For it to show up in the output file, the cluster-wise pvalue must be <
.05 (CWT). To see all the clusters regardless of significance, run it
with a CWT of 1. If you want to run with a more liberal cluster forming
threshold (CFT), you can try using permutation. See
http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm

On 12/05/2018 11:44 PM, Martin Juneja wrote:
>
>         External Email - Use Caution
>
>
> Dear experts,
>
> Could you please help me in resolving following issue?
>
> Thanks.
> ---------- Forwarded message ---------
> From: *Martin Juneja* <mj70481@gmail.com <mailto:mj70481@gmail.com>>
> Date: Wed, Nov 28, 2018 at 2:23 PM
> Subject: Overall maxima is high and still no significant cluster
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>
>
> Hi FS experts,
>
> I am estimating the group-behavioral thickness interaction using
> contrast 2 FSGD file:
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT < 0.01 and
> CWT < 0.05 at FWHM of 12 mm.
>
> I do not find any significant clusters and my output summary text file
> looks like the following. This file shows that overall maxima is
> 4.58212 (which corresponds to p < 0.0001 because -log (0.0001) = 4, so
> I am just wondering despite the fact that maxima is > 4, why I do not
> see this cluster in the summary/output *.mgh file?
>
> I would really appreciate any clarification and tips to modify my
> input thresholds so that I do not miss any significant findings here.
>
> Thanks.
> -----------------------------
>
> # SearchSpace_mm2 76467.1
> # SearchSpace_vtx 149953
> # Bonferroni 2
> # Minimum Threshold 2
> # Maximum Threshold infinity
> # Threshold Sign    abs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold    0 mm^2
> # CSD thresh  2.000000
> # CSD nreps    10000
> # CSD simtype  null-z
> # CSD contrast NA
> # CSD confint  90.000000
> # Overall max 4.58212 at vertex 10608
> # Overall min -2.84277 at vertex 75476
> # NClusters          0
> # FixMNI = 0
> #
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX  MNIY   MNIZ    CWP   
> CWPLow    CWPHi   NVtxs   WghtVtx   Annot
>
>
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