Hello,

I have just run a number of permutation and mc-z on data that was previously analysed using qdec. Unfortunately none of my clusters reach significance (in some cases there are no clusters found at all) and I am unsure as to what I am doing wrong. I am running freesurfer v4.1.0 on CentOS. My commands were as follows:

mri_glmfit –y y.mgh –fsgd ./qdec.fsgd dods --surf fsaverage lh

--fwhm 15 –glmdir ./glmdir --C ./contrasts/lh-Diff-patient-CONTROL-Intercept-thickness.mat --sim perm 5000 2 ./glmdir/csd1

followed by:

mri_surfcluster --in ./lh-Diff-patient-CONTROL-Intercept-thickness/sig.mgh –csd ./glmdir/csd1-lh-Diff-patient-CONTROL-Intercept-thickness.csd --sum lh-Diff-patient-CONTROL-Intercept-thickness/sig.cluster.sum –cwsig lh-Diff-patient-CONTROL-Intercept-thickness/sig.cluster.mgh

I append a log file of mri_glmfit and the output of mri_surfcluster below – there are clusters listed but none of them reach significance. It is confusing because I was under the impression that permutation thresholding was less conservative than fdr correction.

I have also run these using –sim mc-z 5000 2  - maybe I am not performing enough iterations?

Also: is RFT correction implemented in the latest version of freesurfer?

Any help appreciated,

Rysia

mri_glmfit logfile:

$Id: mri_glmfit.c,v 1.138.2.3 2008/08/27 13:33:05 greve Exp $

cwd /cns_zfs/sphasas

cmdline mri_glmfit --y /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/y.mgh --fsgd /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/qdec.fsgd dods --glmdir /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15 --surf fsaverage rh --label /cns_zfs/sphasas/fsaverage/label/rh.cortex.label --C /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/contrasts/rh-Avg-Intercept-thickness.mat --C /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/contrasts/rh-Diff-OCD-CONTROL-Intercept-thickness.mat

sysname  Linux

hostname haemoglobin.cns.image.iop

machine  x86_64

user     kkvi1114

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

OneSampleGroupMean 0

y    /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/y.mgh

logyflag 0

usedti  0

FSGD /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15/qdec.fsgd

labelmask  /cns_zfs/sphasas/fsaverage/label/rh.cortex.label

maskinv 0

glmdir /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15

DoFFx 0

ResidualFWHM 18.998058

SearchSpace 75188.635931

anattype surface

Output of mri_surfcluster:

cwd /cns_zfs/sphasas/qdec/OCD_CONTROL.lh.cortthick.fwhm15

# sysname  Linux

# hostname haemoglobin.cns.image.iop

# machine  x86_64

# FixVertexAreaFlag = 1

#

# Input      ./lh-Diff-OCD-CONTROL-Intercept-thickness/sig.mgh

# Frame Number      0

# srcsubj fsaverage

# hemi lh

# surface white

# SUBJECTS_DIR /software/system/freesurfer/freesurfer-4.1.0/subjects

# Minimum Threshold 2

# Maximum Threshold infinity

# Threshold Sign    abs

# AdjustThreshWhenOneTail 1

# Area Threshold    0 mm^2

# CSD thresh  2.000000

# CSD nreps    5000

# CSD simtype  perm

# CSD contrast lh-Diff-OCD-CONTROL-Intercept-thickness

# CSD confint  90.000000

# Overall max 2.18803 at vertex 126138

# Overall min -2.94444 at vertex 75849

# NClusters          6

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 1

ClusterNo  Max  VtxMax              Size(mm2)          TalX       TalY       TalZ        CWP      CWPLow             CWPHi   NVtxs

   1           -2.944    75846                    61.98                     -17.6      -37.0      -4.2        0.84860  0.84200               0.85500   142

   2           -2.672    22094                    96.92                     -29.6      0.5         -24.2      0.80680  0.79960               0.81400   182

   3           2.188     126138                  41.24                     -22.1      -56.8      40.5        0.87160  0.86560               0.87760    74

   4           2.095     81711                    45.09                     -32.4      -38.2      39.4        0.86860  0.86240               0.87480   105

   5           2.061     147756                 12.32                     -6.2        -61.7      38.4         0.90520  0.89980               0.91040   20

   6           2.001     133188                 0.60                        -32.0      -44.7      59.0        0.91660  0.91160               0.92160    1