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
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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