All those clusters are pretty small, so it does not surprise me that
they are not sig. Your command-lines look ok. I don't think the results
will change with more iterations.
dogu
Burmicz, Ryzarda wrote:
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 *
------------------------------------------------------------------------
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