I think that could be the problem. I don't think that qdec cleans up after itself, so that is probably a contrast from another analysis. Try rerunning qdec using a different output folder, or just delete that contrast.
doug On 07/29/2014 04:52 PM, Jon Alan Wieser wrote: > I ran the analysis in qdec, not mri_glmfit . I did a few analyses in qdec > > Jon > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@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 >> >> >> >> >> _______________________________________________ >> 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
