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

# 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