0.00020 0.00000 0.00040 744 supramarginal 24 -4.619 114728 83.28 -27.9 -51.9 -5.2 0.03135 0.02820 0.03450 183 lingual 25 -4.522 60548 104.20 -37.6 36.7 -10.4 0.01653 0.01415 0.01891 183 parsorbitalis 26 -4.348 36314 167.21 -33.4 34.9 28.1 0.00180 0.00100 0.00260 273 rostralmiddlefrontal 27 -4.188 65567 110.20 -32.0 49.5 5.2 0.01415 0.01196 0.01633 157 rostralmiddlefrontal |
Surface-based Cluster Summary Table as created by mri_glmfit-sim.
- Lines that begin with '#' are comments
- Each data line is a cluster
- There are 38 clusters
- The value in the first column is the cluster number, which allows linking to the annotation.
- Max indicates the maximum -log10(pvalue) in the cluster
VtxMax is the vertex number at the maximum
- Size - surface area (mm^2) of cluster
- Tal(XYZ) is the talairach (MNI305) coordinate of the maximum
- CWP - clusterwise p-value. This is the p-value of the cluster
- CWPLow and CWPHi - 90% confidence interval for CWP
- NVtxs - number of vertices in cluster (each vertex will not have the exact same area, you can estimate mean vertex area by dividing total surface area by the number of vertices)
Eg, the 13th cluster has a pvalue of p<.006.
# Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2014/04/28-17:24:41-GMT # cmdline mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /mnt/macmini/apps/centos4_x86_64/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white # cwd /mnt/macmini/RW_tutorial_data/nmrclass22/buckner_data/tutorial_subjs/group_analysis_tutorial/glm # sysname Linux # hostname nmrclass22 # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /mnt/macmini/RW_tutorial_data/nmrclass22/buckner_data/tutorial_subjs/group_analysis_tutorial # SearchSpace_mm2 65416.6 # SearchSpace_vtx 149955 # Bonferroni 2 # Minimum Threshold 4 # Maximum Threshold infinity # Threshold Sign neg # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 4.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.09918 at vertex 139021 # Overall min -13.2556 at vertex 41081 # NClusters 27 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -13.256 41081 7674.37 -32.9 -32.4 17.6 0.00020 0.00000 0.00040 16861 insula 2 -13.251 134037 4478.93 -11.6 34.2 26.8 0.00020 0.00000 0.00040 8528 superiorfrontal 3 -10.087 33898 853.18 -11.2 -56.5 29.8 0.00020 0.00000 0.00040 1970 precuneus 4 -8.756 8836 909.75 -31.7 -45.5 38.6 0.00020 0.00000 0.00040 2500 superiorparietal 5 -8.310 90999 990.06 -21.0 -69.8 1.1 0.00020 0.00000 0.00040 2010 lingual 6 -8.039 135316 1059.05 -43.2 -51.4 10.2 0.00020 0.00000 0.00040 2151 bankssts 7 -8.026 117530 719.04 -57.0 -37.9 41.0 0.00020 0.00000 0.00040 1622 supramarginal 8 -7.902 105523 912.75 -43.1 -10.3 51.6 0.00020 0.00000 0.00040 2095 precentral 9 -7.508 127827 675.17 -45.4 -66.3 -4.3 0.00020 0.00000 0.00040 1076 lateraloccipital 10 -7.155 52076 920.09 -28.5 -80.5 12.7 0.00020 0.00000 0.00040 1653 inferiorparietal 11 -7.112 120332 166.83 -20.3 -69.0 23.1 0.00180 0.00100 0.00260 330 precuneus 12 -6.113 81547 194.03 -28.6 -40.6 51.2 0.00040 0.00000 0.00080 410 superiorparietal 13 -5.981 101953 361.51 -45.3 -44.5 -14.5 0.00020 0.00000 0.00040 536 inferiortemporal 14 -5.980 157254 105.36 -46.6 -31.1 -5.3 0.01554 0.01336 0.01772 304 superiortemporal 15 -5.824 96719 145.57 -42.9 -71.1 11.9 0.00300 0.00200 0.00400 284 inferiorparietal 16 -5.703 120950 292.32 -30.3 -70.6 -9.4 0.00020 0.00000 0.00040 443 fusiform 17 -5.556 108035 114.50 -54.5 -5.1 41.0 0.01236 0.01037 0.01435 271 precentral 18 -5.482 81929 93.78 -9.2 -21.4 58.6 0.02287 0.02010 0.02563 215 paracentral 19 -5.469 176 111.52 -23.4 53.7 11.1 0.01375 0.01177 0.01594 140 rostralmiddlefrontal 20 -5.335 56417 98.52 -49.8 -53.9 43.8 0.02049 0.01792 0.02307 237 supramarginal 21 -4.976 16136 82.28 -12.4 -59.2 56.6 0.03233 0.02918 0.03548 186 superiorparietal 22 -4.712 136899 96.51 -46.7 -7.3 -31.8 0.02109 0.01851 0.02366 134 inferiortemporal 23 -4.677 78263 331.41 -43.6 -55.3 37.9 0.00020 0.00000 0.00040 744 supramarginal 24 -4.619 114728 83.28 -27.9 -51.9 -5.2 0.03135 0.02820 0.03450 183 lingual 25 -4.522 60548 104.20 -37.6 36.7 -10.4 0.01653 0.01415 0.01891 183 parsorbitalis 26 -4.348 36314 167.21 -33.4 34.9 28.1 0.00180 0.00100 0.00260 273 rostralmiddlefrontal 27 -4.188 65567 110.20 -32.0 49.5 5.2 0.01415 0.01196 0.01633 157 rostralmiddlefrontal