Please note that this extension for voxel-wise thresholding is now natively part of FSL (as of version 5.0.10). This repository is therefore no longer maintained.
FSL extension for voxel-wise thresholding
FSLDIRUP=/usr/local/fsl_MODIFIED
cd ${FSLDIRUP}/src/cluster
make
${FSLDIR}/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.0902 -d 0.700797 --volume=38344 -r 6.60989
--othresh=thresh_zstat1_2 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z
--voxthresh
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) COPE-MAX COPE-MAX X (vox)
COPE-MAX Y (vox) COPE-MAX Z (vox) COPE-MEAN
20 27 7.47 19 40 18 18.8 40.3 17.9 420 18 42 19 243
19 13 7.49 16 25 20 15.9 25 19.9 222 16 25 20 159
18 11 7.26 49 34 20 48.8 34.5 19.4 194 50 34 20 153
17 10 6.76 21 10 11 21.7 10.2 10.6 323 23 9 10 226
16 10 6.1 23 44 13 23.4 43.8 13.6 235 23 44 13 186
15 8 6.03 36 37 23 35.9 36.8 22.5 222 35 37 23 167
14 6 5.86 25 9 14 24.2 9.49 13.7 323 24 9 14 236
[...]
${FSLDIR}/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.0902 -d 0.700797 --volume=38344 -r 6.60989
--othresh=thresh_zstat1_2 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z
--voxuncthresh
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) COPE-MAX COPE-MAX X (vox)
COPE-MAX Y (vox) COPE-MAX Z (vox) COPE-MEAN
147 795 7.47 19 40 18 24.7 41.7 18.4 632 28 56 17 168
146 243 7.49 16 25 20 16.4 21.6 18.8 428 17 19 23 135
145 161 4.56 42 43 14 39.3 44.2 15.1 479 33 36 11 199
144 152 7.26 49 34 20 47.7 35 19.7 218 52 38 16 117
143 66 6.76 21 10 11 22.3 10.9 11.3 323 23 9 10 171
142 65 5.04 46 23 20 45.3 20.7 20 242 41 16 21 131
141 42 4.95 49 46 17 48.1 45.7 17.9 357 47 47 17 184
[...]
${FSLDIR}/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -d 0.700797 --volume=38344 -r 6.60989
--othresh=thresh_zstat1_2 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -p 0.05
Cluster Index Voxels P -log10(P) Z-MAX Z-MAX X (vox) Z-MAX Y (vox) Z-MAX Z (vox)
Z-COG X (vox) Z-COG Y (voxZ-COG Z (vox) COPE-MAX COPE-MAX X (vox) COPE-MAX Y (vox)
COPE-MAX Z (vox) COPE-MEAN
7 3130 0 68.9 7.47 19 40 18 32.5 39.9 18.1 632 28 56 17 139
6 521 6.02e-20 19.2 7.49 16 25 20 16 22.4 17.5 428 17 19 23 110
5 167 1.7e-08 7.77 4.71 39 8 12 43.9 14.9 9.45 533 43 16 7 146
4 99 1.58e-05 4.8 6.76 21 10 11 23.1 10.5 11.5 323 23 9 10 143
3 43 0.017 1.77 4.03 36 7 6 35.5 8.35 3.75 200 31 8 4 128
2 41 0.0227 1.64 4.41 27 18 17 27.9 14.6 17.6 263 28 13 18 131
1 40 0.0263 1.58 4.77 47 21 15 48 20.8 14 200 48 19 14 102