On Thu, May 26, 2016 at 11:59 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Design matrix, not contrast matrix. It was printed out as part of the
terminal output. It can also be found in glmdir/Xg.dat

On 05/26/2016 01:48 PM, Hanbyul Cho wrote:
> Dear Douglas N Greve,
>
> The Contrast matrix was = [1 -1 0 0 0 0]
> I attached the Xg.dat printed by unended mri_glmfit process.
>
> Thank you.
>
> Han.
>
> On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> Please send the design matrix
>
> On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> > Today, I tested the previous group analysis on other computer,
> and saw
> > the same error massage.
> >
> > I attached the tested fsgd and mtx files.
> >
> > command:
> > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage
> lh --C
> > 052416_contrast.mtx
> >
> > Thank you,
> >
> > Best wishes,
> >
> > Han
> >
> >
> >
> >
> >
> > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > If you seek help with this problem, make sure to send:
> > 1. Your command line:
> > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> > 2. The FSGD file (if using one)
> > 3. And the design matrix above
> >
> > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > Dear FreeSurfer Team,
> > >
> > > I processed the Group analysis by FreeSurfer 5.3.0
> > >
> > > Our data has two groups (Patient, Control) and two
> covariate values
> > > (age, extra value)
> > > mtx, contrast is 1 -1 0 0 0 0
> > > The mris_preproc, and mri_surf2surf command were completed
> > without error.
> > >
> > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi
> lh --meas
> > > thickness --out lh.**G2V2.dods.mgh
> > > mri_surf2surf --hemi lh --s fsaverage --sval
> lh.**G2V2.dods.mgh
> > --fwhm
> > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >
> > > After mri_glmfit command, I saw the error message.
> > >
> > > =========================================================
> > > ERROR: matrix is ill-conditioned or badly scaled, condno =
> 1e+08
> > > --------------------------------
> > > 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.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > > 2. The FSGD file (if using one)
> > > 3. And the design matrix above
> > > =========================================================
> > >
> > > I think our fsgd and mtx compositions are equal to the
> g2v2.fsgd
> > which
> > > FreeSurfer wiki example.
> > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> > >
> > > In this situation, how can I correct my fsgd or mtx files?
> Is there
> > > any other command option?
> > >
> > > Best Regards,
> > >
> > > Han
> > >
> > >
> > > _______________________________________________
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> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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