Hi Steve & fellow FSLers,
I tried following your recommendation of using --minclustersize=XXX. However, output table still give me the same table regardless of what I put as minclustersize (e.g. 27 vs 123). See below for table output...
How do I use --minclustersize option? If I do cluster -h, --minclustersize has the following description, but nothing else: --minclustersize prints out minimum significant cluster size
Thanks for your help in advance!
[puku:stats] (nmr-stable5.1-env) cluster --in=zstat1.nii.gz --thresh=2.3 --minclustersize=27
Cluster Index Voxels Z-MAX Z-MAX X (vox) Z-MAX Y (vox) Z-MAX Z (vox) Z-COG X (vox) Z-COG Y (vox) Z-COG Z (vox)
158 772 3.54 28 90 47 26.7 85.7 46.6
157 255 3.22 61 15 33 63.1 17.3 38.4
156 249 3.15 21 33 37 23.5 32 38.6
155 156 3.25 66 54 69 66.9 60.2 67.2
154 151 3.43 33 14 34 33.3 13.7 37
153 143 3.4 32 19 56 32.4 19.2 56.2
152 111 2.88 37 98 43 37.8 95.5 40.7
151 99 3.24 60 16 51 60 16.4 50.4
150 90 3.07 25 38 68 27.8 39.9 66.7
149 80 3.26 38 75 70 36.3 76.9 68.2
148 79 3.37 56 33 72 56.9 30.7 70.6
147 75 3.19 62 71 50 62.4 73.3 47.9
146 57 3.06 23 19 36 23.7 19.9 34.4
145 52 3.23 26 69 69 24.6 69.3 67
144 48 2.79 58 38 62 58.1 38.6 62.9
143 48 3.05 74 38 44 74.6 39.7 43.4
142 48 3.69 51 89 23 49.4 91.1 23.5
141 45 2.91 31 41 74 33.1 38.6 70.6
140 38 3.11 21 27 44 20.7 26.9 43.8
139 36 2.93 60 47 27 60.6 47.5 27.2
138 33 2.62 20 73 38 18 70.5 38.1
137 32 2.85 60 91 49 60.3 90.2 48.8
136 31 2.8 43 76 59 44.1 75.6 60.1
135 28 2.99 65 72 65 65.1 71.6 64.8
134 28 2.9 37 74 57 37.5 74.2 57.7
133 27 2.68 48 70 57 47.5 69.7 57.3
132 24 3.37 52 79 67 51.6 79.7 66.8
131 24 2.91 57 60 62 57.6 60.1 62.5
130 24 2.66 35 26 55 34.7 26.1 55.4
129 24 2.87 29 73 46 29.2 73.2 46.5
128 24 2.9 71 29 31 70.8 28.8 30.8
127 23 2.71 65 35 28 64.9 36.3 28.9
126 22 2.62 56 89 43 55.4 88.9 43.8
125 21 3.03 32 71 71 31.2 69.8 70.7
124 21 2.62 19 68 52 19.9 67.5 53.3
123 21 3.07 78 51 52 77.8 50.3 51.6
122 20 2.72 16 70 57 17 69.8 58.2
121 19 2.93 42 85 57 42.3 85.7 56.6
120 18 2.67 64 60 27 64 60 27
119 17 2.65 61 45 73 61.2 45.3 72.2
118 17 3.02 76 44 59 76 44.8 59.5
117 17 2.85 35 79 56 34.4 78.6 56.7
116 16 2.87 12 56 55 12.7 55.4 55.3
115 16 2.78 56 13 46 56.3 13.6 46.2
114 16 2.63 41 48 40 40.2 47.6 39.8
113 16 2.66 50 20 28 50.1 21.1 27.9
112 14 2.75 38 88 57 37.6 87.9 56.9
111 13 2.66 29 60 63 29 59.6 62.6
110 13 2.59 74 54 54 73.7 54 53.3
109 13 2.93 34 64 37 34.2 64.2 37.4
108 12 2.61 37 81 66 36.7 81.9 64.9
107 12 2.82 74 72 51 73.6 71.9 50.7
106 12 2.77 52 93 43 52.3 92.6 42.9
105 11 2.48 24 56 70 23.5 56.5 69.5
104 11 2.64 17 50 62 17.7 49.6 62.2
103 11 2.61 50 10 41 50 9.74 40.9
102 11 2.55 58 87 26 60.2 88 26.2
101 10 2.6 64 56 61 63.8 56 60.9
100 10 2.76 70 51 56 69.6 50.9 55.9
99 10 2.46 48 84 44 49 84.9 43.9
98 9 2.63 23 62 62 23.2 61.8 61.9
97 9 2.73 39 13 47 38.3 12.9 47
96 9 2.58 45 24 27 45.3 24 27
95 9 3.05 37 94 25 36.7 93.9 25.4
94 8 2.57 31 35 65 30 35.4 64.6
93 8 2.58 13 66 38 12.5 66.2 38.4
92 8 2.98 40 80 23 39.5 81 22.6
91 7 2.61 15 70 50 15.4 69.9 50.3
90 7 2.45 17 74 50 16.8 73.9 49.9
89 7 2.51 16 44 50 15.6 44.3 49.3
88 7 2.57 65 56 47 65.3 55.7 46.3
87 7 2.72 63 91 42 62.6 90.6 41.6
86 7 2.45 26 76 38 26 75.7 38.1
85 7 2.56 60 33 29 58.6 31.9 29.7
84 7 2.69 47 29 27 46.6 28.6 26.4
83 6 2.51 39 37 65 38.5 36.7 65.2
82 6 2.48 49 93 49 48.7 93.3 48.5
81 6 2.57 36 79 47 35 78.8 47.7
80 6 2.44 12 69 46 12.7 69.7 46.2
79 6 2.6 66 39 42 66.2 38.5 42.2
78 6 2.52 51 13 34 50.5 12.5 34.2
77 6 2.57 15 47 24 15 47.5 24
76 6 2.64 32 85 24 32.5 85.8 23.8
75 6 3.07 33 84 22 32.7 82.6 22
74 5 2.47 27 47 59 26.8 47 58.8
73 5 2.44 73 50 56 73.8 50.4 56.4
72 5 2.54 55 21 49 54.4 20.2 49.8
71 5 2.57 67 45 47 67.2 44.4 46.4
70 5 2.62 52 95 46 52.2 95.2 46
69 5 2.43 30 29 43 30.8 29.2 43.2
68 5 2.49 68 61 39 68 61.4 38.6
67 5 2.65 64 52 25 64.4 51.8 25
66 4 2.53 67 40 68 67 40.5 67.5
65 4 2.44 17 53 54 16.3 53.5 53.7
64 4 2.49 15 69 47 15.2 68.7 47.2
63 4 2.42 59 28 48 58.8 27.5 47.7
62 4 2.46 42 90 40 42.2 90.5 39.8
61 4 2.42 18 28 38 18.5 27.8 37.5
60 4 2.46 62 92 36 62 91.7 36
59 4 2.83 47 97 32 47.3 97.3 32
58 4 2.42 59 36 29 59.5 35.8 29.2
57 3 2.37 43 58 71 43 58.3 70.3
56 3 2.4 27 67 54 27.3 67.7 54
55 3 2.59 63 85 52 63 84 52
54 3 2.36 71 65 35 71.3 65.3 34.3
53 3 2.41 46 51 35 46 50.7 34.7
52 3 2.49 25 31 34 24.4 31.6 33.7
51 3 2.38 67 60 32 67.7 60 31
50 3 2.42 21 92 30 21.7 92 29.7
49 3 2.41 20 35 25 20.3 35.3 25
48 3 2.5 41 91 24 41 91 23.7
47 2 2.46 22 42 70 22.5 42 70
46 2 2.38 64 35 67 64.5 35 67
45 2 2.33 17 59 63 17 58.5 63
44 2 2.39 42 70 61 42 70.5 61
43 2 2.32 43 72 57 43 71.5 57
42 2 2.36 66 40 56 65.5 40 55.5
41 2 2.43 41 95 50 40.5 94.5 50
40 2 2.49 68 82 50 68 82 50.5
39 2 2.47 27 82 42 26.5 82 42
38 2 2.41 39 13 42 39 12.5 42
37 2 2.44 66 63 41 66 63 41.5
36 2 2.37 57 43 41 57 43.5 41
35 2 2.37 54 31 38 54 31.5 38
34 2 2.53 74 73 37 74.5 73 37.5
33 2 2.49 10 46 36 10 46.5 36
32 2 2.34 75 72 34 75 72.5 34.5
31 2 2.45 32 22 31 32 22 31.5
30 2 2.66 21 29 29 20.5 29 29
29 2 2.45 41 95 28 41 95 28.5
28 1 2.43 64 40 70 64 40 70
27 1 2.31 55 76 68 55 76 68
26 1 2.32 66 60 66 66 60 66
25 1 2.33 33 34 66 33 34 66
24 1 2.42 73 58 63 73 58 63
23 1 2.33 14 50 57 14 50 57
22 1 2.34 15 71 53 15 71 53
21 1 2.34 40 83 52 40 83 52
20 1 2.41 13 41 50 13 41 50
19 1 2.32 61 22 47 61 22 47
18 1 2.36 49 98 44 49 98 44
17 1 2.31 63 90 44 63 90 44
16 1 2.3 64 81 44 64 81 44
15 1 2.33 33 96 43 33 96 43
14 1 2.37 23 55 42 23 55 42
13 1 2.35 40 93 41 40 93 41
12 1 2.4 69 52 41 69 52 41
11 1 2.3 25 56 39 25 56 39
10 1 2.32 60 13 39 60 13 39
9 1 2.31 24 66 36 24 66 36
8 1 2.36 55 97 33 55 97 33
7 1 2.37 55 96 31 55 96 31
6 1 2.42 67 26 29 67 26 29
5 1 2.46 68 33 28 68 33 28
4 1 2.51 40 94 25 40 94 25
3 1 2.43 61 73 25 61 73 25
2 1 2.37 51 71 24 51 71 24
1 1 2.3 30 83 22 30 83 22
[puku:stats] (nmr-stable5.1-env) cluster --in=zstat1.nii.gz --thresh=2.3 --minclustersize=123
Cluster Index Voxels Z-MAX Z-MAX X (vox) Z-MAX Y (vox) Z-MAX Z (vox) Z-COG X (vox) Z-COG Y (vox) Z-COG Z (vox)
158 772 3.54 28 90 47 26.7 85.7 46.6
157 255 3.22 61 15 33 63.1 17.3 38.4
156 249 3.15 21 33 37 23.5 32 38.6
155 156 3.25 66 54 69 66.9 60.2 67.2
154 151 3.43 33 14 34 33.3 13.7 37
153 143 3.4 32 19 56 32.4 19.2 56.2
152 111 2.88 37 98 43 37.8 95.5 40.7
151 99 3.24 60 16 51 60 16.4 50.4
150 90 3.07 25 38 68 27.8 39.9 66.7
149 80 3.26 38 75 70 36.3 76.9 68.2
148 79 3.37 56 33 72 56.9 30.7 70.6
147 75 3.19 62 71 50 62.4 73.3 47.9
146 57 3.06 23 19 36 23.7 19.9 34.4
145 52 3.23 26 69 69 24.6 69.3 67
144 48 2.79 58 38 62 58.1 38.6 62.9
143 48 3.05 74 38 44 74.6 39.7 43.4
142 48 3.69 51 89 23 49.4 91.1 23.5
141 45 2.91 31 41 74 33.1 38.6 70.6
140 38 3.11 21 27 44 20.7 26.9 43.8
139 36 2.93 60 47 27 60.6 47.5 27.2
138 33 2.62 20 73 38 18 70.5 38.1
137 32 2.85 60 91 49 60.3 90.2 48.8
136 31 2.8 43 76 59 44.1 75.6 60.1
135 28 2.99 65 72 65 65.1 71.6 64.8
134 28 2.9 37 74 57 37.5 74.2 57.7
133 27 2.68 48 70 57 47.5 69.7 57.3
132 24 3.37 52 79 67 51.6 79.7 66.8
131 24 2.91 57 60 62 57.6 60.1 62.5
130 24 2.66 35 26 55 34.7 26.1 55.4
129 24 2.87 29 73 46 29.2 73.2 46.5
128 24 2.9 71 29 31 70.8 28.8 30.8
127 23 2.71 65 35 28 64.9 36.3 28.9
126 22 2.62 56 89 43 55.4 88.9 43.8
125 21 3.03 32 71 71 31.2 69.8 70.7
124 21 2.62 19 68 52 19.9 67.5 53.3
123 21 3.07 78 51 52 77.8 50.3 51.6
122 20 2.72 16 70 57 17 69.8 58.2
121 19 2.93 42 85 57 42.3 85.7 56.6
120 18 2.67 64 60 27 64 60 27
119 17 2.65 61 45 73 61.2 45.3 72.2
118 17 3.02 76 44 59 76 44.8 59.5
117 17 2.85 35 79 56 34.4 78.6 56.7
116 16 2.87 12 56 55 12.7 55.4 55.3
115 16 2.78 56 13 46 56.3 13.6 46.2
114 16 2.63 41 48 40 40.2 47.6 39.8
113 16 2.66 50 20 28 50.1 21.1 27.9
112 14 2.75 38 88 57 37.6 87.9 56.9
111 13 2.66 29 60 63 29 59.6 62.6
110 13 2.59 74 54 54 73.7 54 53.3
109 13 2.93 34 64 37 34.2 64.2 37.4
108 12 2.61 37 81 66 36.7 81.9 64.9
107 12 2.82 74 72 51 73.6 71.9 50.7
106 12 2.77 52 93 43 52.3 92.6 42.9
105 11 2.48 24 56 70 23.5 56.5 69.5
104 11 2.64 17 50 62 17.7 49.6 62.2
103 11 2.61 50 10 41 50 9.74 40.9
102 11 2.55 58 87 26 60.2 88 26.2
101 10 2.6 64 56 61 63.8 56 60.9
100 10 2.76 70 51 56 69.6 50.9 55.9
99 10 2.46 48 84 44 49 84.9 43.9
98 9 2.63 23 62 62 23.2 61.8 61.9
97 9 2.73 39 13 47 38.3 12.9 47
96 9 2.58 45 24 27 45.3 24 27
95 9 3.05 37 94 25 36.7 93.9 25.4
94 8 2.57 31 35 65 30 35.4 64.6
93 8 2.58 13 66 38 12.5 66.2 38.4
92 8 2.98 40 80 23 39.5 81 22.6
91 7 2.61 15 70 50 15.4 69.9 50.3
90 7 2.45 17 74 50 16.8 73.9 49.9
89 7 2.51 16 44 50 15.6 44.3 49.3
88 7 2.57 65 56 47 65.3 55.7 46.3
87 7 2.72 63 91 42 62.6 90.6 41.6
86 7 2.45 26 76 38 26 75.7 38.1
85 7 2.56 60 33 29 58.6 31.9 29.7
84 7 2.69 47 29 27 46.6 28.6 26.4
83 6 2.51 39 37 65 38.5 36.7 65.2
82 6 2.48 49 93 49 48.7 93.3 48.5
81 6 2.57 36 79 47 35 78.8 47.7
80 6 2.44 12 69 46 12.7 69.7 46.2
79 6 2.6 66 39 42 66.2 38.5 42.2
78 6 2.52 51 13 34 50.5 12.5 34.2
77 6 2.57 15 47 24 15 47.5 24
76 6 2.64 32 85 24 32.5 85.8 23.8
75 6 3.07 33 84 22 32.7 82.6 22
74 5 2.47 27 47 59 26.8 47 58.8
73 5 2.44 73 50 56 73.8 50.4 56.4
72 5 2.54 55 21 49 54.4 20.2 49.8
71 5 2.57 67 45 47 67.2 44.4 46.4
70 5 2.62 52 95 46 52.2 95.2 46
69 5 2.43 30 29 43 30.8 29.2 43.2
68 5 2.49 68 61 39 68 61.4 38.6
67 5 2.65 64 52 25 64.4 51.8 25
66 4 2.53 67 40 68 67 40.5 67.5
65 4 2.44 17 53 54 16.3 53.5 53.7
64 4 2.49 15 69 47 15.2 68.7 47.2
63 4 2.42 59 28 48 58.8 27.5 47.7
62 4 2.46 42 90 40 42.2 90.5 39.8
61 4 2.42 18 28 38 18.5 27.8 37.5
60 4 2.46 62 92 36 62 91.7 36
59 4 2.83 47 97 32 47.3 97.3 32
58 4 2.42 59 36 29 59.5 35.8 29.2
57 3 2.37 43 58 71 43 58.3 70.3
56 3 2.4 27 67 54 27.3 67.7 54
55 3 2.59 63 85 52 63 84 52
54 3 2.36 71 65 35 71.3 65.3 34.3
53 3 2.41 46 51 35 46 50.7 34.7
52 3 2.49 25 31 34 24.4 31.6 33.7
51 3 2.38 67 60 32 67.7 60 31
50 3 2.42 21 92 30 21.7 92 29.7
49 3 2.41 20 35 25 20.3 35.3 25
48 3 2.5 41 91 24 41 91 23.7
47 2 2.46 22 42 70 22.5 42 70
46 2 2.38 64 35 67 64.5 35 67
45 2 2.33 17 59 63 17 58.5 63
44 2 2.39 42 70 61 42 70.5 61
43 2 2.32 43 72 57 43 71.5 57
42 2 2.36 66 40 56 65.5 40 55.5
41 2 2.43 41 95 50 40.5 94.5 50
40 2 2.49 68 82 50 68 82 50.5
39 2 2.47 27 82 42 26.5 82 42
38 2 2.41 39 13 42 39 12.5 42
37 2 2.44 66 63 41 66 63 41.5
36 2 2.37 57 43 41 57 43.5 41
35 2 2.37 54 31 38 54 31.5 38
34 2 2.53 74 73 37 74.5 73 37.5
33 2 2.49 10 46 36 10 46.5 36
32 2 2.34 75 72 34 75 72.5 34.5
31 2 2.45 32 22 31 32 22 31.5
30 2 2.66 21 29 29 20.5 29 29
29 2 2.45 41 95 28 41 95 28.5
28 1 2.43 64 40 70 64 40 70
27 1 2.31 55 76 68 55 76 68
26 1 2.32 66 60 66 66 60 66
25 1 2.33 33 34 66 33 34 66
24 1 2.42 73 58 63 73 58 63
23 1 2.33 14 50 57 14 50 57
22 1 2.34 15 71 53 15 71 53
21 1 2.34 40 83 52 40 83 52
20 1 2.41 13 41 50 13 41 50
19 1 2.32 61 22 47 61 22 47
18 1 2.36 49 98 44 49 98 44
17 1 2.31 63 90 44 63 90 44
16 1 2.3 64 81 44 64 81 44
15 1 2.33 33 96 43 33 96 43
14 1 2.37 23 55 42 23 55 42
13 1 2.35 40 93 41 40 93 41
12 1 2.4 69 52 41 69 52 41
11 1 2.3 25 56 39 25 56 39
10 1 2.32 60 13 39 60 13 39
9 1 2.31 24 66 36 24 66 36
8 1 2.36 55 97 33 55 97 33
7 1 2.37 55 96 31 55 96 31
6 1 2.42 67 26 29 67 26 29
5 1 2.46 68 33 28 68 33 28
4 1 2.51 40 94 25 40 94 25
3 1 2.43 61 73 25 61 73 25
2 1 2.37 51 71 24 51 71 24
1 1 2.3 30 83 22 30 83 22
On Nov 6, 2012, at 5:43 PM, Stephen Smith <[log in to unmask]<mailto:[log in to unmask]>> wrote:
need something like --minclustersize=123
On 6 Nov 2012, at 21:09, Sang wrote:
I am trying to use '--minclustersize' option in 'cluster' command, but not quite sure how to use the option correctly.
cluster --in=zstat1.nii.gz --thresh=2.3 --minclustersize > zstat1_cluster_info.txt
output txt file exactly the same as when I run the cluster command without '--minclustersize'....
Thank you for your help.
From Sang
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve
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