You will need more like 10000 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: > Hello Freesurfer experts-- > > I ran mri_glmfit-sim to validate the group level GLM result (which was > already done using mri_glmfit), but I was not able to get any result > out of it. > > Even with a quite liberal threshold (2), no vertices came out (below > is what I typed in for the random permutation). > > mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign > abs --overwrite > > What is strange is that I was clearly see a number of clusters when I > overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster > shows up in perm.abs.2.sig.cluster.mgh. > I should be able to see the identical map between those right? > > FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. > As can be seen, nothing is listed in the stats table. > > Any of your help would be greatly appreciated. > -Glen > > > > > > > # Cluster Growing Summary (mri_surfcluster) > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > # CreationTime 2013/06/03-20:19:31-GMT > # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd > GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig > GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig > GLM/osgm/perm.abs.2.sig.voxel.mgh --sum > GLM/osgm/perm.abs.2.sig.cluster.summary --ocn > GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot > GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf > GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o > GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white > # cwd /glen/2D/results/LH > # sysname Linux > # hostname sumo.uphs.upenn.edu <http://sumo.uphs.upenn.edu> > # machine x86_64 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input GLM/osgm/sig.mgh > # Frame Number 0 > # srcsubj fsaverage_sym > # hemi lh > # surface white > # annot aparc > # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects > # SearchSpace_mm2 59961.4 > # SearchSpace_vtx 82070 > # Bonferroni 0 > # 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 100 > # CSD simtype perm > # CSD contrast osgm > # CSD confint 90.000000 > # Overall max 3.495 at vertex 61659 > # Overall min -4.18843 at vertex 73402 > # NClusters 0 > # Total Cortical Surface Area 59961.4 (mm^2) > # FixMNI = 0 > # > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > CWPLow CWPHi NVtxs Annot > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
