I ran the analysis in qdec, not mri_glmfit . I did a few analyses in qdec
Jon ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 29, 2014 3:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRI_glmfit-sim error
I'm not sure how that could have happened. Did you run mri_glmfit multiple times by any chance?
On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:
I'm running a monte carlo sim and am getting an error:
command line:
mri_glmfit-sim \ --glmdir MTA_persistanceCP \ --sim mc-z 1000 1.3 mc-z.negative \ --sim-sign abs --cwpvalthresh 0.999 \ --overwrite
output:
cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label /Studies/MTA/fsaverage/label/rh.aparc.label --C /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat SURFACE: fsaverage rh log file is MTA_persistanceCP/mc-z.negative.mri_glmfit-sim.log
cd /Studies/MTA/qdec /Applications/freesurfer/bin/mri_glmfit-sim --glmdir MTA_persistanceCP --sim mc-z 1000 1.3 mc-z.negative --sim-sign abs --cwpvalthresh 0.999 --overwrite
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Tue Jul 29 14:08:52 CDT 2014 Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 wieser setenv SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd /Studies/MTA/qdec/MTA_persistanceCP/qdec.fsgd dods --glmdir /Studies/MTA/qdec/MTA_persistanceCP --surf fsaverage rh --label /Studies/MTA/fsaverage/label/rh.aparc.label --C /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Avg-Intercept-thickness.mat --C /Studies/MTA/qdec/MTA_persistanceCP/contrasts/rh-Diff-F-M-Intercept-thickness.mat
DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 14.370530 nSimPerJob = 1000 1/1 Tue Jul 29 14:08:52 CDT 2014 mri_glmfit --y MTA_persistanceCP/y.mgh --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-F-M-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-thickness-Gender-Cor.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-F-M-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx --mask MTA_persistanceCP/mask.mgh --sim mc-z 1000 1.3 MTA_persistanceCP/csd/mc-z.negative.j001 --sim-sign abs --fwhm 14.370530 --fsgd MTA_persistanceCP/y.fsgd dods --label /Studies/MTA/fsaverage/label/rh.aparc.label --surf fsaverage rh white INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed simbase MTA_persistanceCP/csd/mc-z.negative.j001 FWHM = 14.370530 gdfReadHeader: reading MTA_persistanceCP/y.fsgd INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 Age 23.9348 1.40499 Class Means of each Continuous Variable 1 Gender_MFF 23.8000 2 Gender_MFM 23.9722 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 Surface smoothing by fwhm=14.370530, niters=152.000000
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Studies/MTA/Qdec cmdline mri_glmfit --y MTA_persistanceCP/y.mgh --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-C-P-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-Control-MJuser-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Diff-F-M-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Avg-thickness-Gender-Cor.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-C-P-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-Control-MJuser-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-Diff-F-M-Intercept-thickness.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Cor-thickness-Gender.mtx --C MTA_persistanceCP/tmp.mri_glmfit-sim-68749/rh-X-ADHD_Persist-MJ_group-Intercept-thickness.mtx --mask MTA_persistanceCP/mask.mgh --sim mc-z 1000 1.3 MTA_persistanceCP/csd/mc-z.negative.j001 --sim-sign abs --fwhm 14.370530 --fsgd MTA_persistanceCP/y.fsgd dods --label /Studies/MTA/fsaverage/label/rh.aparc.label --surf fsaverage rh white sysname Darwin hostname psy-blackbird.ad.uwm.edu machine x86_64 user wieser FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 14.370530 niters 152.000000 OneSampleGroupMean 0 y /Studies/MTA/Qdec/MTA_persistanceCP/y.mgh logyflag 0 usedti 0 FSGD MTA_persistanceCP/y.fsgd labelmask /Studies/MTA/fsaverage/label/rh.aparc.label maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Studies/MTA/Qdec/MTA_persistanceCP/y.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 1366.76 Matrix condition is 712602 Found 148495 points in label. Found 148495 voxels in mask Reshaping mriglm->mask... search space = 73776.320066 ERROR: dimension mismatch between X and contrast MTA_persistanceCP/tmp.mri_glmfit-sim-68749/lh-Avg-thickness-Gender-Cor.mtx X has 4 cols, C has 12 cols
How do I fix this dimension masmatch?
thanks
Jon
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