Having run randomize with the --T2 option I get one large significant cluster, whereas with -c and a t level I get several rational clusters that are similar to an SPM output.
randomise -i ctrl-hivp_skeleton -o tbss -m mean_FA_ctrl_skeleton_mask -d ctrl-hivp_design.mat -t ctrl-hivp_design.con -n 500 --T2
Further, using the "cluster" command the report varies depending on the command threshold - I would have thought the main cluster would be the same regardless of the threshold for the cluster description.
cluster1.cluster:dolf[118]> cluster -i ctrl-hivp_tfce_corrp_tstat1.nii.gz -t .80 -o ctrl-hivp_tfce_clusters > cluster_list.txt
cluster1.cluster:dolf[119]> more cluster_list.txt
Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z (vox) COG X (vox) COG Y (vox) COG Z (vox)
3 77562 0.998 163 121 41 118 104 79.3
2 8 0.802 122 129 69 122 129 69.9
1 5 0.8 95 61 48 94.6 62.2 48
cluster1.cluster:dolf[120]> cluster -i ctrl-hivp_tfce_corrp_tstat1.nii.gz -t .90 -o ctrl-hivp_tfce_clusters > cluster_list.txt
cluster1.cluster:dolf[121]> more cluster_list.txt
Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z (vox) COG X (vox) COG Y (vox) COG Z (vox)
4 65928 0.998 163 121 41 118 106 83.1
3 1813 0.932 95 88 28 100 83.9 32.1
2 742 0.918 141 81 30 139 79.4 34.8
1 167 0.91 141 60 32 140 58.9 33.2
cluster1.cluster:dolf[122]> cluster -i ctrl-hivp_tfce_corrp_tstat1.nii.gz -t .95 -o ctrl-hivp_tfce_clusters > cluster_list.txt
cluster1.cluster:dolf[123]> more cluster_list.txt
Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z (vox) COG X (vox) COG Y (vox) COG Z (vox)
1 60332 0.998 163 121 41 118 106 83.4
___________________________
Adolf Pfefferbaum, MD
Neuroscience Program
SRI International
650-859-2927 phone
650-859-2743 FAX
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