Thanks for the suggestions Doug, I have a few clarifying questions below, to make sure I understand everything.
On Tue, Oct 22, 2013 at 8:02 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > The duration of illnessis always 0 for your healthy controls(which is > obviously reasonable). The problem is that mri_glmfit is creating a > regressor of all 0s to model this duration and this is causing the > ill-conditionedness. There are several things you can do: > > 1. Create your own design matrix so that HCs do not have a column for > duration. You can edit the one created by mri_glmfit from the fsgd. You > can then feed this matrix into mri_glmfit instead of the fsgd file. > Would I do this for both medication and duration columns? What is the flag for feeding mri_glmfit an .mtx instead of an fsgd? > > 2. Run mri_glmfit with DOSS instead of DODS. This is appropriateif all > four groupshave the same slope with age, mean thickness, medication, and > duration. > i.e. if there are no group differences on age, mean thickness, medication, or duration of illness I can run DOSS? My groups are matched on age and ,mean thickness, but there are obviously group differences in medications and illness duration... thus wouldn't I expect them to have different slopes? > > 3. Recode the HCs be SZs with 0 duration illness. This maynot make sense > with your other variables (like medication). > i.e. collapse them into one group? But, the analysis I am interested in is detecting group differences in thickness whilst controlling for confounds such as age, medication, and duration of illness... if I recoded the HC group wouldn't this change the analysis from between group to within? > > doug > > On 10/21/2013 11:01 PM, Laura M. Tully wrote: > > Hello freesurfers, > > > > I'm trying to run mri_glmfit between groups analysis (patients vs. > > controls) with gender, age, medication (continuous), and duration of > > illness as covariates. The problem is, only the patients have > > medication and duration of illness values - by virtue of being control > > participants, the control group have values of zero for medication and > > duration of illness. This causes issues with the matrix and I'm trying > > to figure out how to get around it. Suggestions would be most > > appreciated. See output and details below, plus attached files. > > > > Thanks! > > > > Laura. > > > > *Command line: * > > mri_glmfit --y lh_grpDiffs_thickness10.mgh --fsgd > > grpdiffs_thickness_lh_Med_Dur.fsgd --fsgd-rescale --C > > Contrast1A_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex > > --glmdir lh_grpdiffs_lh_thickness_Med_Dur.glmdir > > * > > * > > *Output:* > > gdfReadHeader: reading grpdiffs_thickness_lh_Med_Dur.fsgd > > INFO: demeaning continuous variables > > Continuous Variable Means (all subjects) > > 0 Age 36.0909 11.4927 > > 1 LH_Mean_Thick 2.34931 0.118499 > > 2 medication 204.545 330.217 > > 3 duration_illness 7.74545 11.4005 > > Class Means of each Continuous Variable > > 1 HCmale 34.3000 2.3799 0.0000 0.0000 > > 2 HCfemale 32.5556 2.3723 0.0000 0.0000 > > 3 SZmale 36.5000 2.3124 391.2500 14.6875 > > 4 SZfemale 42.2000 2.3265 499.0000 19.1000 > > INFO: gd2mtx_method is dods > > Reading source surface > > /ncf/snp/04/SCORE/freesurfer_analysis/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 /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis > > cmdline mri_glmfit --y lh_grpDiffs_thickness10.mgh --fsgd > > grpdiffs_thickness_lh_Med_Dur.fsgd --fsgd-rescale --C > > Contrast1A_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex > > --glmdir lh_grpdiffs_lh_thickness_Med_Dur.glmdir > > sysname Linux > > hostname ncfws14.rc.fas.harvard.edu <http://ncfws14.rc.fas.harvard.edu> > > machine x86_64 > > user ltully > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y > > > > /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh > > logyflag 0 > > usedti 0 > > FSGD grpdiffs_thickness_lh_Med_Dur.fsgd > > labelmask > > /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.cortex.label > > maskinv 0 > > glmdir lh_grpdiffs_lh_thickness_Med_Dur.glmdir > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory lh_grpdiffs_lh_thickness_Med_Dur.glmdir > > Loading y from > > > /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to lh_grpdiffs_lh_thickness_Med_Dur.glmdir/Xg.dat > > Normalized matrix condition is 1e+08 > > Design matrix ------------------ > > 0.000 0.000 1.000 0.000 0.000 0.000 0.740 0.000 0.000 > > 0.000 -1.700 0.000 0.000 0.000 0.329 0.000 0.000 0.000 > > 0.817 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 -0.392 0.000 0.000 > > 0.000 0.233 0.000 0.000 0.000 0.632 0.000 0.000 0.000 > > -0.148 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.191 0.000 > > 0.000 0.000 0.013 0.000 0.000 0.000 -1.511 0.000 0.000 > > 0.000 -0.272; > > 0.000 0.000 1.000 0.000 0.000 0.000 0.479 0.000 0.000 > > 0.000 0.427 0.000 0.000 0.000 0.212 0.000 0.000 0.000 > > 0.729 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.940 0.000 > > 0.000 0.000 -0.907 0.000 0.000 0.000 0.912 0.000 0.000 > > 0.000 -0.009; > > 0.000 0.000 1.000 0.000 0.000 0.000 1.436 0.000 0.000 > > 0.000 -0.029 0.000 0.000 0.000 -0.276 0.000 0.000 > > 0.000 1.431 0.000; > > 1.000 0.000 0.000 0.000 0.757 0.000 0.000 0.000 -0.235 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 1.018 0.000 0.000 0.000 -0.775 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 1.627 0.000 0.000 0.000 -0.032 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 1.000 0.000 0.000 0.000 1.953 0.000 0.000 0.000 > > -0.070 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 1.105 0.000 0.000 0.000 0.854 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 1.000 0.000 0.000 0.000 1.518 0.000 0.000 0.000 > > -0.864 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.713 0.000 > > 0.000 0.000 0.359 0.000 0.000 0.000 -0.784 0.000 0.000 > > 0.000 -0.886; > > 0.000 1.000 0.000 0.000 0.000 1.083 0.000 0.000 0.000 > > 0.428 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 -1.088 0.000 0.000 > > 0.000 0.190 0.000 0.000 0.000 0.632 0.000 0.000 0.000 > > -0.937 0.000; > > 1.000 0.000 0.000 0.000 -0.548 0.000 0.000 0.000 -0.454 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.375 0.000 > > 0.000 0.000 0.612 0.000 0.000 0.000 1.517 0.000 0.000 > > 0.000 1.395; > > 1.000 0.000 0.000 0.000 0.496 0.000 0.000 0.000 0.010 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 0.131 0.000 0.000 > > 0.000 0.435 0.000 0.000 0.000 -1.185 0.000 0.000 > > 0.000 0.378 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 -1.001 0.000 0.000 > > 0.000 -0.864 0.000 0.000 0.000 0.212 0.000 0.000 0.000 > > -1.201 0.000; > > 0.000 1.000 0.000 0.000 0.000 -0.222 0.000 0.000 0.000 > > -2.138 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 0.931 0.000 0.000 0.000 -1.214 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 1.088 0.000 0.000 > > 0.000 -0.856 0.000 0.000 0.000 -0.943 0.000 0.000 > > 0.000 0.992 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.070 0.000 > > 0.000 0.000 0.401 0.000 0.000 0.000 -1.208 0.000 0.000 > > 0.000 0.342; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.114 0.000 > > 0.000 0.000 -1.051 0.000 0.000 0.000 1.214 0.000 0.000 > > 0.000 2.009; > > 0.000 0.000 1.000 0.000 0.000 0.000 -1.088 0.000 0.000 > > 0.000 -0.147 0.000 0.000 0.000 0.212 0.000 0.000 0.000 > > -1.113 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.017 0.000 > > 0.000 0.000 -1.219 0.000 0.000 0.000 0.306 0.000 0.000 > > 0.000 0.868; > > 0.000 0.000 1.000 0.000 0.000 0.000 0.218 0.000 0.000 > > 0.000 -0.721 0.000 0.000 0.000 -0.983 0.000 0.000 > > 0.000 -0.323 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.149 0.000 > > 0.000 0.000 2.139 0.000 0.000 0.000 0.154 0.000 0.000 > > 0.000 -1.325; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.452 0.000 > > 0.000 0.000 -0.325 0.000 0.000 0.000 -0.300 0.000 0.000 > > 0.000 -1.061; > > 0.000 0.000 1.000 0.000 0.000 0.000 -0.044 0.000 0.000 > > 0.000 0.486 0.000 0.000 0.000 -1.064 0.000 0.000 > > 0.000 -0.060 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 0.653 0.000 0.000 > > 0.000 -0.392 0.000 0.000 0.000 -0.912 0.000 0.000 > > 0.000 1.080 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.975 0.000 > > 0.000 0.000 -0.021 0.000 0.000 0.000 -0.300 0.000 0.000 > > 0.000 -1.061; > > 0.000 0.000 1.000 0.000 0.000 0.000 -1.349 0.000 0.000 > > 0.000 0.579 0.000 0.000 0.000 0.026 0.000 0.000 0.000 > > -1.113 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 -0.566 0.000 0.000 > > 0.000 1.895 0.000 0.000 0.000 0.632 0.000 0.000 0.000 > > -0.850 0.000; > > 1.000 0.000 0.000 0.000 0.670 0.000 0.000 0.000 -0.809 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 -0.722 0.000 0.000 0.000 -0.716 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 1.000 0.000 0.000 0.000 -0.831 0.000 0.000 0.000 > > 1.398 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 1.453 0.000 0.000 0.000 -0.978 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 0.670 0.000 0.000 0.000 -2.429 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 1.000 0.000 0.000 0.000 -0.744 0.000 0.000 0.000 > > -0.121 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 1.000 0.000 0.000 0.000 -0.657 0.000 0.000 0.000 > > 0.082 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 1.018 0.000 0.000 0.000 1.318 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 -1.244 0.000 0.000 0.000 1.208 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 1.000 0.000 0.000 0.000 -1.179 0.000 0.000 0.000 > > 0.444 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 -1.244 0.000 0.000 0.000 0.364 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 -0.809 0.000 0.000 0.000 1.790 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 -0.983 0.000 0.000 0.000 0.558 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 -1.157 0.000 0.000 0.000 0.254 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 -1.157 0.000 0.000 0.000 0.752 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 1.000 0.000 0.000 0.000 -0.918 0.000 0.000 0.000 > > 0.841 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 1.088 0.000 0.000 > > 0.000 -1.354 0.000 0.000 0.000 3.660 0.000 0.000 0.000 > > 1.343 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 -0.305 0.000 0.000 > > 0.000 1.819 0.000 0.000 0.000 -1.185 0.000 0.000 > > 0.000 -1.025 0.000; > > 1.000 0.000 0.000 0.000 -0.461 0.000 0.000 0.000 0.870 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > 1.000 0.000 0.000 0.000 -1.418 0.000 0.000 0.000 -0.336 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > > 0.000 0.000; > > -------------------------------- > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > > > > > -- > > -- > > Laura M. Tully, PhD > > Post-Doctoral Fellow in Psychiatry > > UC Davis Imaging Research Center > > 4701 X Street, > > Sacramento, CA 95817 > > Phone: (916) 734-7927 > > Fax: (916) 734-8750 > > > > Alumnus of Social Neuroscience & Psychopathology Lab, Harvard University > > ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu> > > > > Follow me on twitter: @tully_laura > > -- > > > > > > > > _______________________________________________ > > 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 > > > 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. > > -- -- Laura M. Tully, PhD Post-Doctoral Fellow in Psychiatry UC Davis Imaging Research Center 4701 X Street, Sacramento, CA 95817 Phone: (916) 734-7927 Fax: (916) 734-8750 Alumnus of Social Neuroscience & Psychopathology Lab, Harvard University ltu...@fas.harvard.edu Follow me on twitter: @tully_laura --
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