Hi Matthew,

Thanks very much for your helpful reply.
Does 'in descending order' mean that the six local maxima with the 6 highest p-values are reported?

Now that I read cluster's functions, I'm also wondering what  -p,--pthresh (p-threshold for clusters) means? How is it different from --thresh ?

Thanks again for your help,
Bart

PS:
To place our use of the cluster-command in context: We are doing a meta-analysis and want to include a study that found changes within most part of the TBSS skeleton, conglomerating into one giant cluster (even at p<0.001 using threshold-free cluster enhancement). Therefore want to get local maxima indicating areas of change relative to the whole skeleton.


> Date: Fri, 8 Apr 2011 11:55:19 +0100
> From: [log in to unmask]
> Subject: Re: [FSL] cluster command & local maxima
> To: [log in to unmask]
>
> Hello,
> The --olmax option reports in descending order the local maxima in a cluster ( those voxels whose surrounding voxels are all of lower intensities ). By default only 6 local maxima are reported per cluster, but this can be changed with the -n option. For local maxima, the co-ordinates reported should be the location of the peak score.
>
> Many Regards
>
> Matthew
>
> > Dear FSLers,
> >
> > I have used --olmax in 'cluster' to get local maxima of a very big cluster in TBSS, which covered more or less the whole skeleton, with:
> >
> > cluster --in=..._tfce_corrp_tstat file --thresh=0.99 --mm --olmax= bart_FA_99_plus_olmax
> >
> > It produced 6 coordinates out of the big cluster. That made me wonder what exactly –-olmax does, how it determines what the local maxima are within a cluster?
> >
> > Also, when using –olmax the output file is like this:
> >
> > Cluster Index Z x y z
> >
> > Are these coordinates of the peak t-score or are they COG coordinates?
> >
> >
> > Any clarification on these two questions would be very much appreciated!
> >
> > Thanks in advance,
> > Bart
> >
> >
> > Bart D. Peters, MD, PhD
> > Research Fellow
> > Zucker Hillside Hospital
> > Feinstein Institute for Medical Research
> > North Shore-LIJ Health System
> > 75-59 263rd Street
> > Glen Oaks, NY 11004
> > Ph: 718-470-8168
> >