cd /Applications/freesurfer/subjects/PDM_cortical_thickness /Applications/freesurfer/bin/mri_glmfit-sim --glmdir ./rh.CP.paired-diff --sim perm 10000 3 perm.abs.3 --sim-sign abs --overwrite --cwpvalthresh .05 --bg 4 $Id: mri_glmfit-sim,v 1.36.2.3 2011/05/25 20:23:08 greve Exp $ Thu Jun 21 11:19:49 CST 2012 Darwin fmripc2.vghtpe.gov.tw 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 IBRU setenv SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh.CP.paired-diff --y rh.thickness.fwhm10.fsaverage.mgh --fsgd paired-diff_CP.fsgd --C control_main.mtx --C pdm_main.mtx --C control-pdm.mtx --surface fsaverage rh DoSim = 1 UseCache = 0 DoPoll = 1 DoPBSubmit = 0 DoBackground = 1 DiagCluster = 0 gd2mtx = dods fwhm = 0 nSimPerJob = 2500 1/4 Thu Jun 21 11:19:49 CST 2012 mri_glmfit --y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control-pdm.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control_main.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/pdm_main.mtx --mask ./rh.CP.paired-diff/mask.mgh --sim perm 2500 3 ./rh.CP.paired-diff/csd/perm.abs.3.j001 --sim-sign abs --fwhm 0 --fsgd ./rh.CP.paired-diff/y.fsgd dods --surf fsaverage rh white --sim-done ./rh.CP.paired-diff/csd/poll/done.perm.abs.3.j001 2/4 Thu Jun 21 11:19:49 CST 2012 mri_glmfit --y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control-pdm.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control_main.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/pdm_main.mtx --mask ./rh.CP.paired-diff/mask.mgh --sim perm 2500 3 ./rh.CP.paired-diff/csd/perm.abs.3.j002 --sim-sign abs --fwhm 0 --fsgd ./rh.CP.paired-diff/y.fsgd dods --surf fsaverage rh white --sim-done ./rh.CP.paired-diff/csd/poll/done.perm.abs.3.j002 3/4 Thu Jun 21 11:19:49 CST 2012 mri_glmfit --y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control-pdm.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control_main.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/pdm_main.mtx --mask ./rh.CP.paired-diff/mask.mgh --sim perm 2500 3 ./rh.CP.paired-diff/csd/perm.abs.3.j003 --sim-sign abs --fwhm 0 --fsgd ./rh.CP.paired-diff/y.fsgd dods --surf fsaverage rh white --sim-done ./rh.CP.paired-diff/csd/poll/done.perm.abs.3.j003 4/4 Thu Jun 21 11:19:49 CST 2012 mri_glmfit --y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control-pdm.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control_main.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/pdm_main.mtx --mask ./rh.CP.paired-diff/mask.mgh --sim perm 2500 3 ./rh.CP.paired-diff/csd/perm.abs.3.j004 --sim-sign abs --fwhm 0 --fsgd ./rh.CP.paired-diff/y.fsgd dods --surf fsaverage rh white --sim-done ./rh.CP.paired-diff/csd/poll/done.perm.abs.3.j004 Polling Poll 1 job 1 Thu Jun 21 11:19:49 CST 2012 INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed simbase ./rh.CP.paired-diff/csd/perm.abs.3.j003 gdfReadHeader: reading ./rh.CP.paired-diff/y.fsgd INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 stai 3.26562 11.21 1 cesd 2.17188 6.98112 Class Means of each Continuous Variable 1 control -2.2188 -0.5938 2 PDM 8.7500 4.9375 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Applications/freesurfer/subjects/PDM_cortical_thickness cmdline mri_glmfit --y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control-pdm.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control_main.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/pdm_main.mtx --mask ./rh.CP.paired-diff/mask.mgh --sim perm 2500 3 ./rh.CP.paired-diff/csd/perm.abs.3.j003 --sim-sign abs --fwhm 0 --fsgd ./rh.CP.paired-diff/y.fsgd dods --surf fsaverage rh white --sim-done ./rh.CP.paired-diff/csd/poll/done.perm.abs.3.j003 sysname Darwin hostname fmripc2.vghtpe.gov.tw machine x86_64 user IBRU FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh logyflag 0 usedti 0 FSGD ./rh.CP.paired-diff/y.fsgd mask ./rh.CP.paired-diff/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 6.72042 Matrix condition is 430.174 Found 149926 voxels in mask Reshaping mriglm->mask... search space = 74490.928733 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force simbase ./rh.CP.paired-diff/csd/perm.abs.3.j002 gdfReadHeader: reading ./rh.CP.paired-diff/y.fsgd INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 stai 3.26562 11.21 1 cesd 2.17188 6.98112 Class Means of each Continuous Variable 1 control -2.2188 -0.5938 2 PDM 8.7500 4.9375 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Applications/freesurfer/subjects/PDM_cortical_thickness cmdline mri_glmfit --y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control-pdm.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control_main.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/pdm_main.mtx --mask ./rh.CP.paired-diff/mask.mgh --sim perm 2500 3 ./rh.CP.paired-diff/csd/perm.abs.3.j002 --sim-sign abs --fwhm 0 --fsgd ./rh.CP.paired-diff/y.fsgd dods --surf fsaverage rh white --sim-done ./rh.CP.paired-diff/csd/poll/done.perm.abs.3.j002 sysname Darwin hostname fmripc2.vghtpe.gov.tw machine x86_64 user IBRU FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh logyflag 0 usedti 0 FSGD ./rh.CP.paired-diff/y.fsgd mask ./rh.CP.paired-diff/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 6.72042 Matrix condition is 430.174 Found 149926 voxels in mask Reshaping mriglm->mask... search space = 74490.928733 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force simbase ./rh.CP.paired-diff/csd/perm.abs.3.j001 gdfReadHeader: reading ./rh.CP.paired-diff/y.fsgd INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 stai 3.26562 11.21 1 cesd 2.17188 6.98112 Class Means of each Continuous Variable 1 control -2.2188 -0.5938 2 PDM 8.7500 4.9375 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Applications/freesurfer/subjects/PDM_cortical_thickness cmdline mri_glmfit --y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control-pdm.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control_main.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/pdm_main.mtx --mask ./rh.CP.paired-diff/mask.mgh --sim perm 2500 3 ./rh.CP.paired-diff/csd/perm.abs.3.j001 --sim-sign abs --fwhm 0 --fsgd ./rh.CP.paired-diff/y.fsgd dods --surf fsaverage rh white --sim-done ./rh.CP.paired-diff/csd/poll/done.perm.abs.3.j001 sysname Darwin hostname fmripc2.vghtpe.gov.tw machine x86_64 user IBRU FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh logyflag 0 usedti 0 FSGD ./rh.CP.paired-diff/y.fsgd mask ./rh.CP.paired-diff/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 6.72042 Matrix condition is 430.174 Found 149926 voxels in mask Reshaping mriglm->mask... search space = 74490.928733 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force simbase ./rh.CP.paired-diff/csd/perm.abs.3.j004 gdfReadHeader: reading ./rh.CP.paired-diff/y.fsgd INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 stai 3.26562 11.21 1 cesd 2.17188 6.98112 Class Means of each Continuous Variable 1 control -2.2188 -0.5938 2 PDM 8.7500 4.9375 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Applications/freesurfer/subjects/PDM_cortical_thickness cmdline mri_glmfit --y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control-pdm.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/control_main.mtx --C ./rh.CP.paired-diff/tmp.mri_glmfit-sim-27056/pdm_main.mtx --mask ./rh.CP.paired-diff/mask.mgh --sim perm 2500 3 ./rh.CP.paired-diff/csd/perm.abs.3.j004 --sim-sign abs --fwhm 0 --fsgd ./rh.CP.paired-diff/y.fsgd dods --surf fsaverage rh white --sim-done ./rh.CP.paired-diff/csd/poll/done.perm.abs.3.j004 sysname Darwin hostname fmripc2.vghtpe.gov.tw machine x86_64 user IBRU FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh logyflag 0 usedti 0 FSGD ./rh.CP.paired-diff/y.fsgd mask ./rh.CP.paired-diff/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Applications/freesurfer/subjects/PDM_cortical_thickness/rh.thickness.fwhm10.fsaverage.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 6.72042 Matrix condition is 430.174 Found 149926 voxels in mask Reshaping mriglm->mask... search space = 74490.928733 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force Poll 2 job 1 Thu Jun 21 11:19:59 CST 2012 Poll 3 job 1 Thu Jun 21 11:20:09 CST 2012 Poll 4 job 1 Thu Jun 21 11:20:19 CST 2012 Poll 5 job 1 Thu Jun 21 11:20:29 CST 2012 Poll 6 job 1 Thu Jun 21 11:20:39 CST 2012 [deleted] Poll 434990 job 1 Fri Aug 10 20:41:03 CST 2012 Poll 434991 job 1 Fri Aug 10 20:41:13 CST 2012 Poll 434992 job 1 Fri Aug 10 20:41:23 CST 2012 Poll 434993 job 1 Fri Aug 10 20:41:33 CST 2012 Poll 434994 job 1 Fri Aug 10 20:41:43 CST 2012 Poll 434995 job 1 Fri Aug 10 20:41:53 CST 2012 Poll 434996 job 1 Fri Aug 10 20:42:03 CST 2012