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 . 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