On Thursday, April 11, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

Hi Amrita, first of all, thanks for following the instructions on
submitting the bug report! It helps us a lot to get all the information
the first time. As for your issue, there is a confound between the
Female class and the NSI_1 variable. All the Females have a NSI_1 value
of 0, meaning that you cannot compute a slope for the Females group.
What to do next depends a little on what you think is happening in the
data. You could run it with different-offset same-slope (mri_glmfit
--fsgd TEST.fsgd DOSS ...). This would force a single slope for both
males and females. This is not a problem for the NSI_1 variable because
there is no slope for females. If you think this is ok for CAPS_C, then
just do it. If not, then things get harder, but I can probably step you
through it.

On 4/11/19 8:40 AM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
>
>
> ---------- Forwarded message ----------
> From: *abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edu>*
> <abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edu>>
> Date: Thursday, April 11, 2019
> Subject: Fw: mriglmfit error
> To: Amrita Bedi <amibedi273@gmail.com <mailto:amibedi273@gmail.com>>
>
>
>
>
> Amrita Bedi
> /Biomedical Engineering - Class of 2018/
> /The City College of New York - CUNY/
>
>
>
> ------------------------------------------------------------------------
> *From:* abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edu>
> *Sent:* Thursday, April 11, 2019 8:38 AM
> *To:* Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> *Subject:* mriglmfit error
>
> Good morning Freesurfer developers,
>
>
> While using the mri-glmfit command on 20 subjects. I got the following
> error-
>
> --------------------------------
> 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.bin --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx
> --surf fsaverage lh --cortex --glmdir test.glmdir
> 2. The FSGD file (if using one)
> 3. And the design matrix above
> Attempting to diagnose further
> SumSq: Min=0.000000 (col 6), Max=228.790298 (col 3)
> The scale is much different between columns 6 and 3, you may want to
> normalize by subtracting the mean and dividing by the standard deviation.
> Column 6, all values are 0.
>
> 1. My command line used was-
>
> mri_glmfit --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf
> fsaverage lh --cortex --glmdir test.glmdir
>
>
> 2. My fsgd file and design matrix file are attached.
>
> Thank you for your help.
>
>
>
>
> Amrita Bedi
>
>
>
>
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