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>> 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>
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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
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/

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