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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

Back to Group Analysis

Surface-based Cluster Summary Table as created by mri_glmfit-sim.

  1. Lines that begin with '#' are comments
  2. Each data line is a cluster
  3. There are 38 clusters
  4. The value in the first column is the cluster number, which allows linking to the annotation.
  5. Max indicates the maximum -log10(pvalue) in the cluster

  6. VtxMax is the vertex number at the maximum

  7. Size - surface area (mm^2) of cluster
  8. Tal(XYZ) is the talairach (MNI305) coordinate of the maximum
  9. CWP - clusterwise p-value. This is the p-value of the cluster
  10. CWPLow and CWPHi - 90% confidence interval for CWP
  11. 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

FsTutorial/GroupAnalysisClusterSummary (last edited 2016-03-28 18:15:36 by LeeTirrell)