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: levy@nmr.mgh.harvard.edu
phone: 617-726-1908
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab