thanks Doug.

just tried, but I still got no clusters.

below is the output of perm.abs.2.sig.cluster.summary.

# CreationTime 2013/06/05-18:52:23-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 rage.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 /derek/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 20000

# 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

On Wed, Jun 5, 2013 at 2:44 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

try

mri_glmfit-sim --glmdir GLM --no-sim perm.abs.2

doug

On 06/05/2013 02:26 PM, Glen Lee wrote:

On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

what was your original mri_glmfit-sim command?

mri_glmfit-sim --glmdir GLM --sim perm 20000 2 perm.abs.2
--sim-sign abs --overwrite

Then, I tried no-sim on the generated csd file with the following
command:

mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim
--overwrite /csd/perm.abs.2.j001-osgm.csd

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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