Thank you doug. Is there a command for normalising in fsgd file. I know DeMeaning is DeMeanFlag 1. Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Friday, July 22, 2016 6:45 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] mri_glmfit problem/2 group 6 covariates Try demeaning and normalizing your continuous covariates in the FSGD file. On 07/22/2016 06:17 PM, miracle ozzoude wrote: > > Hello doug, > > while running the mir_glmfit problem, i encountered this problem “ > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 Age 39.9375 17.3312 > > 1 Education 15.5625 1.99902 > > 2 Firstscore 1.03375 0.341785 > > 3 Secondscore 1.03906 0.370678 > > 4 Thirdscore 1.13844 0.4768 > > 5 Averagescore 1.07375 0.364046 > > Class Means of each Continuous Variable > > 1 Group1 35.6316 15.0526 1.0342 1.2111 1.4289 1.2305 > > 2 Group2 46.2308 16.3077 1.0331 0.7877 0.7138 0.8446 > > INFO: gd2mtx_method is dods > > Reading source surface > /Users/paul/Desktop/improvervsdeclinermri/fsaverage/surf/lh.white > > Number of vertices 163842 > > Number of faces 327680 > > Total area 65416.648438 > > AvgVtxArea 0.399267 > > AvgVtxDist 0.721953 > > StdVtxDist 0.195470 > > $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ > > cwd /Users/paul/Desktop/improvervsdeclinermri > > cmdline mri_glmfit --y lh.new.MOT.thickness.10B.mgh --fsgd > new.MOT.fsgd dods --C new.firstmatrix.mtx --C new.secondmatrix.mtx --C > new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C new.fifthmatrix.mtx > --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C > new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx > --surf fsaverage lh --cortex --glmdir lh.new.MOT.glmdir > > sysname Darwin > > hostname TC-CT-LAB4-iMAC.local > > machine x86_64 > > user paul > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /Users/paul/Desktop/improvervsdeclinermri/lh.new.MOT.thickness.10B.mgh > > logyflag 0 > > usedti 0 > > FSGD new.MOT.fsgd > > labelmask > /Users/paul/Desktop/improvervsdeclinermri/fsaverage/label/lh.cortex.label > > maskinv 0 > > glmdir lh.new.MOT.glmdir > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory lh.new.MOT.glmdir > > Loading y from > /Users/paul/Desktop/improvervsdeclinermri/lh.new.MOT.thickness.10B.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to lh.new.MOT.glmdir/Xg.dat > > Normalized matrix condition is 1.27568e+06 > > Design matrix ------------------ > > 1.000 0.000 23.000 0.000 15.000 0.000 1.680 0.000 > 1.780 0.000 2.110 0.000 1.860 0.000; > > 1.000 0.000 43.000 0.000 16.000 0.000 0.840 0.000 > 0.890 0.000 1.190 0.000 0.970 0.000; > > 1.000 0.000 39.000 0.000 17.000 0.000 0.790 0.000 > 0.840 0.000 1.220 0.000 0.950 0.000; > > 1.000 0.000 19.000 0.000 13.000 0.000 0.840 0.000 > 1.060 0.000 1.260 0.000 1.050 0.000; > > 1.000 0.000 28.000 0.000 13.000 0.000 1.060 0.000 > 1.120 0.000 1.370 0.000 1.180 0.000 > > …………………………………………………………………………………………………………………... > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1.27568e+06 > > -------------------------------- > > Possible problem with experimental design: > > Check for duplicate entries and/or lack of range of > > continuous variables within a class. > > If you seek help with this problem, make sure to send: > > 1. Your command line: > > mri_glmfit --y lh.new.MOT.thickness.10B.mgh --fsgd new.MOT.fsgd > dods --C new.firstmatrix.mtx —C new.secondmatrix.mtx --C > new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C new.fifthmatrix.mtx > --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C > new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx > --surf fsaverage lh --cortex --glmdir lh.new.MOT.glmdir > > 2. The FSGD file (if using one) > > 3. And the design matrix above” > > Below are my fsgd file and contrast matrix. I can’t add DeMeanFlag 1 > because I am using dods and interested in group difference. Also, none > of the responses from people with similar error helped me. I am using > version 5.1 > > Thank you very much. > > Paul > > > > GroupDescriptorFile 1 > > Title MOT > > Class Group1 > > Class Group2 > > Variables Age Education Firstscore > Secondscore Thirdscore Averagescore > > Input 01053p/fsdir Group1 23 15 1.68 > 1.78 2.11 1.86 > > Input 01054p/fsdir Group1 43 16 0.84 > 0.89 1.19 0.97 > > Input 01061p/fsdir Group1 39 17 0.79 > 0.84 1.22 0.95 > > Input 01062p/fsdir Group1 19 13 0.84 > 1.06 1.26 1.05 > > Input 01074p/fsdir Group1 28 13 1.06 > 1.12 1.37 1.18 > > Input 01080p/fsdir Group1 28 18 0.97 > 1.26 1.33 1.19 > > Input 01099p/fsdir Group1 37 16 0.87 > 1.15 1.37 1.13 > > Input 01101p/fsdir Group1 20 14 1.00 > 1.37 1.45 1.27 > > Input 01102p/fsdir Group1 58 16 0.97 > 1.12 1.41 1.27 > > Input 01121p/fsdir Group1 28 18 0.87 > 1.00 1.00 0.96 > > Input 01127p/fsdir Group1 46 16 0.77 > 1.06 1.58 1.14 > > Input 01128p/fsdir Group1 21 16 1.58 > 1.78 1.78 1.71 > > Input 01130p/fsdir Group1 22 16 1.50 > 1.22 1.63 1.45 > > Input 01131p/fsdir Group1 19 13 1.54 > 1.68 2.11 1.78 > > Input 01141p/fsdir Group1 17 12 1.00 > 1.09 1.30 1.13 > > Input 1044pp/fsdir Group1 51 16 0.94 > 1.54 1.68 1.39 > > Input 1053pp/fsdir Group1 44 16 1.22 > 1.30 1.50 1.34 > > Input 1058pp/fsdir Group1 78 12 0.61 > 1.12 1.15 0.96 > > Input 1060pp/fsdir Group1 56 13 0.60 > 0.63 0.71 0.65 > > Input 01047p/fsdir Group2 50 18 1.12 > 0.94 0.94 1.00 > > Input 01075p/fsdir Group2 20 15 1.12 > 0.84 0.60 0.85 > > Input 01077p/fsdir Group2 48 16 0.43 > 0.35 0.35 0.38 > > Input 01091p/fsdir Group2 23 16 1.58 > 1.22 1.22 1.34 > > Input 01096p/fsdir Group2 17 17 1.50 > 1.26 1.19 1.32 > > Input 01113p/fsdir Group2 51 18 0.75 > 0.69 0.60 0.68 > > Input 01124p/fsdir Group2 43 18 1.33 > 0.89 0.87 1.03 > > Input 01134p/fsdir Group2 59 16 0.82 > 0.60 0.60 0.67 > > Input 1004pp/fsdir Group2 46 19 0.82 > 0.79 0.71 0.77 > > Input 1040pp/fsdir Group2 64 13 0.92 > 0.55 0.46 0.64 > > Input 1043pp/fsdir Group2 49 16 1.58 > 1.03 0.89 1.17 > > Input 1064pp/fsdir Group2 78 12 0.40 > 0.11 0.10 0.20 > > Input 1067pp/fsdir Group2 53 18 1.06 > 0.97 0.75 0.93 > > > first contrast matrix > > 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 > > group1 greater than group 2 regressing out age, education, first, > second, third and average > > second constrast matrix > > -1 1 0 0 0 0 0 0 0 0 0 0 0 0 > > group 2 greater than group 1 regressing out age, education, first, > second, third and average > > third contrast matrix > > 0 0 0 0 0 0 0.5 -0.5 0 0 0 0 0 0 > > group 1 showing increasing correlation with first score compared to > group 2 > > fourth contrast matrix > > 0 0 0 0 0 0 -0.5 0.5 0 0 0 0 0 0 > > group2 showing showing increasing correlation with first score > compared to group 1 > > fifth contrast matrix > > 0 0 0 0 0 0 0 0 0.5 -0.5 0 0 0 0 > > group1 showing showing increasing correlation with second score > compared to group 2 > > sixth contrast matrix > > 0 0 0 0 0 0 0 0 -0.5 0.5 0 0 0 0 > > group2 showing showing increasing correlation with second score > compared to group 1 > > seventh contrast matrix > > 0 0 0 0 0 0 0 0 0 0 0.5 -0.5 0 0 > > group1 showing showing increasing correlation with third score > compared to group 2 > > eighth contrast matrix > > 0 0 0 0 0 0 0 0 0 0 -0.5 0.5 0 0 > > group2 showing showing increasing correlation with third score > compared to group 1 > > ninety contrast matrix > > 0 0 0 0 0 0 0 0 0 0 0 0 0.5 -0.5 > > group1 showing showing increasing correlation with average score > compared to group 2 > > tenth contrast matrix > > 0 0 0 0 0 0 0 0 0 0 0 0 -0.5 0.5 > > group2 showing showing increasing correlation with average score > compared to group 1 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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