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
>
>

> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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