Differences between revisions 4 and 5
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 1.56 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
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# hostname crash # hostname sangwoo
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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 # group_avg_surface_area 82220
# group_avg_vtxarea_loaded 1
# annot aparc
# SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/group_study_fs5.3.0_unedited
# SearchSpace_mm2 65416.6
# SearchSpace_vtx 149955
# Bonferroni 0
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# CW PValue Threshold: 0.4
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# CSD nreps 1000 # CSD nreps 5
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# Overall max 5.48597 at vertex 84216
# Overall min -12.7661 at vertex 10349
# NClusters 38 		# Overall max 4.09919 at vertex 139021
# Overall min -13.2556 at vertex 41081
# NClusters 35
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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 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

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 1.56 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
# sysname  Linux
# hostname sangwoo
# 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
# group_avg_surface_area 82220
# group_avg_vtxarea_loaded 1
# annot aparc
# SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/group_study_fs5.3.0_unedited
# SearchSpace_mm2 65416.6
# SearchSpace_vtx 149955
# Bonferroni 0
# Minimum Threshold 4
# Maximum Threshold infinity
# Threshold Sign    neg
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.4 
# Area Threshold    0 mm^2
# CSD thresh  4.000000
# CSD nreps    5
# CSD simtype  mc-z
# CSD contrast lh-Avg-thickness-age-Cor
# CSD confint  90.000000
# Overall max 4.09919 at vertex 139021
# Overall min -13.2556 at vertex 41081
# NClusters          35
# Total Cortical Surface Area 65416.6 (mm^2)
# FixMNI = 0
# 
# 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

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