Hi, I tested for a difference between the groups on age slope using DODS and there was a difference. Does this mean I cannot re-run the model using DOSS? Please let me know if there is a way I can still test for the difference in thickness between groups.
Thanks again, Allie On Mon, May 7, 2012 at 3:01 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > The right way to do it is to remove the column entirely. You can't do this > inside of the FSGD unless you use DOSS. You can use DOSS if there is no > difference between the groups in the age slope. In fact, it is a good idea > to run this test first. So, create an FSGD with just the age. Create a > contrast to test for a difference between the groups on age slope (and use > DODS). If there are no differences, then re-run your original model using > DOSS (you will need to change the contrast vector). > > doug > > > On 05/07/2012 02:50 PM, Allie Rosen wrote: > >> Hi Doug, >> >> Is there a different number I can substitute into the fifth column so the >> numbers are not all zeroes? >> >> Thank you, >> Allie >> >> >> >> On Mon, May 7, 2012 at 12:39 PM, Allie Rosen <rosen.al...@gmail.com<mailto: >> rosen.al...@gmail.com>**> wrote: >> >> Hi Doug, >> >> Thanks for the help. The fifth column is all zeroes because the >> covariate - length of disease - isn't applicable to control >> subjects. In the end, I want to test the difference in thickness >> between the two groups, regressing out the effect of both >> covariates (age and length of disease). I think this means the >> difference in intercepts between the two groups. >> >> Thanks again, >> Allie >> >> >> >> On Mon, May 7, 2012 at 12:29 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> Hi Allie, the 5th column of your design matrix is all 0s, >> which causes >> the ill conditioning. I don't think this design fits into our >> standard >> framework. You can still analyze and test, we'll just have to >> figure out >> exactly what needs to be done. In the end, what is it that you >> want to >> test? Just a difference in intercepts between the two groups? >> doug >> >> On 05/07/2012 09:38 AM, Allie Rosen wrote: >> > Hello, >> > >> > I am analyzing cortical thickness in a patient and control >> group. I >> > have two covariates: age and length of disease. I am using >> the model from: >> > >> > >> http://surfer.nmr.mgh.harvard.**edu/fswiki/Fsgdf2G2V<http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V> >> > >> > However, for the control group I put length of disease as 0 >> in my FSGD >> > file. When I run the GLM, I get the following error message: >> > >> > matrix is ill-conditioned or badly scaled, condno = 1e+08 >> > >> > Can you please tell me what I am doing wrong? Below is the >> required >> > information. >> > >> > 1. Your command line: >> > >> > mri_glmfit --y lh.disease_length.thickness.**20.mgz --fsgd >> > fsgd_disease_length.txt dods --glmdir >> > lh.disease_length.thickness.**20.glmdir --surf fsaverage lh --C >> > groupdiff_length_disease.mat >> > >> > 2. The FSGD file >> > >> > GroupDescriptorFile 1 >> > Title Anorexia vs Controls >> > Class Control plus blue >> > Class Patient circle green >> > Variables Age Disease_Length >> > >> > Input C07 Control 37 0 >> > Input C28 Control 28 0 >> > Input C39 Control 37 0 >> > Input C54 Control 40 0 >> > Input C57 Control 32 0 >> > Input C10 Control 54 0 >> > Input C33 Control 31 0 >> > Input C29 Control 22 0 >> > Input A01 Patient 39 20 >> > Input A02 Patient 24 11 >> > Input A03 Patient 35 15 >> > Input A04 Patient 40 10 >> > Input A05 Patient 35 20 >> > Input A06 Patient 57 20 >> > Input A07 Patient 31 16 >> > Input A08 Patient 20 8 >> > >> > 3. And the design matrix >> > >> > Design matrix ------------------ >> > 1.000 0.000 37.000 0.000 0.000 0.000; >> > 1.000 0.000 28.000 0.000 0.000 0.000; >> > 1.000 0.000 37.000 0.000 0.000 0.000; >> > 1.000 0.000 40.000 0.000 0.000 0.000; >> > 1.000 0.000 32.000 0.000 0.000 0.000; >> > 1.000 0.000 54.000 0.000 0.000 0.000; >> > 1.000 0.000 31.000 0.000 0.000 0.000; >> > 1.000 0.000 22.000 0.000 0.000 0.000; >> > 0.000 1.000 0.000 39.000 0.000 20.000; >> > 0.000 1.000 0.000 24.000 0.000 11.000; >> > 0.000 1.000 0.000 35.000 0.000 15.000; >> > 0.000 1.000 0.000 40.000 0.000 10.000; >> > 0.000 1.000 0.000 35.000 0.000 20.000; >> > 0.000 1.000 0.000 57.000 0.000 20.000; >> > 0.000 1.000 0.000 31.000 0.000 16.000; >> > 0.000 1.000 0.000 20.000 0.000 8.000; >> > ------------------------------**-- >> > >> > Thank you, >> > Allie >> > >> > >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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> >> >> <http://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> >> >> <http://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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> >> > -- > 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<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> > >
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