I think the issue may be the use of commas (,) instead of decimal points
(.). You an convert it easily with
cat yourfsgd | sed 's/,/\./g' > yournewfsgd
On 1/12/2022 12:10 PM, Laura Willers de Souza wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I want to perform an analysis of the difference between two groups in
cortical thickness, having cortisol levels as covariate.
This is my model: cortical thickness ~ diagnosis (CU/CI) + plasma
cortisol + diagnosis*plasma cortisol
I am now performing a glm dods analysis to see if the diagnosis*plasma
cortisol interaction is significant.
I'm using this contrast: 0 0 1 -1
The fsgd file is attached. Cortisol values are converted to log.
But when I run the mri_glmfit command it gives the following error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
-------- ERROR: READ THIS -----------------
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.CU_CI_plasma.thickness.10.mgh --fsgd
CU_CI_plasma.fsgd dods --C group-x-cortisol_pl.mtx --surf fsaverage lh
--cortex --glmdir lh.CU_CI_plasma.glmdir --eres-save
2. The terminal output of this program (ie, everything it prints to
the screen)
3. The FSGD file (CU_CI_plasma.fsgd) - ATTACHED
4. The design matrix lh.CU_CI_plasma.glmdir/Xg.dat - ATTACHED
Attempting to diagnose further SumSq: Min=0.000000 (col 3),
Max=22.135944 (col 2)
The scale is much different between columns 3 and 2, you may want to
normalize by subtracting the mean and dividing by the standard deviation.
Column 3, all values are 0
Column 4, all values are 0
Columns 3 and 4 are the same
Could this error be because the n of the CU group is 54 and of the CI
group is 490?
Thanks in advance!
*Laura Willers de Souza *
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
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