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
>
>
>
>
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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