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Deletions are marked like this. Additions are marked like this.
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# $Id: mri_surfcluster.c,v 1.39.2.3 2009/01/15 01:06:01 greve Exp $
# $Id: mrisurf.c,v 1.557.2.17 2009/01/08 17:16:51 nicks Exp $
# CreationTime 2009/01/17-23:15:29-GMT
# cmdline mri_surfcluster --in lh.gender_age.glmdir.dng/lh-Avg-thickness-age-Cor/sig.mgh --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j001-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j002-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j003-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j004-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j005-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j006-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j007-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j008-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j009-lh-Avg-thickness-age-Cor.csd --csd lh.gender_age.glmdir.dng/csd/mc-z.neg4.j010-lh-Avg-thickness-age-Cor.csd --mask lh.gender_age.glmdir.dng/mask.mgh --cwsig lh.gender_age.glmdir.dng/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.cluster.mgh --vwsig lh.gender_age.glmdir.dng/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.voxel.mgh --sum lh.gender_age.glmdir.dng/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.cluster.summary --ocn lh.gender_age.glmdir.dng/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.mgh --oannot lh.gender_age.glmdir.dng/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot
# cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/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 crash # hostname nmrclass22
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# Input lh.gender_age.glmdir.dng/lh-Avg-thickness-age-Cor/sig.mgh # Input lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh
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# SUBJECTS_DIR /homes/4/greve/subjects # 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
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# CW PValue Threshold: 0.05
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# CSD nreps 1000
# 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 5.48597 at vertex 84216
# Overall min -12.7661 at vertex 10349
# NClusters 38		 # Overall max 4.09918 at vertex 139021
# Overall min -13.2556 at vertex 41081
# NClusters 27
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# FixMNI = 1 # FixMNI = 0
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# ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs
   1 -12.766 10349 4044.79 -32.9 -30.5 16.2 0.00100 0.00000 0.00200 9674
   2 -9.373 87074 1061.40 -29.3 -65.4 24.8 0.00100 0.00000 0.00200 1827
   3 -9.099 94747 1753.72 -33.2 -16.8 35.9 0.00100 0.00000 0.00200 3826
   4 -8.378 124347 857.47 -8.0 9.5 54.0 0.00100 0.00000 0.00200 1562
   5 -7.655 134038 270.11 -10.0 31.7 26.3 0.00100 0.00000 0.00200 406
   6 -7.207 151199 495.56 -27.2 -46.6 39.8 0.00100 0.00000 0.00200 1428
   7 -7.146 135320 225.86 -44.7 -48.5 10.0 0.00100 0.00000 0.00200 502
   8 -7.054 56027 1620.84 -17.2 -73.7 11.9 0.00100 0.00000 0.00200 2812
   9 -6.792 8949 560.63 -16.3 43.6 32.5 0.00100 0.00000 0.00200 1026
  10 -6.735 96031 362.26 -20.2 8.9 56.5 0.00100 0.00000 0.00200 663
  11 -6.550 8820 285.91 -28.9 -35.3 49.0 0.00100 0.00000 0.00200 628
  12 -6.523 143993 207.58 -28.2 -76.0 -2.8 0.00100 0.00000 0.00200 254
  13 -6.186 50351 94.58 -9.6 -20.1 54.7 0.00600 0.00300 0.00900 218
  14 -6.165 156572 366.23 -42.7 -80.1 4.3 0.00100 0.00000 0.00200 536
  15 -6.149 88337 269.18 -8.4 -43.1 30.0 0.00100 0.00000 0.00200 611
  16 -5.961 12488 241.14 -10.4 8.9 37.4 0.00100 0.00000 0.00200 664
  17 -5.918 63623 150.17 -49.0 -48.8 43.3 0.00100 0.00000 0.00200 351
  18 -5.629 64694 91.13 -17.9 -37.6 47.5 0.00600 0.00300 0.00900 275
  19 -5.599 12705 272.83 -57.0 -34.2 34.0 0.00100 0.00000 0.00200 608
  20 -5.558 43501 86.84 -41.2 -62.0 8.0 0.00800 0.00500 0.01200 178
  21 -5.536 155028 36.06 -27.1 27.0 1.5 0.07700 0.06600 0.08800 110
  22 -5.467 147033 252.12 -57.0 -50.1 19.2 0.00100 0.00000 0.00200 561
  23 -5.452 160783 63.52 -24.7 -11.9 -25.1 0.02900 0.02200 0.03600 176
  24 -5.130 108644 379.76 -18.4 -59.4 59.1 0.00100 0.00000 0.00200 912
  25 -4.751 17102 174.99 -20.2 -65.7 24.3 0.00100 0.00000 0.00200 349
  26 -4.592 106761 74.44 -49.2 -55.3 27.6 0.01500 0.01000 0.02000 152
  27 -4.576 37880 27.15 -38.1 16.0 7.6 0.11600 0.10300 0.12900 73
  28 -4.443 39303 25.56 -16.7 -23.5 35.7 0.12200 0.10900 0.13500 77
  29 -4.347 27994 75.48 -8.6 -42.2 47.1 0.01300 0.00900 0.01800 158
  30 -4.281 45716 117.41 -50.7 28.4 1.1 0.00100 0.00000 0.00200 166
  31 -4.230 89384 0.86 -20.2 6.1 -13.1 0.29700 0.27900 0.31600 2
  32 -4.144 99466 70.11 -47.5 -58.5 40.6 0.02000 0.01400 0.02600 168
  33 -4.124 99664 14.11 -36.2 1.5 -10.2 0.19400 0.17800 0.21000 40
  34 -4.107 162791 22.65 -9.1 -75.8 1.1 0.14000 0.12600 0.15400 26
  35 -4.103 129139 7.53 -47.6 -25.2 -4.4 0.24500 0.22800 0.26200 23
  36 -4.079 92916 32.15 -8.5 -9.8 52.3 0.09000 0.07800 0.10200 62
  37 -3.880 42435 18.70 -18.5 -18.1 66.7 0.16000 0.14500 0.17500 59
  38 -3.775 161351 3.11 -57.6 -6.3 -22.0 0.27900 0.26100 0.29700 6		 # 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)