# 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.eduMessage-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