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README.md


Important note

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 This repository is therefore no longer maintained.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

FSL extension for voxel-wise thresholding

Make

FSLDIRUP=/usr/local/fsl_MODIFIED
cd ${FSLDIRUP}/src/cluster
make

Examples of usage for the updated cluster command

Voxel-wise corrected
${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
[...]
Voxel-wise uncorrected
${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
[...]

Cluster-wise corrected (same as before)
${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

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