Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

I'm not sure what the difference is. Compute the mean of the 2nd column, then subtract that number from the values in the 2nd column. doug

On 2/2/16 7:30 AM, Nabin Koirala wrote:

Thank you for your response . Sorry but for my understanding, should i substract the mean from the data (demean) or you mean to remove the value which is equal to the mean ?

Thank you.

Regards, Nabin

On Mon, Feb 1, 2016 at 5:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Try removing the mean from your covariate

On 01/30/2016 01:31 PM, Nabin Koirala wrote:
> Dear Freesurfer forum,
>
> 'I am trying to run qdec analysis for a group of subjects to see if
> correlation exists but I am getting this error only for this
>  particular set of data but could not figure out what is exactly
wrong
> with it. Your suggestion would be greatly appreciated.
>
> Following is the terminal output for the process:
> ..........
> Saving design matrix to
/g/f/h/s/freesurfer/subjects/qdec/Untitled/Xg.dat
> Normalized matrix condition is 27492.1
> Design matrix ------------------
>  1.000   0.408;
>  1.000   0.417;
>  1.000   0.417;
>  1.000   0.405;
>  1.000   0.412;
>  1.000   0.412;
>  1.000   0.411;
>  1.000   0.417;
>  1.000   0.405;
>  1.000   0.406;
>  1.000   0.402;
>  1.000   0.419;
>  1.000   0.413;
>  1.000   0.413;
> --------------------------------
> ERROR: matrix is ill-conditioned or badly scaled, condno = 27492.1
> --------------------------------
> 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 /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh
> --fsgd /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods
> --glmdir /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage
> lh --label
/g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label
> --C
>
/g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
> --C
>
/g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat
>
>   2. The FSGD file (if using one)
>   3. And the design matrix above
> Error in Analyze: command failed: mri_glmfit --y
> /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd
> /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir
> /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage lh
--label
> /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label --C
>
/g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
> --C
>
/g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat
>
> Many thanks in advance.
>
> Regards,
> Nabin
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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