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> 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 CautionDear 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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