you have to at least remove the commas
On 10/4/17 1:09 PM, Dowling, Kevin Francis wrote:
Dear Freesurfer experts,
I'm trying to run a between groups analysis for two groups with a matrix set up for DOSS regressing out 5 covariates (contrast is 1 -1 0 0 0 0 0). I am trying to run this with DOSS as one of the covariates is an interaction term that would lead to colinearity issues in DODS. However, I am having some difficulty reading in my matrix. When I send in a standard matlab matrix (attached as a .mat) I get the following, "MatrixReadTXT: could not scan value [1][1] \ ERROR:in uncompressing," which I assume means that my matrix isn't being read properly (full output below under Output 1). I noticed a similar issue was discussed on the forum previously (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034582.... using an ASCII file seemed to resolve the issue. When I convert my matlab file into an ASCII text file (using dlmwrite in matlab, also attached as a .txt file) I get the following error (full output below under Output 2), "MatrixReadTxt: could not scan value [2][1] \ Invalid argument \ WARNING:matlab elment type is 758132281, which is not a matrix."
I'm running Freesurfer version 5.3 on a CentOs 7 system.
I suspect this is probably a simple mistake on my part, but I would greatly appreciate any guidance or further troubleshooting suggestions you might have!
Output 1: [dauntless:RPDR_Manual_Edits] (nmr-stable53-env) mri_glmfit --y /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_map_usingfsgd.mgh --X /cluster/roffman/users/fsgd/matrix/RPDR/99PostFortification_Minus_100PreFortification_DOSS_Nuisance_ZAgeGST_ZAgeXGrp_Matrix.mat --C /cluster/roffman/users/fsgd/RPDR_083115/Test_TwoGroups_RegressOutFiveCovariates_OddSyntax.mtx --glmdir /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_fwhm22/FS53Test_TopMinusBottomRegressoutZAgeGST_ZAgeXGrp_DOSS --surf fsaverage rh --fwhm 22 --no-prune Reading source surface /cluster/roffman2/users/RPDR_Manual_Edits//fsaverage/surf/rh.white FWHM = 22.000000 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=22.000000, niters=356.000000 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /autofs/cluster/roffman2/users/RPDR_Manual_Edits cmdline mri_glmfit --y /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_map_usingfsgd.mgh --X /cluster/roffman/users/fsgd/matrix/RPDR/99PostFortification_Minus_100PreFortification_DOSS_Nuisance_ZAgeGST_ZAgeXGrp_Matrix.mat --C /cluster/roffman/users/fsgd/RPDR_083115/Test_TwoGroups_RegressOutFiveCovariates_OddSyntax.mtx --glmdir /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_fwhm22/FS53Test_TopMinusBottomRegressoutZAgeGST_ZAgeXGrp_DOSS --surf fsaverage rh --fwhm 22 --no-prune sysname Linux hostname dauntless.nmr.mgh.harvard.edu machine x86_64 user kfd11 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 22.000000 niters 356.000000 OneSampleGroupMean 0 y /autofs/cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_map_usingfsgd.mgh logyflag 0 X /cluster/roffman/users/fsgd/matrix/RPDR/99PostFortification_Minus_100PreFortification_DOSS_Nuisance_ZAgeGST_ZAgeXGrp_Matrix.mat usedti 0 labelmask /cluster/roffman2/users/RPDR_Manual_Edits//fsaverage/label/rh.cortex.label maskinv 0 glmdir /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_fwhm22/FS53Test_TopMinusBottomRegressoutZAgeGST_ZAgeXGrp_DOSS IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_fwhm22/FS53Test_TopMinusBottomRegressoutZAgeGST_ZAgeXGrp_DOSS Loading y from /autofs/cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_map_usingfsgd.mgh MatrixReadTxT: could not scan value [1][1] Invalid argument ERROR: in uncompressing not enough memory in buffer Cannot allocate memory Segmentation fault (core dumped)Output 2:
[dauntless:RPDR_Manual_Edits] (nmr-stable53-env) mri_glmfit --y /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_map_usingfsgd.mgh --X /cluster/roffman/users/fsgd/matrix/RPDR/99PostFortification_Minus_100PreFortification_DOSS_Nuisance_ZAgeGST_ZAgeXGrp_Matrix_ASCII.txt --C /cluster/roffman/users/fsgd/RPDR_083115/Test_TwoGroups_RegressOutFiveCovariates_OddSyntax.mtx --glmdir /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_fwhm22/FS53Test_TopMinusBottomRegressoutZAgeGST_ZAgeXGrp_DOSS --surf fsaverage rh --fwhm 22 --no-prune Reading source surface /cluster/roffman2/users/RPDR_Manual_Edits//fsaverage/surf/rh.white FWHM = 22.000000 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=22.000000, niters=356.000000
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /autofs/cluster/roffman2/users/RPDR_Manual_Edits cmdline mri_glmfit --y /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_map_usingfsgd.mgh --X /cluster/roffman/users/fsgd/matrix/RPDR/99PostFortification_Minus_100PreFortification_DOSS_Nuisance_ZAgeGST_ZAgeXGrp_Matrix_ASCII.txt --C /cluster/roffman/users/fsgd/RPDR_083115/Test_TwoGroups_RegressOutFiveCovariates_OddSyntax --glmdir /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_fwhm22/FS53Test_TopMinusBottomRegressoutZAgeGST_ZAgeXGrp_DOSS --surf fsaverage rh --fwhm 22 --no-prune sysname Linux hostname dauntless.nmr.mgh.harvard.edu machine x86_64 user kfd11 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 22.000000 niters 356.000000 OneSampleGroupMean 0 y /autofs/cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_map_usingfsgd.mgh logyflag 0 X /cluster/roffman/users/fsgd/matrix/RPDR/99PostFortification_Minus_100PreFortification_DOSS_Nuisance_ZAgeGST_ZAgeXGrp_Matrix_ASCII.txt usedti 0 labelmask /cluster/roffman2/users/RPDR_Manual_Edits//fsaverage/label/rh.cortex.label maskinv 0 glmdir /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_fwhm22/FS53Test_TopMinusBottomRegressoutZAgeGST_ZAgeXGrp_DOSS IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_fwhm22/FS53Test_TopMinusBottomRegressoutZAgeGST_ZAgeXGrp_DOSS Loading y from /autofs/cluster/roffman2/users/RPDR_Manual_Edits/Analyses_Thickness/199_PrePostFort/RH/rh_thickness_map_usingfsgd.mgh MatrixReadTxT: could not scan value [2][1]
Invalid argument WARNING: matlab elment type is 758132281, which is not a matrix.
Kind regards, Kevin
*Kevin F. Dowling * Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.2479
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