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# 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		  Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $
# $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $
# CreationTime 2016/03/18-19:41:27-GMT
# cmdline mri_surfcluster.bin --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /home/nmrclass/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 /home/nmrclass/freesurfer/subjects/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm
Line 32: Line 27:
# hostname sangwoo # hostname nmrclass19
Line 43: Line 38:
# group_avg_vtxarea_loaded 1 # group_avg_vtxarea_loaded 0
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# SUBJECTS_DIR /autofs/space/birn_045/users/BWH/buckner_data/group_study_fs5.3.0_unedited # SUBJECTS_DIR /home/nmrclass/freesurfer/subjects/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial
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# SearchSpace_vtx 149955
# Bonferroni 0		 # SearchSpace_vtx 149953
# 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 min -13.2556 at vertex 41081
# NClusters 35		 # Overall max 3.74095 at vertex 153106
# Overall min -11.5636 at vertex 134036
# NClusters 20
Line 67: Line 62:
   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		    1 -11.564 134036 3685.09 -11.1 34.5 27.2 0.00020 0.00000 0.00040 8495 -46427.05 superiorfrontal
   2 -11.479 136827 7353.19 -49.4 5.9 -16.9 0.00020 0.00000 0.00040 18945 -105891.25 superiortemporal
   3 -9.462 38853 1414.27 -25.4 -75.9 18.6 0.00020 0.00000 0.00040 3450 -18026.77 superiorparietal
   4 -8.836 38022 150.27 -27.5 28.3 2.1 0.00280 0.00180 0.00380 408 -2297.87 lateralorbitofrontal
   5 -8.379 95475 1068.72 -20.6 -49.4 -2.3 0.00020 0.00000 0.00040 2549 -13274.34 lingual
   6 -8.323 133346 445.15 -33.0 -36.8 37.5 0.00020 0.00000 0.00040 1684 -8583.54 supramarginal
   7 -8.081 101082 329.73 -44.4 -50.4 9.2 0.00020 0.00000 0.00040 984 -4973.56 bankssts
   8 -7.915 120330 402.71 -20.2 -66.9 24.4 0.00020 0.00000 0.00040 1025 -4941.69 precuneus
   9 -7.409 10899 413.74 -12.1 -54.9 28.8 0.00020 0.00000 0.00040 1050 -5410.59 precuneus
  10 -6.724 155919 341.74 -56.8 -38.8 40.2 0.00020 0.00000 0.00040 1175 -5467.80 supramarginal
  11 -6.583 120934 494.68 -27.6 -79.9 -8.1 0.00020 0.00000 0.00040 1075 -5092.23 fusiform
  12 -6.567 80571 208.72 -31.2 34.1 25.6 0.00020 0.00000 0.00040 491 -2320.33 rostralmiddlefrontal
  13 -5.987 62853 260.64 -52.0 -49.3 -19.0 0.00020 0.00000 0.00040 514 -2449.65 inferiortemporal
  14 -5.577 81545 156.62 -28.8 -39.1 51.2 0.00260 0.00180 0.00360 487 -2192.27 superiorparietal
  15 -5.389 159131 242.49 -10.4 -43.9 41.1 0.00020 0.00000 0.00040 655 -2765.41 precuneus
  16 -5.248 81927 84.70 -9.1 -21.2 59.9 0.02938 0.02642 0.03253 207 -906.86 paracentral
  17 -4.646 108705 84.31 -30.5 -55.0 62.5 0.03017 0.02702 0.03332 277 -1134.21 superiorparietal
  18 -4.563 63135 73.74 -33.4 -43.5 -15.9 0.04273 0.03901 0.04645 124 -509.13 fusiform
  19 -4.370 35855 194.37 -62.8 -44.5 -4.4 0.00040 0.00000 0.00080 551 -2199.50 middletemporal
  20 -4.281 33706 89.60 -36.1 -72.7 43.9 0.02623 0.02326 0.02918 261 -1029.40 inferiorparietal

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 1.57 2014/03/06 17:02:46 greve Exp $
# $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $
# CreationTime 2016/03/18-19:41:27-GMT
# cmdline mri_surfcluster.bin --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /home/nmrclass/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 /home/nmrclass/freesurfer/subjects/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm
# sysname  Linux
# hostname nmrclass19
# 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 0
# annot aparc
# SUBJECTS_DIR /home/nmrclass/freesurfer/subjects/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial
# SearchSpace_mm2 65416.6
# SearchSpace_vtx 149953
# 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 3.74095 at vertex 153106
# Overall min -11.5636 at vertex 134036
# NClusters          20
# 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      -11.564  134036   3685.09    -11.1   34.5   27.2  0.00020  0.00000  0.00040   8495   -46427.05  superiorfrontal
   2      -11.479  136827   7353.19    -49.4    5.9  -16.9  0.00020  0.00000  0.00040  18945  -105891.25  superiortemporal
   3       -9.462   38853   1414.27    -25.4  -75.9   18.6  0.00020  0.00000  0.00040   3450   -18026.77  superiorparietal
   4       -8.836   38022    150.27    -27.5   28.3    2.1  0.00280  0.00180  0.00380    408    -2297.87  lateralorbitofrontal
   5       -8.379   95475   1068.72    -20.6  -49.4   -2.3  0.00020  0.00000  0.00040   2549   -13274.34  lingual
   6       -8.323  133346    445.15    -33.0  -36.8   37.5  0.00020  0.00000  0.00040   1684    -8583.54  supramarginal
   7       -8.081  101082    329.73    -44.4  -50.4    9.2  0.00020  0.00000  0.00040    984    -4973.56  bankssts
   8       -7.915  120330    402.71    -20.2  -66.9   24.4  0.00020  0.00000  0.00040   1025    -4941.69  precuneus
   9       -7.409   10899    413.74    -12.1  -54.9   28.8  0.00020  0.00000  0.00040   1050    -5410.59  precuneus
  10       -6.724  155919    341.74    -56.8  -38.8   40.2  0.00020  0.00000  0.00040   1175    -5467.80  supramarginal
  11       -6.583  120934    494.68    -27.6  -79.9   -8.1  0.00020  0.00000  0.00040   1075    -5092.23  fusiform
  12       -6.567   80571    208.72    -31.2   34.1   25.6  0.00020  0.00000  0.00040    491    -2320.33  rostralmiddlefrontal
  13       -5.987   62853    260.64    -52.0  -49.3  -19.0  0.00020  0.00000  0.00040    514    -2449.65  inferiortemporal
  14       -5.577   81545    156.62    -28.8  -39.1   51.2  0.00260  0.00180  0.00360    487    -2192.27  superiorparietal
  15       -5.389  159131    242.49    -10.4  -43.9   41.1  0.00020  0.00000  0.00040    655    -2765.41  precuneus
  16       -5.248   81927     84.70     -9.1  -21.2   59.9  0.02938  0.02642  0.03253    207     -906.86  paracentral
  17       -4.646  108705     84.31    -30.5  -55.0   62.5  0.03017  0.02702  0.03332    277    -1134.21  superiorparietal
  18       -4.563   63135     73.74    -33.4  -43.5  -15.9  0.04273  0.03901  0.04645    124     -509.13  fusiform
  19       -4.370   35855    194.37    -62.8  -44.5   -4.4  0.00040  0.00000  0.00080    551    -2199.50  middletemporal
  20       -4.281   33706     89.60    -36.1  -72.7   43.9  0.02623  0.02326  0.02918    261    -1029.40  inferiorparietal

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