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.
- My command line used was-
mri_glmfit --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir
- My fsgd file and design matrix file are attached.
Thank you for your help.
Amrita Bedi
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