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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did you do this?

First, install a new version of mri_glmfit-sim from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim (copy it to $FREESURFER_HOME/bin and make it executable with chmod a+rx mri_glmfit-sim).

On 12/06/2018 01:28 PM, Martin Juneja wrote:

External Email - Use Caution

Thanks Dough for your suggestions. I tried to use permutation method, but its giving me following error:

ERROR: design matrix is not orthogonal, cannot be used with permutation.

If this something you really want to do, run with --perm-force

Can you please tell me how can I fix this issue or if I can run with --perm-force?

Thanks for the help.

On Thu, Dec 6, 2018 at 9:37 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:

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> <mailto: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>
> <mailto: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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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