Hello,
I tried a between group comparison using mri_glmfit, correcting for
multiple comparisons using the z-based monte carlo method. This
differed from previous similar analyses I had run in that I did not
constrain the analysis with a ROI (not in the glmfit, but I did in
surfcluster when outputting corrected results). It seems like
something is buggy about this output, but it may actually be correct but
I just don't know how to interpret it correctly. The negative CWPLow
probability values for certain clusters are what seems puzzling. I
don't know what a negative p value could possibly mean [ it is beyond
impossible for the cluster to be unreal? : ) ], though I'm sure it's not
a real p value. These are not significant clusters regardless, but
these are impossible statistics and so I was concerned that something
was breaking down in the process that would invalidate the other results.
The second part of what I tried possibly shows that there is something
going wrong in the code, just because it is drastically different when I
would only expect a minor difference (and probably in the opposite
direction actually). I ran surfcluster with no ROI, and the same
cluster became much more significant than it was reported as being before.
This seems strange, so I don't know whether the other results in the
same unconstrained analysis are correct. I have included some of the
surfcluster output (and attached both of the example files), and the
environment and commands.
Thanks,
Rob
before correcting for multiple comparisons
rh ASvfix 8s BwGroupError5
ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs
1 -3.474 14231 1786.39 6.3 30.8 20.9 2551
2 -1.476 42121 13.60 3.2 -6.6 21.6 27
3 -1.354 106598 3.66 10.3 -9.8 32.2 8
after correcting for multiple comparisons
rh ASvfix 8s BwGroupError5
ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP
CWPLow CWPHi NVtxs
1 -3.474 14231 1190.92 6.3 30.8 20.9 0.07400
0.07070 0.07740 2551
2 -1.476 42121 9.07 3.2 -6.6 21.6 1.00000
-0.00010 1.00000 27
3 -1.354 106598 2.44 10.3 -9.8 32.2 1.00000
-0.00010 1.00000 8
some of the output when running surfcluster without using an ROI
# ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP
CWPLow CWPHi NVtxs
1 -3.474 14231 2007.09 6.3 30.8 20.9 0.00160
0.00110 0.00210 3998
2 -3.362 125672 356.48 4.5 -25.9 21.3 0.99010
0.98880 0.99140 907
3 -2.749 95384 360.56 8.3 -38.6 -12.7 0.98830
0.98690 0.98970 993
4 -2.572 132812 143.54 26.1 37.5 27.5 1.00000
-0.00010 1.00000 415
5 -2.531 48150 242.73 20.1 -10.2 -24.3 1.00000
-0.00010 1.00000 563
6 -2.373 80761 156.38 2.6 -32.6 29.3 1.00000
-0.00010 1.00000 421
...
-------- freesurfer-Linux-centos4_x86_64-dev-20070729 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/dev
FSFAST_HOME /usr/local/freesurfer/dev/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR
MNI_DIR /usr/local/freesurfer/dev/mni
FSL_DIR /usr/local/freesurfer/dev/fsl
hostname: vantz
pwd: $SUBJECTS_DIR
*
# rh: perform analysis*
/space/greve/1/users/greve/freesurfer/bin/mri_glmfit \
--really-use-average7 \
--y rh.ASvfix_8s_BwGroupError5.fsfast.mgh \
--fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \
--glmdir
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir
\
--surf average7 rh \
--pca \
--C fsgd_and_contrast_files/BwGroupError5.mat \
--fwhm 4.6
*# rh: report clusters found in analysis before threshold*
mri_surfcluster \
--really-use-average7 \
--src
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh
\
--sum
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.rh.ASvfix_8s_BwGroupError5.fsfast.sum
\
--ocp
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.rh.ASvfix_8s_BwGroupError5.fsfast.mgh
\
--clabel average7/label/dACC_rACC_final-rh.label \
--hemi rh \
--srcsubj average7 \
--thmin 1.3 \
--thmax infinity
*
# rh: apply simulation data to get cluster size threshold*
mri_surfcluster \
--src
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM01-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM02-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM03-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM04-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM05-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM06-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM07-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM08-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM09-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM10-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM11-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM12-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM13-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM14-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM15-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM16-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM17-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM18-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM19-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM20-BwGroupError5.csd
\
--clabel average7/label/dACC_rACC_final-rh.label \
--sum
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh.sum
\
--ocp
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh.mgh
\
--thmax infinity
*# rh: apply simulation data to get cluster size threshold (no ROI) *
mri_surfcluster \
--src
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM01-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM02-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM03-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM04-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM05-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM06-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM07-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM08-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM09-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM10-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM11-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM12-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM13-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM14-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM15-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM16-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM17-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM18-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM19-BwGroupError5.csd
\
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM20-BwGroupError5.csd
\
--sum
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh_noroi.sum
\
--thmax infinity
--
Robert P. Levy, B.A.
Research Assistant, Manoach Lab
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St., Room 2656
Charlestown, MA 02129
email: [EMAIL PROTECTED]
phone: 617-726-1908
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.37 2007/04/20 20:46:05 greve Exp $
# $Id: mrisurf.c,v 1.551 2007/07/24 19:34:25 kteich Exp $
# CreationTime 2007/07/30-02:48:57-GMT
# cmdline mri_surfcluster --src
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM01-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM02-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM03-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM04-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM05-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM06-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM07-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM08-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM09-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM10-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM11-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM12-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM13-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM14-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM15-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM16-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM17-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM18-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM19-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM20-BwGroupError5.csd
--clabel average7/label/dACC_rACC_final-rh.label --sum
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh.sum
--ocp
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh.mgh
--thmax infinity
# cwd /autofs/space/ventzl_001/users/SUBJECTS_DIR
# sysname Linux
# hostname vantz
# machine x86_64
# FixVertexAreaFlag = 1
#
# Input
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh
# Frame Number 0
# srcsubj average7
# hemi rh
# surface white
# SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR
# Minimum Threshold 1.3
# Maximum Threshold inf
# Threshold Sign abs
# AdjustThreshWhenOneTail 1
# Area Threshold 0 mm^2
# clabelfile average7/label/dACC_rACC_final-rh.label
# clabelinv 0
# CSD thresh 1.300000
# CSD nreps 10000
# CSD simtype mc-z
# CSD contrast BwGroupError5
# CSD confint 90.000000
# Overall max 0 at vertex 0
# Overall min -3.47414 at vertex 14231
# NClusters 3
# Total Cortical Surface Area 65350.2 (mm^2)
# FixMNI = 1
#
# ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow
CWPHi NVtxs
1 -3.474 14231 1190.92 6.3 30.8 20.9 0.07400 0.07070
0.07740 2551
2 -1.476 42121 9.07 3.2 -6.6 21.6 1.00000 -0.00010
1.00000 27
3 -1.354 106598 2.44 10.3 -9.8 32.2 1.00000 -0.00010
1.00000 8
# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.37 2007/04/20 20:46:05 greve Exp $
# $Id: mrisurf.c,v 1.551 2007/07/24 19:34:25 kteich Exp $
# CreationTime 2007/07/31-01:27:21-GMT
# cmdline mri_surfcluster --src
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM01-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM02-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM03-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM04-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM05-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM06-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM07-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM08-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM09-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM10-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM11-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM12-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM13-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM14-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM15-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM16-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM17-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM18-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM19-BwGroupError5.csd
--csd
BwGroupError5_wholebrain_mriglmfit/ASevASc_8s_p05_z_rhMCSIM20-BwGroupError5.csd
--sum
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.clusterMCSIM_rh_noroi.sum
--thmax infinity
# cwd /autofs/space/ventzl_001/users/SUBJECTS_DIR
# sysname Linux
# hostname vantz
# machine x86_64
# FixVertexAreaFlag = 1
#
# Input
BwGroupError5_wholebrain_mriglmfit/rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/BwGroupError5/sig.mgh
# Frame Number 0
# srcsubj average7
# hemi rh
# surface white
# SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR
# Minimum Threshold 1.3
# Maximum Threshold inf
# Threshold Sign abs
# AdjustThreshWhenOneTail 1
# Area Threshold 0 mm^2
# CSD thresh 1.300000
# CSD nreps 10000
# CSD simtype mc-z
# CSD contrast BwGroupError5
# CSD confint 90.000000
# Overall max 2.04638 at vertex 151209
# Overall min -3.47414 at vertex 14231
# NClusters 42
# Total Cortical Surface Area 65350.2 (mm^2)
# FixMNI = 1
#
# ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow
CWPHi NVtxs
1 -3.474 14231 2007.09 6.3 30.8 20.9 0.00160 0.00110
0.00210 3998
2 -3.362 125672 356.48 4.5 -25.9 21.3 0.99010 0.98880
0.99140 907
3 -2.749 95384 360.56 8.3 -38.6 -12.7 0.98830 0.98690
0.98970 993
4 -2.572 132812 143.54 26.1 37.5 27.5 1.00000 -0.00010
1.00000 415
5 -2.531 48150 242.73 20.1 -10.2 -24.3 1.00000 -0.00010
1.00000 563
6 -2.373 80761 156.38 2.6 -32.6 29.3 1.00000 -0.00010
1.00000 421
7 -2.311 122659 135.90 15.2 -14.1 -21.2 1.00000 -0.00010
1.00000 231
8 -2.269 109398 87.32 48.1 24.5 17.9 1.00000 -0.00010
1.00000 194
9 -2.184 2154 66.84 45.7 -5.2 -10.2 1.00000 -0.00010
1.00000 167
10 -2.110 114979 330.99 57.3 -15.5 -16.2 0.99600 0.99520
0.99680 651
11 2.046 151209 59.59 13.4 -69.9 32.6 1.00000 -0.00010
1.00000 258
12 2.013 39130 44.30 36.5 -85.0 1.2 1.00000 -0.00010
1.00000 100
13 -1.920 29514 53.60 7.3 -24.9 -5.4 1.00000 -0.00010
1.00000 118
14 -1.906 64313 65.04 23.9 56.5 4.4 1.00000 -0.00010
1.00000 95
15 -1.896 67841 69.34 27.5 24.1 -1.7 1.00000 -0.00010
1.00000 152
16 -1.850 151774 113.33 35.6 -30.5 20.6 1.00000 -0.00010
1.00000 312
17 -1.842 45709 71.17 18.0 64.5 14.5 1.00000 -0.00010
1.00000 110
18 -1.795 67367 45.74 46.8 9.9 20.1 1.00000 -0.00010
1.00000 134
19 -1.795 124903 51.58 35.2 2.2 -8.0 1.00000 -0.00010
1.00000 142
20 -1.780 44424 148.33 29.8 11.1 6.7 1.00000 -0.00010
1.00000 383
21 -1.769 68495 34.75 4.6 -22.8 8.2 1.00000 -0.00010
1.00000 87
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