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
In the first case, the corrected p-value is very close to 1 (ie, no significance), and so it has a large uncertainty (error bars -1,0), there appears to be a slight error in the computation of the lower bound.
In the 2nd case, when you don't use an ROI, the size of the cluster almost doubles, and so the p-value improves.
doug
Robert Levy wrote:
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
# 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 22 -1.700 115699 19.10 7.8 -20.5 34.4 1.00000 -0.00010 1.00000 74 23 -1.655 155650 96.64 0.1 -9.7 -15.1 1.00000 -0.00010 1.00000 156 24 -1.650 32879 51.99 8.6 0.1 48.4 1.00000 -0.00010 1.00000 142 25 -1.644 76413 66.97 25.4 -41.1 30.3 1.00000 -0.00010 1.00000 178 26 -1.621 128318 20.26 37.4 -44.7 -30.8 1.00000 -0.00010 1.00000 37 27 -1.549 116042 31.69 23.6 -8.3 35.9 1.00000 -0.00010 1.00000 118 28 -1.542 141754 31.22 3.0 -9.1 20.3 1.00000 -0.00010 1.00000 83 29 -1.519 103341 24.62 18.7 -45.2 39.3 1.00000 -0.00010 1.00000 53 30 -1.469 92147 37.18 37.9 -25.6 -28.1 1.00000 -0.00010 1.00000 107 31 -1.411 137447 7.46 39.3 -48.3 -30.3 1.00000 -0.00010 1.00000 20 32 -1.407 35200 15.63 9.6 -11.3 31.9 1.00000 -0.00010 1.00000 60 33 -1.397 108543 9.91 6.0 -6.5 40.5 1.00000 -0.00010 1.00000 33 34 -1.387 71979 10.28 17.9 26.9 38.3 1.00000 -0.00010 1.00000 26 35 -1.368 3990 2.61 18.2 -24.8 39.3 1.00000 -0.00010 1.00000 10 36 -1.354 97916 0.71 38.3 -27.5 -29.4 1.00000 -0.00010 1.00000 2 37 -1.353 134902 6.18 11.8 18.7 -0.0 1.00000 -0.00010 1.00000 10 38 -1.330 117096 2.94 54.4 0.0 19.5 1.00000 -0.00010 1.00000 7 39 -1.325 17909 5.02 30.4 -42.2 25.7 1.00000 -0.00010 1.00000 16 40 -1.312 98368 1.37 53.6 -13.0 25.0 1.00000 -0.00010 1.00000 4 41 -1.310 151969 0.90 38.8 -38.7 19.0 1.00000 -0.00010 1.00000 3 42 -1.303 29812 0.23 50.5 21.8 11.4 1.00000 -0.00010 1.00000 1
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, this makes sense. I think the second part should have been obvious to me, but I was confused by the lower bound being strange. From what you wrote, it sounds like the error affecting the lower bound value would not also affect the p value for the cluster.
Rob
Doug Greve wrote:
In the first case, the corrected p-value is very close to 1 (ie, no significance), and so it has a large uncertainty (error bars -1,0), there appears to be a slight error in the computation of the lower bound.
In the 2nd case, when you don't use an ROI, the size of the cluster almost doubles, and so the p-value improves.
doug
Robert Levy wrote:
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
# 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*0096394* # 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 --th max 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 22 -1.700 115699 19.10 7.8 -20.5 34.4 1.00000 -0.00010 1.00000 74 23 -1.655 155650 96.64 0.1 -9.7 -15.1 1.00000 -0.00010 1.00000 156 24 -1.650 32879 51.99 8.6 0.1 48.4 1.00000 -0.00010 1.00000 142 25 -1.644 76413 66.97 25.4 -41.1 30.3 1.00000 -0.00010 1.00000 178 26 -1.621 128318 20.26 37.4 -44.7 -30.8 1.00000 -0.00010 1.00000 37 27 -1.549 116042 31.69 23.6 -8.3 35.9 1.00000 -0.00010 1.00000 118 28 -1.542 141754 31.22 3.0 -9.1 20.3 1.00000 -0.00010 1.00000 83 29 -1.519 103341 24.62 18.7 -45.2 39.3 1.00000 -0.00010 1.00000 53 30 -1.469 92147 37.18 37.9 -25.6 -28.1 1.00000 -0.00010 1.00000 107 31 -1.411 137447 7.46 39.3 -48.3 -30.3 1.00000 -0.00010 1.00000 20 32 -1.407 35200 15.63 9.6 -11.3 31.9 1.00000 -0.00010 1.00000 60 33 -1.397 108543 9.91 6.0 -6.5 40.5 1.00000 -0.00010 1.00000 33 34 -1.387 71979 10.28 17.9 26.9 38.3 1.00000 -0.00010 1.00000 26 35 -1.368 3990 2.61 18.2 -24.8 39.3 1.00000 -0.00010 1.00000 10 36 -1.354 97916 0.71 38.3 -27.5 -29.4 1.00000 -0.00010 1.00000 2 37 -1.353 134902 6.18 11.8 18.7 -0.0 1.00000 -0.00010 1.00000 10 38 -1.330 117096 2.94 54.4 0.0 19.5 1.00000 -0.00010 1.00000 7 39 -1.325 17909 5.02 30.4 -42.2 25.7 1.00000 -0.00010 1.00000 16 40 -1.312 98368 1.37 53.6 -13.0 25.0 1.00000 -0.00010 1.00000 4 41 -1.310 151969 0.90 38.8 -38.7 19.0 1.00000 -0.00010 1.00000 3 42 -1.303 29812 0.23 50.5 21.8 11.4 1.00000 -0.00010 1.00000 1
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Robert Levy