Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong?
FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > 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. > >
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