Hello,
--thresh is the value used to threshold the input image before any clustering occurs ( any voxels below this value are set to 0, and hence ignored by the clustering algorithm ).
Many Regards
Matthew
> Dear all,
>
> Does the 'cluster' program use the input parameter --thresh to identify local maxima to form clusters? Or is --thresh used to threshold based on cluster mean?
>
> I see that the output listed in, say, cluster_zstat1_std.html, lists cluster indices and max z-score.
>
> But I wonder if the clusters are (or can be) initially defined by thresholding based on the mean of the candidate cluster.
>
> I know I can find the cluster mean with a combination of 'cluster' and 'fslstats', something like so:
>
> cluster --in=zstat1 --thresh=2.5 --oindex=outIdx
> clusterNum=5
> fslmaths outIdx -thr $clusterNum -uthr $clusterNum -bin outMask
> fslstats zstat1 -k outMask -m
>
> But this is after the fact, that is, after the cluster has already been identified.
>
> Thank you,
> - BettyAnn
>
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