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Dear Martin,
actually, when your primary problem is very high local maxima on p-map, but no significant cluster-wise p after thresholding, I guess, that you should try the opposite, i.e. increase cluster forming threshold. This will increase sensitivity to clusters with smaller extent but comprising larger p-values before thresholding.
Antonin Skoch
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:
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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. <dgr...@mgh.harvard.edu mailto:dgr...@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* <mj70...@gmail.com <mailto:mj70...@gmail.com> <mailto:mj70...@gmail.com <mailto:mj70...@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 _______________________________________________ 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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