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