Differences between revisions 1 and 7 (spanning 6 versions)
⇤ ← Revision 1 as of 2009-01-17 20:28:51 →
Size: 5349
Editor: crash
Comment:
← Revision 7 as of 2016-03-28 18:15:36 → ⇥
Size: 5614
Editor: LeeTirrell
Comment:
Deletions are marked like this. Additions are marked like this.
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  1. The value in the first column is the cluster number, which allows linking to the annotation.
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  1. NVtxs - number of vertices in cluster   1. 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)
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# Cluster Growing Summary (mri_surfcluster)
# $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
# cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/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
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# hostname crash # hostname nmrclass19
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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 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
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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 3.74095 at vertex 153106
# Overall min -11.5636 at vertex 134036
# NClusters 20
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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 -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)