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?

Laura Willers de Souza

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil