[Freesurfer] Fw: mriglmfit error

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Hi Dr Greve,

Is the idea behind removing one column for the NS 1 column in the design matrix meant to remove the columns for females? And how do we know which of the two columns for the Ns_1 in the design matrix are for which gender?

In the contrast (0 0 0 0 1-1) which column of the last two for the Ns_1 would be removed?

For the DOSS, say it works for the caps score since female scores for Ns_1 are 0 and we can say that the ---------- Forwarded message ---------- From: *Greve, Douglas N.,Ph.D.* DGREVE@mgh.harvard.edu Date: Thursday, April 11, 2019 Subject: Fw: mriglmfit error To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu

In that case, you will have to create your own design matrix. The easiest way to do that is to start with the DODS Xg.dat matrix that you sent. There will be two columns for the NSI_1 variable (one for males, one for females). You need to reduce it down to one column. In the Xg.dat that you sent, the two columns are the last two columns; in this case, you can just remove the last column. Your contrast matrix will then need one less column.

On 4/11/19 2:08 PM, Amrita Bedi wrote:

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Hi Dr Greve,

I can’t do the Fsgd in the DOSS format since it won’t be ok for my other 6 variables. I would appreciate it if you could guide me through it.

Best Amrita

On Thursday, April 11, 2019, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto: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:
>
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>
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> ---------- Forwarded message ----------
> From: *abedi000@citymail.cuny.edu
<mailto:abedi000@citymail.cuny.edu>
<mailto:abedi000@citymail.cuny.edu
<mailto:abedi000@citymail.cuny.edu>>*
> <abedi000@citymail.cuny.edu <mailto:abedi000@citymail.cuny.edu>
<mailto: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> <mailto:amibedi273@gmail.com
<mailto:amibedi273@gmail.com>>>
>
>
>
>
> Amrita Bedi
> /Biomedical Engineering - Class of 2018/
> /The City College of New York - CUNY/
>
>
>
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-----------------------------------------------------------

-------------

> *From:* abedi000@citymail.cuny.edu
<mailto:abedi000@citymail.cuny.edu>
<mailto: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>
> <mailto: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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