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 greve@nmr.mgh.harvard.eduwrote:
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:
- 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?
- 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?
- 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 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu
Follow me on twitter: @tully_laura
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