In matlab Xsss = sqrt(sum(X.^2)); Xn = X ./ repmat(Xsss,[ntptot 1]); Then look at the condition of Xn
On 06/12/2012 06:12 PM, mdkrue...@uwalumni.com wrote: > due to their similarity is it not possible to run this analysis? also > how did you adjust for the scale presented here? > > On Tue, Jun 12, 2012 at 5:06 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > When I adjusted for the scale, the matrix is still ill-conditioned. It > looks like some of the columns are very similar to each other. > doug > > On 06/12/2012 05:15 PM, mdkrue...@uwalumni.com > <mailto:mdkrue...@uwalumni.com> wrote: > > Hello- > > > > I am trying to analyze the cortical thickness between two groups of > > subjects Cl1 and CL2. When i run the GLM i receive the error: > > > > matrix is ill-conditioned or badly scaled, condno = 1e+08 > > > > I am under the impression the error could be due to the > > non-uniformity in the range/scale of the regressors. > > > > here is my information: > > > > contrast is 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > > > > > > 1) mri_glmfit --y lh.PvNPeverything.10.mgh --fsgd > PvNPeverything.fsgd > > dods --C PvNP_everything.mtx --surf UNM_ALLGOOD lh --cortex --glmdir > > lh.PvNPeverything.glmdir > > > > 2) (sample of my fsgd) - there are no columns with all 0's in them > > GroupDescriptorFile 1 > > Title Methedone Comparison > > Class Cl1 > > Class Cl2 > > Variables > > WAISIQtrait_anxietyalcohol_yearheroin_yearcocaine_yearcannabis_yearmeth_yearamphetamines_yearmeth_amphet_yearhallucinogens_year > > > > > > inhalants_yearmethodne_yearopiates_yearpills_yearopitates_pills_yearother_year > > total_years > > InputM87160505Cl18633103911011180066049 > > InputM87161888Cl11095900722000000000032 > > InputM87107477Cl1893412091309961001910057 > > InputM87199897Cl11174402301000000915015360 > > InputM87146570Cl1944226038000000000637 > > InputM87189755Cl111159110.52150331.500000036 > > InputM87169696Cl18622201114000000000025 > > InputM87187366Cl11065128027002020000000075 > > InputM87178857Cl211748044805570400.080.08042.08 > > InputM87165923Cl21034052015000000011023 > > InputM87110556Cl21346040115000000000020 > > InputM87183811Cl2974315083000000000026 > > > > 3) design matrix > > > > 1 0 86 0 33 0 10 0 3 > 0 9 0 11 0 0 0 1 > 0 1 0 > > 1 0 8 0 0 0 0 0 6 > 0 6 0 0 0 49 0 > > 1 0 109 0 59 0 0 0 0 > 0 7 0 22 0 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 32 0 > > 1 0 89 0 34 0 12 0 0 > 0 9 0 13 0 0 0 9 > 0 9 0 > > 6 0 10 0 0 0 1 0 9 > 0 10 0 0 0 57 0 > > 1 0 89 0 40 0 15 0 5 > 0 2 0 30 0 10 0 0 > 0 > > 10 0 2 0 0 0 0 0 0 > 0 0 0 0 0 0 0 59 > 0 > > 1 0 77 0 44 0 0 0 0 > 0 3 0 0 0 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 3 0 > > 1 0 91 0 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> > 0 0.5 0 0 0 0 0 0 0 > 0 0 0 0 0 0 14 > > 0 1 0 91 0 37 0 0 0 > 0 0 0 0 8 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 12 > > 0 1 0 91 0 48 0 0 0 > 0 0 0 0 1 0 0 0 > 0 0 0 0 > > 0.25 0 0 0 0 0 0 0 0 > 0 0 0 0 0 4.25 > > 0 1 0 94 0 58 0 1 0 > 0 0 0.67 0 4 0 5 0 > 0 0 > > 5 0 0 0 3 0 0 0 0 > 0 0 0 0 0 0 0 13.67 > > 0 1 0 114 0 48 0 17 0 > 0 0 6 0 17 0 0 0 > 7 0 > > 7 0 5 0 0 0 0 0 0 > 0 2 0 2 0 0 0 50 > > 0 1 0 106 0 54 0 15 0 > 0 0 7 0 15 0 0 0 > 15 0 > > 15 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 44 > > 0 1 0 74 0 46 0 0 0 > 0 0 0 0 5 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 5 > > 0 1 0 91 0 43 0 0 0 > 0 0 0 0 0 0 0 0 > 0.33 0 > > 0.33 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0.33 > > 0 1 0 80 0 27 0 3 0 > 30 0 0 0 30 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 60 > > 0 1 0 97 0 33 0 0.5 0 > 0 0 0.25 0 2 0 2 0 > 0 0 > > 2 0 0 0 0.17 0 0 0 0 > 0 0 0 0 0 0 0 4.92 > > 0 1 0 100 0 31 0 6 0 > 0 0 0 0 5 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 9 > > 0 1 0 109 0 29 0 0 0 > 0 0 0 0 13 0 0 0 > 10 0 > > 10 0 1 0 0 0 0 0 0 > 0 0 0 0 0 0 0 24 > > 0 1 0 80 0 37 0 0 0 > 0 0 8 0 8 0 0.5 0 > 0 0 > > 0.5 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 16.5 > > 0 1 0 72 0 55 0 10 0 > 0 0 0 0 10 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 20 > > 0 1 0 103 0 40 0 0 0 > 0.5 0 1 0 8 0 0.67 0 > 0 0 > > 0.67 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 10.17 > > 0 1 0 77 0 32 0 0 0 > 0.5 0 0 0 12 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 12.5 > > 0 1 0 120 0 28 0 0 0 > 0 0 4 0 12 0 0 0 > 7 0 7 > > 0 4 0 0 0 0 0 0 0 > 0 0 0 0 7 0 34 > > 0 1 0 86 0 32 0 11 0 > 0 0 8 0 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 19 > > 0 1 0 91 0 44 0 2 0 > 0 0 1 0 0 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 3 > > 0 1 0 94 0 50 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 > > 0 1 0 100 0 29 0 5 0 > 0 0 0 0 16 0 17 0 > 0 0 > > 17 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 38 > > 0 1 0 94 0 25 0 4 0 > 0 0 0.5 0 10 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 12.5 > > 0 1 0 74 0 51 0 10 0 > 0 0 0 0 20 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 30 > > 0 1 0 97 0 36 0 30 0 > 0 0 20 0 33 0 5 0 > 6 0 > > 11 0 6 0 0 0 0 0 0 > 0 0 0 0 0 0 0 90 > > 0 1 0 117 0 35 0 0 0 > 0 0 0 0 3 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 5 > > 0 1 0 80 0 51 0 7 0 > 4 0 0 0 8 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 19 > > 0 1 0 103 0 28 0 9 0 > 0 0 1 0 1 0 0 0 > 8 0 > > 8 0 8 0 0 0 0 0 0 > 0 0 0 0 0 0 0 27 > > 0 1 0 103 0 74 0 6 0 > 0 0 0 0 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 6 > > 0 1 0 89 0 57 0 10 0 > 0 0 0 0 0 0 15 0 > 0 0 > > 15 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 18 > > 0 1 0 109 0 33 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > > 0 1 0 109 0 28 0 3 0 > 0 0 2 0 2 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 5 > > 0 1 0 91 0 27 0 20 0 > 0 0 15 0 0 0 3 0 > 0 0 3 > > 0 0 0 0 0 0 0 17 0 > 0 0 17 0 0 0 55 > > 0 1 0 89 0 48 0 9 0 > 0 0 0.25 0 10 0 20 0 > 0 0 > > 20 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 39.25 > > 0 1 0 97 0 28 0 10 0 > 0 0 4 0 10 0 5 0 > 0 0 5 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 29 > > 0 1 0 100 0 40 0 3 0 > 0 0 0 0 0.17 0 0 0 > 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > 3.17 > > 0 1 0 89 0 21 0 20 0 > 8 0 25 0 25 0 10 0 > 0 0 > > 10 0 0 0 2 0 0 0 0 > 0 0 0 0 0 0 0 90 > > 0 1 0 103 0 54 0 10 0 > 0 0 2 0 0 0 0 0 > 2 0 2 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 12 > > 0 1 0 77 0 49 0 0 0 > 0 0 10 0 12 0 0 0 > 4 0 4 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 2 0 42 > > 0 1 0 89 0 42 0 0 0 > 0 0 4 0 10 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 14 > > 0 1 0 117 0 34 0 25 0 > 0 0 2 0 25 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 52 > > 0 1 0 83 0 56 0 12 0 > 0 0 0 0 15 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 15 > > 0 1 0 91 0 33 0 0 0 > 0 0 0 0 2 0 0 0 > 0 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 2 > > 0 1 0 106 0 36 0 0 0 > 0 0 0 0 0 0 0 0 > 0 0 > > 0 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 > > 0 1 0 120 0 50 0 1 0 > 0 0 0 0 2 0 1 0 > 0 0 > > 1 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 6 > > > > > > -- > > Michael D. Kruepke > > PhD - University of Illinois at Urbana-Champaign > > BA - Psych - University of Wisconsin-Madison > > mdkrue...@gmail.com <mailto:mdkrue...@gmail.com> > <mailto:mdkrue...@gmail.com <mailto:mdkrue...@gmail.com>> > > (262)-483-7449 <tel:%28262%29-483-7449> > > > > > > > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > 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. > > > > > -- > Michael D. Kruepke > PhD - University of Illinois at Urbana-Champaign > BA - Psych - University of Wisconsin-Madison > mdkrue...@gmail.com <mailto:mdkrue...@gmail.com> > (262)-483-7449 <tel:%28262%29-483-7449> > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
