Hello Lee,
--minclustersize only works if you have a p-threshold specified using the -p option ( the outputs is the minimum significant clustersize for that p-threshold ). You don't need to specify any value for the parameter, --minclustersize is a binary option.
Kind Regards
Matthew
> 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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