Sure, here it is:
# Cluster Growing Summary (mri_volcluster) # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $ # cwd /autofs/cluster/maury/users/gcoombs/College_Risk/ObjectLooming/allSBQ_061213/st4-obj_ns-4runs/face_v_car # cmdline mri_volcluster --in tal.sm.wls.pct.rfx//group/sig.mgh --csd tal.sm.wls.pct.rfx//csd/HvL.SBQ.2.pos.j001-group.csd --mask tal.sm.wls.pct.rfx//mask.mgh --cwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.mgh --vwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.voxel.mgh --sum tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.summary --ocn tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.ocn.mgh --csdpdf tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.pdf.dat # sysname Linux # hostname compute-0-114 # machine x86_64 # user eboeke01 # Input Volume: tal.sm.wls.pct.rfx//group/sig.mgh # Frame Number: 0 # Minimum Threshold: 2 # Maximum Threshold: inifinity # Threshold Sign: pos # AdjustThreshWhenOneTail 1 # Size Threshold: 0 mm^3 # Size Threshold: 0 voxels # Voxel Size: 8 mm^3 # Registration: None : Tal Coords invalid # Mask Vol: tal.sm.wls.pct.rfx//mask.mgh # Mask Thresh: 0.500000 # Mask Sign: abs # Mask Invert: 0 # AllowDiag: 0 # NClusters 192 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast group # CSD confint 90.000000 # # Reporting Coordinates in Voxel Indices # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ Max# CWP CWPLow CWPHi 1 597 4776.0 30.00 50.00 65.00 5.94673 0.02490 0.02290 0.02690 2 730 5840.0 27.00 28.00 86.00 5.56628 0.00720 0.00610 0.00830 3 1124 8992.0 5.00 18.00 38.00 5.01850 0.00010 0.00000 0.00020 4 259 2072.0 59.00 20.00 78.00 5.01465 0.68360 0.67760 0.68960 5 279 2232.0 18.00 22.00 73.00 3.94952 0.58840 0.58210 0.59470 6 194 1552.0 35.00 66.00 76.00 3.94297 0.93630 0.93320 0.93940 7 664 5312.0 32.00 15.00 60.00 3.68551 0.01400 0.01250 0.01550 8 293 2344.0 28.00 5.00 58.00 3.66686 0.52560 0.51920 0.53200 9 49 392.0 12.00 52.00 58.00 3.63351 1.00000 -0.00010 1.00000 10 150 1200.0 5.00 4.00 28.00 3.62637 0.99560 0.99470 0.99640 11 298 2384.0 12.00 47.00 86.00 3.58250 0.50260 0.49620 0.50900 12 343 2744.0 13.00 39.00 60.00 3.57829 0.33900 0.33290 0.34510 13 467 3736.0 21.00 42.00 49.00 3.53307 0.09590 0.09210 0.09970 14 276 2208.0 49.00 36.00 56.00 3.51549 0.60280 0.59650 0.60910 15 134 1072.0 70.00 17.00 34.00 3.38623 0.99890 0.99850 0.99930 16 75 600.0 5.00 25.00 55.00 3.09334 1.00000 -0.00010 1.00000 17 74 592.0 13.00 10.00 49.00 3.03017 1.00000 -0.00010 1.00000 18 45 360.0 65.00 39.00 62.00 3.00205 1.00000 -0.00010 1.00000 19 15 120.0 72.00 7.00 42.00 2.96283 1.00000 -0.00010 1.00000 20 55 440.0 62.00 9.00 23.00 2.93121 1.00000 -0.00010 1.00000 21 79 632.0 46.00 60.00 87.00 2.92199 1.00000 -0.00010 1.00000 22 35 280.0 2.00 41.00 48.00 2.84065 1.00000 -0.00010 1.00000 23 44 352.0 6.00 35.00 27.00 2.80109 1.00000 -0.00010 1.00000 24 14 112.0 50.00 3.00 54.00 2.75399 1.00000 -0.00010 1.00000 25 71 568.0 0.00 22.00 9.00 2.75160 1.00000 -0.00010 1.00000 26 5 40.0 28.00 0.00 36.00 2.72535 1.00000 -0.00010 1.00000 27 130 1040.0 40.00 1.00 45.00 2.71826 0.99920 0.99880 0.99950 28 81 648.0 33.00 61.00 86.00 2.70040 1.00000 -0.00010 1.00000 29 73 584.0 67.00 26.00 52.00 2.68744 1.00000 -0.00010 1.00000 30 16 128.0 64.00 48.00 72.00 2.67636 1.00000 -0.00010 1.00000 31 28 224.0 75.00 35.00 88.00 2.65193 1.00000 -0.00010 1.00000 32 11 88.0 15.00 21.00 82.00 2.61771 1.00000 -0.00010 1.00000 33 5 40.0 45.00 0.00 27.00 2.61424 1.00000 -0.00010 1.00000 34 16 128.0 9.00 13.00 70.00 2.58842 1.00000 -0.00010 1.00000 35 23 184.0 15.00 27.00 48.00 2.57410 1.00000 -0.00010 1.00000 36 28 224.0 15.00 31.00 44.00 2.57219 1.00000 -0.00010 1.00000 37 23 184.0 29.00 56.00 78.00 2.55890 1.00000 -0.00010 1.00000 38 7 56.0 0.00 42.00 92.00 2.55525 1.00000 -0.00010 1.00000 39 49 392.0 52.00 40.00 88.00 2.54894 1.00000 -0.00010 1.00000 40 42 336.0 7.00 31.00 63.00 2.52160 1.00000 -0.00010 1.00000 41 37 296.0 22.00 43.00 81.00 2.50557 1.00000 -0.00010 1.00000 42 21 168.0 22.00 58.00 72.00 2.49912 1.00000 -0.00010 1.00000 43 32 256.0 59.00 45.00 91.00 2.44918 1.00000 -0.00010 1.00000 44 12 96.0 31.00 29.00 36.00 2.42939 1.00000 -0.00010 1.00000 45 50 400.0 14.00 34.00 26.00 2.42102 1.00000 -0.00010 1.00000 46 22 176.0 6.00 15.00 55.00 2.41349 1.00000 -0.00010 1.00000 47 12 96.0 9.00 43.00 42.00 2.40593 1.00000 -0.00010 1.00000 48 27 216.0 64.00 17.00 31.00 2.38351 1.00000 -0.00010 1.00000 49 16 128.0 25.00 49.00 81.00 2.37500 1.00000 -0.00010 1.00000 50 37 296.0 12.00 18.00 54.00 2.36836 1.00000 -0.00010 1.00000 51 22 176.0 43.00 50.00 63.00 2.35072 1.00000 -0.00010 1.00000 52 39 312.0 31.00 39.00 46.00 2.31633 1.00000 -0.00010 1.00000 53 7 56.0 75.00 60.00 84.00 2.28945 1.00000 -0.00010 1.00000 54 6 48.0 33.00 25.00 67.00 2.28154 1.00000 -0.00010 1.00000 55 10 80.0 49.00 40.00 33.00 2.27301 1.00000 -0.00010 1.00000 56 13 104.0 26.00 65.00 88.00 2.27017 1.00000 -0.00010 1.00000 57 6 48.0 13.00 25.00 26.00 2.26583 1.00000 -0.00010 1.00000 58 15 120.0 54.00 9.00 20.00 2.25868 1.00000 -0.00010 1.00000 59 16 128.0 63.00 14.00 19.00 2.21490 1.00000 -0.00010 1.00000 60 4 32.0 9.00 25.00 61.00 2.21056 1.00000 -0.00010 1.00000 61 37 296.0 25.00 37.00 62.00 2.21055 1.00000 -0.00010 1.00000 62 10 80.0 59.00 51.00 51.00 2.20982 1.00000 -0.00010 1.00000 63 20 160.0 66.00 41.00 51.00 2.19863 1.00000 -0.00010 1.00000 64 2 16.0 53.00 66.00 72.00 2.18410 1.00000 -0.00010 1.00000 65 9 72.0 37.00 38.00 66.00 2.17739 1.00000 -0.00010 1.00000 66 6 48.0 6.00 44.00 62.00 2.17461 1.00000 -0.00010 1.00000 67 39 312.0 50.00 35.00 70.00 2.16322 1.00000 -0.00010 1.00000 68 11 88.0 52.00 6.00 21.00 2.16002 1.00000 -0.00010 1.00000 69 6 48.0 26.00 0.00 43.00 2.15030 1.00000 -0.00010 1.00000 70 8 64.0 41.00 16.00 19.00 2.14875 1.00000 -0.00010 1.00000 71 4 32.0 51.00 8.00 39.00 2.14592 1.00000 -0.00010 1.00000 72 3 24.0 47.00 9.00 21.00 2.14285 1.00000 -0.00010 1.00000 73 8 64.0 67.00 19.00 27.00 2.14034 1.00000 -0.00010 1.00000 74 12 96.0 3.00 59.00 86.00 2.13879 1.00000 -0.00010 1.00000 75 3 24.0 15.00 6.00 19.00 2.13024 1.00000 -0.00010 1.00000 76 9 72.0 59.00 41.00 41.00 2.12204 1.00000 -0.00010 1.00000 77 18 144.0 35.00 48.00 55.00 2.10334 1.00000 -0.00010 1.00000 78 6 48.0 40.00 57.00 92.00 2.08841 1.00000 -0.00010 1.00000 79 7 56.0 43.00 1.00 17.00 2.07371 1.00000 -0.00010 1.00000 80 6 48.0 41.00 55.00 69.00 2.07007 1.00000 -0.00010 1.00000 81 14 112.0 23.00 35.00 88.00 2.06307 1.00000 -0.00010 1.00000 82 11 88.0 40.00 73.00 82.00 2.05213 1.00000 -0.00010 1.00000 83 5 40.0 39.00 19.00 51.00 2.04809 1.00000 -0.00010 1.00000 84 10 80.0 38.00 24.00 69.00 2.04252 1.00000 -0.00010 1.00000 85 9 72.0 30.00 32.00 67.00 2.04237 1.00000 -0.00010 1.00000 86 7 56.0 54.00 58.00 72.00 2.03645 1.00000 -0.00010 1.00000 87 10 80.0 30.00 13.00 22.00 2.03577 1.00000 -0.00010 1.00000 88 8 64.0 0.00 25.00 72.00 2.03193 1.00000 -0.00010 1.00000 89 5 40.0 7.00 23.00 6.00 2.02805 1.00000 -0.00010 1.00000 90 4 32.0 59.00 28.00 21.00 2.02245 1.00000 -0.00010 1.00000 91 11 88.0 43.00 18.00 63.00 2.01764 1.00000 -0.00010 1.00000 92 5 40.0 14.00 41.00 87.00 2.01255 1.00000 -0.00010 1.00000 93 3 24.0 28.00 50.00 55.00 2.01226 1.00000 -0.00010 1.00000 94 6 48.0 35.00 0.00 43.00 1.99869 1.00000 -0.00010 1.00000 95 1 8.0 59.00 57.00 79.00 1.99505 1.00000 -0.00010 1.00000 96 1 8.0 25.00 2.00 51.00 1.99394 1.00000 -0.00010 1.00000 97 4 32.0 55.00 4.00 36.00 1.98505 1.00000 -0.00010 1.00000 98 2 16.0 66.00 21.00 6.00 1.97461 1.00000 -0.00010 1.00000 99 3 24.0 31.00 51.00 90.00 1.97154 1.00000 -0.00010 1.00000 100 3 24.0 12.00 11.00 23.00 1.95664 1.00000 -0.00010 1.00000 101 5 40.0 38.00 43.00 50.00 1.95222 1.00000 -0.00010 1.00000 102 2 16.0 28.00 22.00 7.00 1.95066 1.00000 -0.00010 1.00000 103 4 32.0 20.00 17.00 69.00 1.94669 1.00000 -0.00010 1.00000 104 5 40.0 1.00 8.00 46.00 1.94587 1.00000 -0.00010 1.00000 105 4 32.0 42.00 15.00 49.00 1.94354 1.00000 -0.00010 1.00000 106 4 32.0 4.00 41.00 54.00 1.93906 1.00000 -0.00010 1.00000 107 3 24.0 15.00 9.00 33.00 1.93848 1.00000 -0.00010 1.00000 108 6 48.0 61.00 28.00 72.00 1.92516 1.00000 -0.00010 1.00000 109 1 8.0 49.00 26.00 88.00 1.92457 1.00000 -0.00010 1.00000 110 3 24.0 65.00 37.00 41.00 1.92365 1.00000 -0.00010 1.00000 111 3 24.0 69.00 29.00 25.00 1.91576 1.00000 -0.00010 1.00000 112 2 16.0 70.00 15.00 9.00 1.89931 1.00000 -0.00010 1.00000 113 2 16.0 65.00 24.00 70.00 1.89719 1.00000 -0.00010 1.00000 114 1 8.0 41.00 24.00 36.00 1.89653 1.00000 -0.00010 1.00000 115 7 56.0 71.00 32.00 91.00 1.89529 1.00000 -0.00010 1.00000 116 6 48.0 24.00 38.00 69.00 1.88993 1.00000 -0.00010 1.00000 117 4 32.0 6.00 22.00 34.00 1.88833 1.00000 -0.00010 1.00000 118 3 24.0 41.00 45.00 51.00 1.87881 1.00000 -0.00010 1.00000 119 2 16.0 18.00 58.00 91.00 1.87841 1.00000 -0.00010 1.00000 120 3 24.0 44.00 10.00 17.00 1.87792 1.00000 -0.00010 1.00000 121 4 32.0 7.00 38.00 71.00 1.87444 1.00000 -0.00010 1.00000 122 2 16.0 39.00 12.00 65.00 1.87242 1.00000 -0.00010 1.00000 123 7 56.0 25.00 35.00 38.00 1.87054 1.00000 -0.00010 1.00000 124 3 24.0 14.00 28.00 25.00 1.86776 1.00000 -0.00010 1.00000 125 4 32.0 64.00 23.00 76.00 1.86629 1.00000 -0.00010 1.00000 126 7 56.0 58.00 44.00 43.00 1.86598 1.00000 -0.00010 1.00000 127 1 8.0 40.00 44.00 63.00 1.86487 1.00000 -0.00010 1.00000 128 1 8.0 19.00 8.00 55.00 1.84677 1.00000 -0.00010 1.00000 129 1 8.0 59.00 58.00 80.00 1.84162 1.00000 -0.00010 1.00000 130 1 8.0 16.00 40.00 92.00 1.83828 1.00000 -0.00010 1.00000 131 2 16.0 21.00 42.00 63.00 1.83258 1.00000 -0.00010 1.00000 132 6 48.0 2.00 19.00 69.00 1.82733 1.00000 -0.00010 1.00000 133 1 8.0 25.00 45.00 73.00 1.81604 1.00000 -0.00010 1.00000 134 1 8.0 6.00 10.00 48.00 1.81496 1.00000 -0.00010 1.00000 135 2 16.0 9.00 7.00 43.00 1.80712 1.00000 -0.00010 1.00000 136 1 8.0 36.00 2.00 53.00 1.80667 1.00000 -0.00010 1.00000 137 1 8.0 19.00 43.00 60.00 1.80358 1.00000 -0.00010 1.00000 138 1 8.0 24.00 0.00 25.00 1.80337 1.00000 -0.00010 1.00000 139 2 16.0 25.00 5.00 42.00 1.79990 1.00000 -0.00010 1.00000 140 4 32.0 69.00 18.00 40.00 1.79854 1.00000 -0.00010 1.00000 141 1 8.0 62.00 48.00 85.00 1.79309 1.00000 -0.00010 1.00000 142 4 32.0 61.00 43.00 84.00 1.78916 1.00000 -0.00010 1.00000 143 1 8.0 13.00 13.00 34.00 1.78877 1.00000 -0.00010 1.00000 144 1 8.0 34.00 28.00 78.00 1.78826 1.00000 -0.00010 1.00000 145 3 24.0 69.00 32.00 83.00 1.78152 1.00000 -0.00010 1.00000 146 1 8.0 14.00 11.00 33.00 1.78004 1.00000 -0.00010 1.00000 147 1 8.0 70.00 19.00 25.00 1.77961 1.00000 -0.00010 1.00000 148 1 8.0 24.00 1.00 50.00 1.77625 1.00000 -0.00010 1.00000 149 1 8.0 3.00 35.00 84.00 1.77073 1.00000 -0.00010 1.00000 150 1 8.0 22.00 43.00 64.00 1.77048 1.00000 -0.00010 1.00000 151 1 8.0 25.00 63.00 83.00 1.76957 1.00000 -0.00010 1.00000 152 1 8.0 52.00 57.00 72.00 1.76913 1.00000 -0.00010 1.00000 153 1 8.0 6.00 24.00 31.00 1.76905 1.00000 -0.00010 1.00000 154 1 8.0 7.00 37.00 72.00 1.76885 1.00000 -0.00010 1.00000 155 2 16.0 75.00 24.00 12.00 1.76788 1.00000 -0.00010 1.00000 156 1 8.0 64.00 38.00 42.00 1.76533 1.00000 -0.00010 1.00000 157 1 8.0 54.00 32.00 84.00 1.76446 1.00000 -0.00010 1.00000 158 1 8.0 23.00 38.00 88.00 1.76098 1.00000 -0.00010 1.00000 159 1 8.0 6.00 40.00 33.00 1.75765 1.00000 -0.00010 1.00000 160 1 8.0 22.00 25.00 9.00 1.75009 1.00000 -0.00010 1.00000 161 2 16.0 67.00 3.00 52.00 1.74760 1.00000 -0.00010 1.00000 162 2 16.0 28.00 67.00 70.00 1.74531 1.00000 -0.00010 1.00000 163 1 8.0 4.00 33.00 30.00 1.74303 1.00000 -0.00010 1.00000 164 1 8.0 69.00 20.00 74.00 1.74160 1.00000 -0.00010 1.00000 165 1 8.0 18.00 21.00 55.00 1.74153 1.00000 -0.00010 1.00000 166 2 16.0 31.00 25.00 80.00 1.73939 1.00000 -0.00010 1.00000 167 2 16.0 22.00 40.00 63.00 1.73425 1.00000 -0.00010 1.00000 168 2 16.0 68.00 21.00 74.00 1.72982 1.00000 -0.00010 1.00000 169 2 16.0 7.00 18.00 27.00 1.72964 1.00000 -0.00010 1.00000 170 1 8.0 11.00 29.00 60.00 1.72963 1.00000 -0.00010 1.00000 171 1 8.0 25.00 65.00 86.00 1.72933 1.00000 -0.00010 1.00000 172 1 8.0 40.00 10.00 56.00 1.72897 1.00000 -0.00010 1.00000 173 2 16.0 40.00 56.00 61.00 1.72244 1.00000 -0.00010 1.00000 174 1 8.0 17.00 67.00 74.00 1.72103 1.00000 -0.00010 1.00000 175 1 8.0 42.00 67.00 70.00 1.71913 1.00000 -0.00010 1.00000 176 1 8.0 25.00 64.00 85.00 1.71646 1.00000 -0.00010 1.00000 177 1 8.0 9.00 38.00 73.00 1.71532 1.00000 -0.00010 1.00000 178 1 8.0 4.00 34.00 31.00 1.71458 1.00000 -0.00010 1.00000 179 1 8.0 3.00 22.00 7.00 1.71416 1.00000 -0.00010 1.00000 180 1 8.0 31.00 50.00 89.00 1.71002 1.00000 -0.00010 1.00000 181 1 8.0 51.00 7.00 19.00 1.70870 1.00000 -0.00010 1.00000 182 1 8.0 43.00 1.00 48.00 1.70621 1.00000 -0.00010 1.00000 183 1 8.0 22.00 36.00 41.00 1.70538 1.00000 -0.00010 1.00000 184 1 8.0 1.00 22.00 71.00 1.70431 1.00000 -0.00010 1.00000 185 1 8.0 65.00 20.00 5.00 1.70426 1.00000 -0.00010 1.00000 186 1 8.0 70.00 10.00 43.00 1.70299 1.00000 -0.00010 1.00000 187 1 8.0 11.00 17.00 62.00 1.70210 1.00000 -0.00010 1.00000 188 1 8.0 1.00 21.00 70.00 1.70207 1.00000 -0.00010 1.00000 189 1 8.0 35.00 26.00 63.00 1.70166 1.00000 -0.00010 1.00000 190 1 8.0 11.00 37.00 66.00 1.70059 1.00000 -0.00010 1.00000 191 1 8.0 22.00 37.00 70.00 1.70035 1.00000 -0.00010 1.00000 192 1 8.0 25.00 14.00 22.00 1.69897 1.00000 -0.00010 1.00000
Date: Tue, 25 Jun 2013 12:22:23 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51C9C3BF.7000000@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
can you send the file?
On 06/25/2013 10:08 AM, Emily Boeke wrote:
Hi All,
I'm running Monte Carlo simulations on functional data, and the coordinate information outputted in the cluster.summary file isn't making sense. Usually the coordinates for the clusters listed are Talairach coordinates, but in the .summary files I'm getting, the coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" and the numbers are clearly not Talairach coordinates. Above the table, it says "Reporting Coordinates in Voxel Indices." I also noted that in the descriptive information above the table, it says "Registration: None: Tal Coords invalid."
However, the .nii files I'm seeing look like I would expect them too.
I'm using the same command line I've run before, so I have no idea why the .summary file looks different. Does anyone know why this would be?
Thanks, Emily
Any thoughts on why this file turned out this way?
Thanks! Emily
On Jun 26, 2013, at 8:09 AM, Emily Boeke wrote:
Sure, here it is:
# Cluster Growing Summary (mri_volcluster) # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $ # cwd /autofs/cluster/maury/users/gcoombs/College_Risk/ObjectLooming/allSBQ_061213/st4-obj_ns-4runs/face_v_car # cmdline mri_volcluster --in tal.sm.wls.pct.rfx//group/sig.mgh --csd tal.sm.wls.pct.rfx//csd/HvL.SBQ.2.pos.j001-group.csd --mask tal.sm.wls.pct.rfx//mask.mgh --cwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.mgh --vwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.voxel.mgh --sum tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.summary --ocn tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.ocn.mgh --csdpdf tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.pdf.dat # sysname Linux # hostname compute-0-114 # machine x86_64 # user eboeke01 # Input Volume: tal.sm.wls.pct.rfx//group/sig.mgh # Frame Number: 0 # Minimum Threshold: 2 # Maximum Threshold: inifinity # Threshold Sign: pos # AdjustThreshWhenOneTail 1 # Size Threshold: 0 mm^3 # Size Threshold: 0 voxels # Voxel Size: 8 mm^3 # Registration: None : Tal Coords invalid # Mask Vol: tal.sm.wls.pct.rfx//mask.mgh # Mask Thresh: 0.500000 # Mask Sign: abs # Mask Invert: 0 # AllowDiag: 0 # NClusters 192 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast group # CSD confint 90.000000 # # Reporting Coordinates in Voxel Indices # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ Max# CWP CWPLow CWPHi 1 597 4776.0 30.00 50.00 65.00 5.94673 0.02490 0.02290 0.02690 2 730 5840.0 27.00 28.00 86.00 5.56628 0.00720 0.00610 0.00830 3 1124 8992.0 5.00 18.00 38.00 5.01850 0.00010 0.00000 0.00020 4 259 2072.0 59.00 20.00 78.00 5.01465 0.68360 0.67760 0.68960 5 279 2232.0 18.00 22.00 73.00 3.94952 0.58840 0.58210 0.59470 6 194 1552.0 35.00 66.00 76.00 3.94297 0.93630 0.93320 0.93940 7 664 5312.0 32.00 15.00 60.00 3.68551 0.01400 0.01250 0.01550 8 293 2344.0 28.00 5.00 58.00 3.66686 0.52560 0.51920 0.53200 9 49 392.0 12.00 52.00 58.00 3.63351 1.00000 -0.00010 1.00000 10 150 1200.0 5.00 4.00 28.00 3.62637 0.99560 0.99470 0.99640 11 298 2384.0 12.00 47.00 86.00 3.58250 0.50260 0.49620 0.50900 12 343 2744.0 13.00 39.00 60.00 3.57829 0.33900 0.33290 0.34510 13 467 3736.0 21.00 42.00 49.00 3.53307 0.09590 0.09210 0.09970 14 276 2208.0 49.00 36.00 56.00 3.51549 0.60280 0.59650 0.60910 15 134 1072.0 70.00 17.00 34.00 3.38623 0.99890 0.99850 0.99930 16 75 600.0 5.00 25.00 55.00 3.09334 1.00000 -0.00010 1.00000 17 74 592.0 13.00 10.00 49.00 3.03017 1.00000 -0.00010 1.00000 18 45 360.0 65.00 39.00 62.00 3.00205 1.00000 -0.00010 1.00000 19 15 120.0 72.00 7.00 42.00 2.96283 1.00000 -0.00010 1.00000 20 55 440.0 62.00 9.00 23.00 2.93121 1.00000 -0.00010 1.00000 21 79 632.0 46.00 60.00 87.00 2.92199 1.00000 -0.00010 1.00000 22 35 280.0 2.00 41.00 48.00 2.84065 1.00000 -0.00010 1.00000 23 44 352.0 6.00 35.00 27.00 2.80109 1.00000 -0.00010 1.00000 24 14 112.0 50.00 3.00 54.00 2.75399 1.00000 -0.00010 1.00000 25 71 568.0 0.00 22.00 9.00 2.75160 1.00000 -0.00010 1.00000 26 5 40.0 28.00 0.00 36.00 2.72535 1.00000 -0.00010 1.00000 27 130 1040.0 40.00 1.00 45.00 2.71826 0.99920 0.99880 0.99950 28 81 648.0 33.00 61.00 86.00 2.70040 1.00000 -0.00010 1.00000 29 73 584.0 67.00 26.00 52.00 2.68744 1.00000 -0.00010 1.00000 30 16 128.0 64.00 48.00 72.00 2.67636 1.00000 -0.00010 1.00000 31 28 224.0 75.00 35.00 88.00 2.65193 1.00000 -0.00010 1.00000 32 11 88.0 15.00 21.00 82.00 2.61771 1.00000 -0.00010 1.00000 33 5 40.0 45.00 0.00 27.00 2.61424 1.00000 -0.00010 1.00000 34 16 128.0 9.00 13.00 70.00 2.58842 1.00000 -0.00010 1.00000 35 23 184.0 15.00 27.00 48.00 2.57410 1.00000 -0.00010 1.00000 36 28 224.0 15.00 31.00 44.00 2.57219 1.00000 -0.00010 1.00000 37 23 184.0 29.00 56.00 78.00 2.55890 1.00000 -0.00010 1.00000 38 7 56.0 0.00 42.00 92.00 2.55525 1.00000 -0.00010 1.00000 39 49 392.0 52.00 40.00 88.00 2.54894 1.00000 -0.00010 1.00000 40 42 336.0 7.00 31.00 63.00 2.52160 1.00000 -0.00010 1.00000 41 37 296.0 22.00 43.00 81.00 2.50557 1.00000 -0.00010 1.00000 42 21 168.0 22.00 58.00 72.00 2.49912 1.00000 -0.00010 1.00000 43 32 256.0 59.00 45.00 91.00 2.44918 1.00000 -0.00010 1.00000 44 12 96.0 31.00 29.00 36.00 2.42939 1.00000 -0.00010 1.00000 45 50 400.0 14.00 34.00 26.00 2.42102 1.00000 -0.00010 1.00000 46 22 176.0 6.00 15.00 55.00 2.41349 1.00000 -0.00010 1.00000 47 12 96.0 9.00 43.00 42.00 2.40593 1.00000 -0.00010 1.00000 48 27 216.0 64.00 17.00 31.00 2.38351 1.00000 -0.00010 1.00000 49 16 128.0 25.00 49.00 81.00 2.37500 1.00000 -0.00010 1.00000 50 37 296.0 12.00 18.00 54.00 2.36836 1.00000 -0.00010 1.00000 51 22 176.0 43.00 50.00 63.00 2.35072 1.00000 -0.00010 1.00000 52 39 312.0 31.00 39.00 46.00 2.31633 1.00000 -0.00010 1.00000 53 7 56.0 75.00 60.00 84.00 2.28945 1.00000 -0.00010 1.00000 54 6 48.0 33.00 25.00 67.00 2.28154 1.00000 -0.00010 1.00000 55 10 80.0 49.00 40.00 33.00 2.27301 1.00000 -0.00010 1.00000 56 13 104.0 26.00 65.00 88.00 2.27017 1.00000 -0.00010 1.00000 57 6 48.0 13.00 25.00 26.00 2.26583 1.00000 -0.00010 1.00000 58 15 120.0 54.00 9.00 20.00 2.25868 1.00000 -0.00010 1.00000 59 16 128.0 63.00 14.00 19.00 2.21490 1.00000 -0.00010 1.00000 60 4 32.0 9.00 25.00 61.00 2.21056 1.00000 -0.00010 1.00000 61 37 296.0 25.00 37.00 62.00 2.21055 1.00000 -0.00010 1.00000 62 10 80.0 59.00 51.00 51.00 2.20982 1.00000 -0.00010 1.00000 63 20 160.0 66.00 41.00 51.00 2.19863 1.00000 -0.00010 1.00000 64 2 16.0 53.00 66.00 72.00 2.18410 1.00000 -0.00010 1.00000 65 9 72.0 37.00 38.00 66.00 2.17739 1.00000 -0.00010 1.00000 66 6 48.0 6.00 44.00 62.00 2.17461 1.00000 -0.00010 1.00000 67 39 312.0 50.00 35.00 70.00 2.16322 1.00000 -0.00010 1.00000 68 11 88.0 52.00 6.00 21.00 2.16002 1.00000 -0.00010 1.00000 69 6 48.0 26.00 0.00 43.00 2.15030 1.00000 -0.00010 1.00000 70 8 64.0 41.00 16.00 19.00 2.14875 1.00000 -0.00010 1.00000 71 4 32.0 51.00 8.00 39.00 2.14592 1.00000 -0.00010 1.00000 72 3 24.0 47.00 9.00 21.00 2.14285 1.00000 -0.00010 1.00000 73 8 64.0 67.00 19.00 27.00 2.14034 1.00000 -0.00010 1.00000 74 12 96.0 3.00 59.00 86.00 2.13879 1.00000 -0.00010 1.00000 75 3 24.0 15.00 6.00 19.00 2.13024 1.00000 -0.00010 1.00000 76 9 72.0 59.00 41.00 41.00 2.12204 1.00000 -0.00010 1.00000 77 18 144.0 35.00 48.00 55.00 2.10334 1.00000 -0.00010 1.00000 78 6 48.0 40.00 57.00 92.00 2.08841 1.00000 -0.00010 1.00000 79 7 56.0 43.00 1.00 17.00 2.07371 1.00000 -0.00010 1.00000 80 6 48.0 41.00 55.00 69.00 2.07007 1.00000 -0.00010 1.00000 81 14 112.0 23.00 35.00 88.00 2.06307 1.00000 -0.00010 1.00000 82 11 88.0 40.00 73.00 82.00 2.05213 1.00000 -0.00010 1.00000 83 5 40.0 39.00 19.00 51.00 2.04809 1.00000 -0.00010 1.00000 84 10 80.0 38.00 24.00 69.00 2.04252 1.00000 -0.00010 1.00000 85 9 72.0 30.00 32.00 67.00 2.04237 1.00000 -0.00010 1.00000 86 7 56.0 54.00 58.00 72.00 2.03645 1.00000 -0.00010 1.00000 87 10 80.0 30.00 13.00 22.00 2.03577 1.00000 -0.00010 1.00000 88 8 64.0 0.00 25.00 72.00 2.03193 1.00000 -0.00010 1.00000 89 5 40.0 7.00 23.00 6.00 2.02805 1.00000 -0.00010 1.00000 90 4 32.0 59.00 28.00 21.00 2.02245 1.00000 -0.00010 1.00000 91 11 88.0 43.00 18.00 63.00 2.01764 1.00000 -0.00010 1.00000 92 5 40.0 14.00 41.00 87.00 2.01255 1.00000 -0.00010 1.00000 93 3 24.0 28.00 50.00 55.00 2.01226 1.00000 -0.00010 1.00000 94 6 48.0 35.00 0.00 43.00 1.99869 1.00000 -0.00010 1.00000 95 1 8.0 59.00 57.00 79.00 1.99505 1.00000 -0.00010 1.00000 96 1 8.0 25.00 2.00 51.00 1.99394 1.00000 -0.00010 1.00000 97 4 32.0 55.00 4.00 36.00 1.98505 1.00000 -0.00010 1.00000 98 2 16.0 66.00 21.00 6.00 1.97461 1.00000 -0.00010 1.00000 99 3 24.0 31.00 51.00 90.00 1.97154 1.00000 -0.00010 1.00000 100 3 24.0 12.00 11.00 23.00 1.95664 1.00000 -0.00010 1.00000 101 5 40.0 38.00 43.00 50.00 1.95222 1.00000 -0.00010 1.00000 102 2 16.0 28.00 22.00 7.00 1.95066 1.00000 -0.00010 1.00000 103 4 32.0 20.00 17.00 69.00 1.94669 1.00000 -0.00010 1.00000 104 5 40.0 1.00 8.00 46.00 1.94587 1.00000 -0.00010 1.00000 105 4 32.0 42.00 15.00 49.00 1.94354 1.00000 -0.00010 1.00000 106 4 32.0 4.00 41.00 54.00 1.93906 1.00000 -0.00010 1.00000 107 3 24.0 15.00 9.00 33.00 1.93848 1.00000 -0.00010 1.00000 108 6 48.0 61.00 28.00 72.00 1.92516 1.00000 -0.00010 1.00000 109 1 8.0 49.00 26.00 88.00 1.92457 1.00000 -0.00010 1.00000 110 3 24.0 65.00 37.00 41.00 1.92365 1.00000 -0.00010 1.00000 111 3 24.0 69.00 29.00 25.00 1.91576 1.00000 -0.00010 1.00000 112 2 16.0 70.00 15.00 9.00 1.89931 1.00000 -0.00010 1.00000 113 2 16.0 65.00 24.00 70.00 1.89719 1.00000 -0.00010 1.00000 114 1 8.0 41.00 24.00 36.00 1.89653 1.00000 -0.00010 1.00000 115 7 56.0 71.00 32.00 91.00 1.89529 1.00000 -0.00010 1.00000 116 6 48.0 24.00 38.00 69.00 1.88993 1.00000 -0.00010 1.00000 117 4 32.0 6.00 22.00 34.00 1.88833 1.00000 -0.00010 1.00000 118 3 24.0 41.00 45.00 51.00 1.87881 1.00000 -0.00010 1.00000 119 2 16.0 18.00 58.00 91.00 1.87841 1.00000 -0.00010 1.00000 120 3 24.0 44.00 10.00 17.00 1.87792 1.00000 -0.00010 1.00000 121 4 32.0 7.00 38.00 71.00 1.87444 1.00000 -0.00010 1.00000 122 2 16.0 39.00 12.00 65.00 1.87242 1.00000 -0.00010 1.00000 123 7 56.0 25.00 35.00 38.00 1.87054 1.00000 -0.00010 1.00000 124 3 24.0 14.00 28.00 25.00 1.86776 1.00000 -0.00010 1.00000 125 4 32.0 64.00 23.00 76.00 1.86629 1.00000 -0.00010 1.00000 126 7 56.0 58.00 44.00 43.00 1.86598 1.00000 -0.00010 1.00000 127 1 8.0 40.00 44.00 63.00 1.86487 1.00000 -0.00010 1.00000 128 1 8.0 19.00 8.00 55.00 1.84677 1.00000 -0.00010 1.00000 129 1 8.0 59.00 58.00 80.00 1.84162 1.00000 -0.00010 1.00000 130 1 8.0 16.00 40.00 92.00 1.83828 1.00000 -0.00010 1.00000 131 2 16.0 21.00 42.00 63.00 1.83258 1.00000 -0.00010 1.00000 132 6 48.0 2.00 19.00 69.00 1.82733 1.00000 -0.00010 1.00000 133 1 8.0 25.00 45.00 73.00 1.81604 1.00000 -0.00010 1.00000 134 1 8.0 6.00 10.00 48.00 1.81496 1.00000 -0.00010 1.00000 135 2 16.0 9.00 7.00 43.00 1.80712 1.00000 -0.00010 1.00000 136 1 8.0 36.00 2.00 53.00 1.80667 1.00000 -0.00010 1.00000 137 1 8.0 19.00 43.00 60.00 1.80358 1.00000 -0.00010 1.00000 138 1 8.0 24.00 0.00 25.00 1.80337 1.00000 -0.00010 1.00000 139 2 16.0 25.00 5.00 42.00 1.79990 1.00000 -0.00010 1.00000 140 4 32.0 69.00 18.00 40.00 1.79854 1.00000 -0.00010 1.00000 141 1 8.0 62.00 48.00 85.00 1.79309 1.00000 -0.00010 1.00000 142 4 32.0 61.00 43.00 84.00 1.78916 1.00000 -0.00010 1.00000 143 1 8.0 13.00 13.00 34.00 1.78877 1.00000 -0.00010 1.00000 144 1 8.0 34.00 28.00 78.00 1.78826 1.00000 -0.00010 1.00000 145 3 24.0 69.00 32.00 83.00 1.78152 1.00000 -0.00010 1.00000 146 1 8.0 14.00 11.00 33.00 1.78004 1.00000 -0.00010 1.00000 147 1 8.0 70.00 19.00 25.00 1.77961 1.00000 -0.00010 1.00000 148 1 8.0 24.00 1.00 50.00 1.77625 1.00000 -0.00010 1.00000 149 1 8.0 3.00 35.00 84.00 1.77073 1.00000 -0.00010 1.00000 150 1 8.0 22.00 43.00 64.00 1.77048 1.00000 -0.00010 1.00000 151 1 8.0 25.00 63.00 83.00 1.76957 1.00000 -0.00010 1.00000 152 1 8.0 52.00 57.00 72.00 1.76913 1.00000 -0.00010 1.00000 153 1 8.0 6.00 24.00 31.00 1.76905 1.00000 -0.00010 1.00000 154 1 8.0 7.00 37.00 72.00 1.76885 1.00000 -0.00010 1.00000 155 2 16.0 75.00 24.00 12.00 1.76788 1.00000 -0.00010 1.00000 156 1 8.0 64.00 38.00 42.00 1.76533 1.00000 -0.00010 1.00000 157 1 8.0 54.00 32.00 84.00 1.76446 1.00000 -0.00010 1.00000 158 1 8.0 23.00 38.00 88.00 1.76098 1.00000 -0.00010 1.00000 159 1 8.0 6.00 40.00 33.00 1.75765 1.00000 -0.00010 1.00000 160 1 8.0 22.00 25.00 9.00 1.75009 1.00000 -0.00010 1.00000 161 2 16.0 67.00 3.00 52.00 1.74760 1.00000 -0.00010 1.00000 162 2 16.0 28.00 67.00 70.00 1.74531 1.00000 -0.00010 1.00000 163 1 8.0 4.00 33.00 30.00 1.74303 1.00000 -0.00010 1.00000 164 1 8.0 69.00 20.00 74.00 1.74160 1.00000 -0.00010 1.00000 165 1 8.0 18.00 21.00 55.00 1.74153 1.00000 -0.00010 1.00000 166 2 16.0 31.00 25.00 80.00 1.73939 1.00000 -0.00010 1.00000 167 2 16.0 22.00 40.00 63.00 1.73425 1.00000 -0.00010 1.00000 168 2 16.0 68.00 21.00 74.00 1.72982 1.00000 -0.00010 1.00000 169 2 16.0 7.00 18.00 27.00 1.72964 1.00000 -0.00010 1.00000 170 1 8.0 11.00 29.00 60.00 1.72963 1.00000 -0.00010 1.00000 171 1 8.0 25.00 65.00 86.00 1.72933 1.00000 -0.00010 1.00000 172 1 8.0 40.00 10.00 56.00 1.72897 1.00000 -0.00010 1.00000 173 2 16.0 40.00 56.00 61.00 1.72244 1.00000 -0.00010 1.00000 174 1 8.0 17.00 67.00 74.00 1.72103 1.00000 -0.00010 1.00000 175 1 8.0 42.00 67.00 70.00 1.71913 1.00000 -0.00010 1.00000 176 1 8.0 25.00 64.00 85.00 1.71646 1.00000 -0.00010 1.00000 177 1 8.0 9.00 38.00 73.00 1.71532 1.00000 -0.00010 1.00000 178 1 8.0 4.00 34.00 31.00 1.71458 1.00000 -0.00010 1.00000 179 1 8.0 3.00 22.00 7.00 1.71416 1.00000 -0.00010 1.00000 180 1 8.0 31.00 50.00 89.00 1.71002 1.00000 -0.00010 1.00000 181 1 8.0 51.00 7.00 19.00 1.70870 1.00000 -0.00010 1.00000 182 1 8.0 43.00 1.00 48.00 1.70621 1.00000 -0.00010 1.00000 183 1 8.0 22.00 36.00 41.00 1.70538 1.00000 -0.00010 1.00000 184 1 8.0 1.00 22.00 71.00 1.70431 1.00000 -0.00010 1.00000 185 1 8.0 65.00 20.00 5.00 1.70426 1.00000 -0.00010 1.00000 186 1 8.0 70.00 10.00 43.00 1.70299 1.00000 -0.00010 1.00000 187 1 8.0 11.00 17.00 62.00 1.70210 1.00000 -0.00010 1.00000 188 1 8.0 1.00 21.00 70.00 1.70207 1.00000 -0.00010 1.00000 189 1 8.0 35.00 26.00 63.00 1.70166 1.00000 -0.00010 1.00000 190 1 8.0 11.00 37.00 66.00 1.70059 1.00000 -0.00010 1.00000 191 1 8.0 22.00 37.00 70.00 1.70035 1.00000 -0.00010 1.00000 192 1 8.0 25.00 14.00 22.00 1.69897 1.00000 -0.00010 1.00000
Date: Tue, 25 Jun 2013 12:22:23 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51C9C3BF.7000000@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
can you send the file?
On 06/25/2013 10:08 AM, Emily Boeke wrote:
Hi All,
I'm running Monte Carlo simulations on functional data, and the coordinate information outputted in the cluster.summary file isn't making sense. Usually the coordinates for the clusters listed are Talairach coordinates, but in the .summary files I'm getting, the coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" and the numbers are clearly not Talairach coordinates. Above the table, it says "Reporting Coordinates in Voxel Indices." I also noted that in the descriptive information above the table, it says "Registration: None: Tal Coords invalid."
However, the .nii files I'm seeing look like I would expect them too.
I'm using the same command line I've run before, so I have no idea why the .summary file looks different. Does anyone know why this would be?
Thanks, Emily
Hi Emily, what is your mri_glmfit-sim command line? doug
On 06/28/2013 02:40 PM, Emily Boeke wrote:
Any thoughts on why this file turned out this way?
Thanks! Emily
On Jun 26, 2013, at 8:09 AM, Emily Boeke wrote:
Sure, here it is:
# Cluster Growing Summary (mri_volcluster) # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $ # cwd /autofs/cluster/maury/users/gcoombs/College_Risk/ObjectLooming/allSBQ_061213/st4-obj_ns-4runs/face_v_car # cmdline mri_volcluster --in tal.sm.wls.pct.rfx//group/sig.mgh --csd tal.sm.wls.pct.rfx//csd/HvL.SBQ.2.pos.j001-group.csd --mask tal.sm.wls.pct.rfx//mask.mgh --cwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.mgh --vwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.voxel.mgh --sum tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.summary --ocn tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.ocn.mgh --csdpdf tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.pdf.dat # sysname Linux # hostname compute-0-114 # machine x86_64 # user eboeke01 # Input Volume: tal.sm.wls.pct.rfx//group/sig.mgh # Frame Number: 0 # Minimum Threshold: 2 # Maximum Threshold: inifinity # Threshold Sign: pos # AdjustThreshWhenOneTail 1 # Size Threshold: 0 mm^3 # Size Threshold: 0 voxels # Voxel Size: 8 mm^3 # Registration: None : Tal Coords invalid # Mask Vol: tal.sm.wls.pct.rfx//mask.mgh # Mask Thresh: 0.500000 # Mask Sign: abs # Mask Invert: 0 # AllowDiag: 0 # NClusters 192 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast group # CSD confint 90.000000 # # Reporting Coordinates in Voxel Indices # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ Max# CWP CWPLow CWPHi 1 597 4776.0 30.00 50.00 65.00 5.94673 0.02490 0.02290 0.02690 2 730 5840.0 27.00 28.00 86.00 5.56628 0.00720 0.00610 0.00830 3 1124 8992.0 5.00 18.00 38.00 5.01850 0.00010 0.00000 0.00020 4 259 2072.0 59.00 20.00 78.00 5.01465 0.68360 0.67760 0.68960 5 279 2232.0 18.00 22.00 73.00 3.94952 0.58840 0.58210 0.59470 6 194 1552.0 35.00 66.00 76.00 3.94297 0.93630 0.93320 0.93940 7 664 5312.0 32.00 15.00 60.00 3.68551 0.01400 0.01250 0.01550 8 293 2344.0 28.00 5.00 58.00 3.66686 0.52560 0.51920 0.53200 9 49 392.0 12.00 52.00 58.00 3.63351 1.00000 -0.00010 1.00000 10 150 1200.0 5.00 4.00 28.00 3.62637 0.99560 0.99470 0.99640 11 298 2384.0 12.00 47.00 86.00 3.58250 0.50260 0.49620 0.50900 12 343 2744.0 13.00 39.00 60.00 3.57829 0.33900 0.33290 0.34510 13 467 3736.0 21.00 42.00 49.00 3.53307 0.09590 0.09210 0.09970 14 276 2208.0 49.00 36.00 56.00 3.51549 0.60280 0.59650 0.60910 15 134 1072.0 70.00 17.00 34.00 3.38623 0.99890 0.99850 0.99930 16 75 600.0 5.00 25.00 55.00 3.09334 1.00000 -0.00010 1.00000 17 74 592.0 13.00 10.00 49.00 3.03017 1.00000 -0.00010 1.00000 18 45 360.0 65.00 39.00 62.00 3.00205 1.00000 -0.00010 1.00000 19 15 120.0 72.00 7.00 42.00 2.96283 1.00000 -0.00010 1.00000 20 55 440.0 62.00 9.00 23.00 2.93121 1.00000 -0.00010 1.00000 21 79 632.0 46.00 60.00 87.00 2.92199 1.00000 -0.00010 1.00000 22 35 280.0 2.00 41.00 48.00 2.84065 1.00000 -0.00010 1.00000 23 44 352.0 6.00 35.00 27.00 2.80109 1.00000 -0.00010 1.00000 24 14 112.0 50.00 3.00 54.00 2.75399 1.00000 -0.00010 1.00000 25 71 568.0 0.00 22.00 9.00 2.75160 1.00000 -0.00010 1.00000 26 5 40.0 28.00 0.00 36.00 2.72535 1.00000 -0.00010 1.00000 27 130 1040.0 40.00 1.00 45.00 2.71826 0.99920 0.99880 0.99950 28 81 648.0 33.00 61.00 86.00 2.70040 1.00000 -0.00010 1.00000 29 73 584.0 67.00 26.00 52.00 2.68744 1.00000 -0.00010 1.00000 30 16 128.0 64.00 48.00 72.00 2.67636 1.00000 -0.00010 1.00000 31 28 224.0 75.00 35.00 88.00 2.65193 1.00000 -0.00010 1.00000 32 11 88.0 15.00 21.00 82.00 2.61771 1.00000 -0.00010 1.00000 33 5 40.0 45.00 0.00 27.00 2.61424 1.00000 -0.00010 1.00000 34 16 128.0 9.00 13.00 70.00 2.58842 1.00000 -0.00010 1.00000 35 23 184.0 15.00 27.00 48.00 2.57410 1.00000 -0.00010 1.00000 36 28 224.0 15.00 31.00 44.00 2.57219 1.00000 -0.00010 1.00000 37 23 184.0 29.00 56.00 78.00 2.55890 1.00000 -0.00010 1.00000 38 7 56.0 0.00 42.00 92.00 2.55525 1.00000 -0.00010 1.00000 39 49 392.0 52.00 40.00 88.00 2.54894 1.00000 -0.00010 1.00000 40 42 336.0 7.00 31.00 63.00 2.52160 1.00000 -0.00010 1.00000 41 37 296.0 22.00 43.00 81.00 2.50557 1.00000 -0.00010 1.00000 42 21 168.0 22.00 58.00 72.00 2.49912 1.00000 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Date: Tue, 25 Jun 2013 12:22:23 -0400 From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <51C9C3BF.7000000@nmr.mgh.harvard.edu mailto:51C9C3BF.7000000@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
can you send the file?
On 06/25/2013 10:08 AM, Emily Boeke wrote:
Hi All,
I'm running Monte Carlo simulations on functional data, and the coordinate information outputted in the cluster.summary file isn't making sense. Usually the coordinates for the clusters listed are Talairach coordinates, but in the .summary files I'm getting, the coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" and the numbers are clearly not Talairach coordinates. Above the table, it says "Reporting Coordinates in Voxel Indices." I also noted that in the descriptive information above the table, it says "Registration: None: Tal Coords invalid."
However, the .nii files I'm seeing look like I would expect them too.
I'm using the same command line I've run before, so I have no idea why the .summary file looks different. Does anyone know why this would be?
Thanks, Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This was the command I ran:
mri_glmfit-sim --glmdir tal.sm.wls.pct.rfx --sim mc-z 10000 2 HvL.SBQ.2.10000.pos --stim-sign pos
On Jun 28, 2013, at 3:29 PM, Douglas N Greve wrote:
Hi Emily, what is your mri_glmfit-sim command line? doug
On 06/28/2013 02:40 PM, Emily Boeke wrote:
Any thoughts on why this file turned out this way?
Thanks! Emily
On Jun 26, 2013, at 8:09 AM, Emily Boeke wrote:
Sure, here it is:
# Cluster Growing Summary (mri_volcluster) # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $ # cwd /autofs/cluster/maury/users/gcoombs/College_Risk/ObjectLooming/allSBQ_061213/st4-obj_ns-4runs/face_v_car # cmdline mri_volcluster --in tal.sm.wls.pct.rfx//group/sig.mgh --csd tal.sm.wls.pct.rfx//csd/HvL.SBQ.2.pos.j001-group.csd --mask tal.sm.wls.pct.rfx//mask.mgh --cwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.mgh --vwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.voxel.mgh --sum tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.summary --ocn tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.ocn.mgh --csdpdf tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.pdf.dat # sysname Linux # hostname compute-0-114 # machine x86_64 # user eboeke01 # Input Volume: tal.sm.wls.pct.rfx//group/sig.mgh # Frame Number: 0 # Minimum Threshold: 2 # Maximum Threshold: inifinity # Threshold Sign: pos # AdjustThreshWhenOneTail 1 # Size Threshold: 0 mm^3 # Size Threshold: 0 voxels # Voxel Size: 8 mm^3 # Registration: None : Tal Coords invalid # Mask Vol: tal.sm.wls.pct.rfx//mask.mgh # Mask Thresh: 0.500000 # Mask Sign: abs # Mask Invert: 0 # AllowDiag: 0 # NClusters 192 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast group # CSD confint 90.000000 # # Reporting Coordinates in Voxel Indices # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ Max# CWP CWPLow CWPHi 1 597 4776.0 30.00 50.00 65.00 5.94673 0.02490 0.02290 0.02690 2 730 5840.0 27.00 28.00 86.00 5.56628 0.00720 0.00610 0.00830 3 1124 8992.0 5.00 18.00 38.00 5.01850 0.00010 0.00000 0.00020 4 259 2072.0 59.00 20.00 78.00 5.01465 0.68360 0.67760 0.68960 5 279 2232.0 18.00 22.00 73.00 3.94952 0.58840 0.58210 0.59470 6 194 1552.0 35.00 66.00 76.00 3.94297 0.93630 0.93320 0.93940 7 664 5312.0 32.00 15.00 60.00 3.68551 0.01400 0.01250 0.01550 8 293 2344.0 28.00 5.00 58.00 3.66686 0.52560 0.51920 0.53200 9 49 392.0 12.00 52.00 58.00 3.63351 1.00000 -0.00010 1.00000 10 150 1200.0 5.00 4.00 28.00 3.62637 0.99560 0.99470 0.99640 11 298 2384.0 12.00 47.00 86.00 3.58250 0.50260 0.49620 0.50900 12 343 2744.0 13.00 39.00 60.00 3.57829 0.33900 0.33290 0.34510 13 467 3736.0 21.00 42.00 49.00 3.53307 0.09590 0.09210 0.09970 14 276 2208.0 49.00 36.00 56.00 3.51549 0.60280 0.59650 0.60910 15 134 1072.0 70.00 17.00 34.00 3.38623 0.99890 0.99850 0.99930 16 75 600.0 5.00 25.00 55.00 3.09334 1.00000 -0.00010 1.00000 17 74 592.0 13.00 10.00 49.00 3.03017 1.00000 -0.00010 1.00000 18 45 360.0 65.00 39.00 62.00 3.00205 1.00000 -0.00010 1.00000 19 15 120.0 72.00 7.00 42.00 2.96283 1.00000 -0.00010 1.00000 20 55 440.0 62.00 9.00 23.00 2.93121 1.00000 -0.00010 1.00000 21 79 632.0 46.00 60.00 87.00 2.92199 1.00000 -0.00010 1.00000 22 35 280.0 2.00 41.00 48.00 2.84065 1.00000 -0.00010 1.00000 23 44 352.0 6.00 35.00 27.00 2.80109 1.00000 -0.00010 1.00000 24 14 112.0 50.00 3.00 54.00 2.75399 1.00000 -0.00010 1.00000 25 71 568.0 0.00 22.00 9.00 2.75160 1.00000 -0.00010 1.00000 26 5 40.0 28.00 0.00 36.00 2.72535 1.00000 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Date: Tue, 25 Jun 2013 12:22:23 -0400 From: Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <51C9C3BF.7000000@nmr.mgh.harvard.edu mailto:51C9C3BF.7000000@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
can you send the file?
On 06/25/2013 10:08 AM, Emily Boeke wrote:
Hi All,
I'm running Monte Carlo simulations on functional data, and the coordinate information outputted in the cluster.summary file isn't making sense. Usually the coordinates for the clusters listed are Talairach coordinates, but in the .summary files I'm getting, the coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" and the numbers are clearly not Talairach coordinates. Above the table, it says "Reporting Coordinates in Voxel Indices." I also noted that in the descriptive information above the table, it says "Registration: None: Tal Coords invalid."
However, the .nii files I'm seeing look like I would expect them too.
I'm using the same command line I've run before, so I have no idea why the .summary file looks different. Does anyone know why this would be?
Thanks, Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Emily Boeke