Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below:
/2D/results/LH/GLM/csd> ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd I'm guessing that I need to define the path for this csd folder? Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite -Glen On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>wrote: > > hi Glen, no cluster will show up if the p-value for all clusters is above > .05. You can change this with --cwpvalthresh to something like .99. That > should give you all the clusters. Also, you don't have to run the full > simulation again; you can use the --no-sim option and it will use the > simulation that you already did. > doug > > > > On 6/3/13 9:45 PM, Glen Lee wrote: > > 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. >> >> > >
_______________________________________________ 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.
