Can you resend the design matrix? On 07/26/2016 11:46 AM, miracle ozzoude wrote: > Hello Doug, > Sure. Here are my new fsgd file and new contrast matrix ( matrix is > the same as the old one). > Best, > Paul > GroupDescriptorFile 1 > Title MOT > Class Group1 > Class Group2 > Variables Age Education Firstscore Secondscore Thirdscore Averagescore > Input 01053p/fsdir Group1 -0.96 -0.17 1.86 1.97 2.01 2.14 > Input 01054p/fsdir Group1 0.17 0.29 -0.56 -0.40 0.11 -0.26 > Input 01061p/fsdir Group1 -0.05 0.75 -0.70 -0.53 0.17 -0.33 > Input 01062p/fsdir Group1 -1.19 -1.10 -0.56 0.06 0.25 -0.05 > Input 01074p/fsdir Group1 -0.68 -1.10 0.08 0.21 0.48 0.31 > Input 01080p/fsdir Group1 -0.68 1.21 -0.18 0.59 0.40 0.32 > Input 01099p/fsdir Group1 -0.17 0.29 -0.47 0.29 0.48 0.16 > Input 01101p/fsdir Group1 -1.13 -0.63 -0.10 0.88 0.64 0.55 > Input 01102p/fsdir Group1 1.03 0.29 -0.18 0.21 0.56 0.26 > Input 01121p/fsdir Group1 -0.68 1.21 -0.47 -0.10 -0.29 -0.31 > Input 01127p/fsdir Group1 0.34 0.29 -0.76 0.06 0.91 0.18 > Input 01128p/fsdir Group1 -1.08 0.29 1.57 1.97 1.32 1.74 > Input 01130p/fsdir Group1 -1.02 0.29 1.34 0.48 1.01 1.03 > Input 01131p/fsdir Group1 -1.19 -1.10 1.46 1.70 2.01 1.92 > Input 01141p/fsdir Group1 -1.30 -1.56 -0.10 0.14 0.33 0.16 > Input 1044pp/fsdir Group1 0.63 0.29 -0.27 1.33 1.12 0.86 > Input 1053pp/fsdir Group1 0.23 0.29 0.54 0.69 0.75 0.73 > Input 1058pp/fsdir Group1 2.16 -1.56 -1.22 0.21 0.02 -0.30 > Input 1060pp/fsdir Group1 0.91 -1.10 -1.25 -1.09 -0.88 -1.15 > Input 01047p/fsdir Group2 0.57 1.21 0.25 -0.26 -0.41 -0.19 > Input 01075p/fsdir Group2 -1.13 -0.17 0.25 -0.53 -1.11 -0.59 > Input 01077p/fsdir Group2 0.46 0.29 -1.74 -1.83 -1.63 -1.89 > Input 01091p/fsdir Group2 -0.96 0.29 1.57 0.48 0.17 0.73 > Input 01096p/fsdir Group2 -1.3 -2.02 1.34 0.59 0.11 0.67 > Input 01113p/fsdir Group2 0.63 1.21 -0.82 -0.93 -1.11 -1.06 > Input 01124p/fsdir Group2 0.17 1.21 0.85 -0.40 -0.55 -0.11 > Input 01134p/fsdir Group2 1.08 0.29 -0.62 -1.17 -1.11 -1.08 > Input 1004pp/fsdir Group2 0.34 1.67 -0.62 -0.66 -0.88 -0.81 > Input 1040pp/fsdir Group2 1.37 -1.10 -0.33 -1.30 -1.40 -1.16 > Input 1043pp/fsdir Group2 0.51 0.29 1.57 -0.02 -0.51 0.26 > Input 1064pp/fsdir Group2 2.16 -1.56 -1.83 -2.47 -2.14 -2.36 > Input 1067pp/fsdir Group2 0.74 1.21 0.08 -0.18 -0.80 -0.39 > > New Contrast Matrix > > 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 > > > > > On Mon, Jul 25, 2016 at 11:19 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Can you send your new fsgd file and new design matrix? > > > On 7/24/16 6:06 PM, miracle ozzoude wrote: >> Hello Doug or Bruce, >> I demeaned and normalize like you suggested but I'm still getting >> the same results. I created a new fsgd file using the demeaned >> and normalized variables (n = (x-mean)/std(x). Any reason why? >> Thank you very much. >> Paul >> >> On Fri, Jul 22, 2016 at 6:43 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> 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 >> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://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 >> <mailto: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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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
