Hello,
Randomise should already output p-value ( actually 1-p ) images for TFCE. You could threshold these at 0.95 with cluster to find discrete "clusters" of significant voxels. However, note that it is not appropriate to use the cluster's GRF options with TFCE output, as TFCE values do not have a known distribution ( randomise is calculating an empirical null ). If you specifically want to obtain clusters with a single p-value, then you should the -c or -C options in randomise, which make fewer assumptions than the GRF options in cluster.
Hope this helps,
Matthew
> Dear experts,
>
> I have run randomise using the TFCE option (-T), producing t-statistic maps. I am using FSL Version 5.0.9. I have subsequently run “cluster" on the randomise output in order to extract significant clusters, but I would like to retrieve the p-value of the clusters using the GRF option.
>
> I know that I need to supply --dlh (smoothness estimate), --volume (number of voxels in mask) and --pthresh (p-value threshold for clusters), where I use the “smoothest" function to determine values for --dlh and --volume.
>
> The “cluster” command I run is:
>
> cluster --in=output_tfce_thresh_tstat2.nii.gz --dlh=0.0239923 --volume=611340 --pthresh=0.95 -t 0.95 --oindex=output_cluster_index.nii.gz --olmax=output_lmax.txt --osize=output_cluster_size.nii.gz
>
>
> Unfortunately, I get “nan” returned for the cluster p-vlaue:
>
> Cluster Index Voxels P -log10(P) MAX MAX X (vox) MAX Y (vox) MAX Z (vox) COG X (vox) COG Y (vox) COG Z (vox)
> 1 1786 nan -nan 17.7 43 86 43 43.2 84 48.2
>
> whereas when I run without any GRF options, I see the following:
>
> Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z (vox) COG X (vox) COG Y (vox) COG Z (vox)
> 1 1786 17.7 43 86 43 43.2 84 48.2
>
>
> I am unsure why I am getting nan values when using GRF options. Any help would be much appreciated!
>
> Cheers,
> Donal
