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Hi freesurfer experts,
I am trying to run a GLM fit between cortical thickness and some other continuous marker. My cortical thickness were stacked before using the mris_preproc and surf2surf commands. I have an FSGD file with the same subjects as used during the stacking of the thickness maps, but I added a new continuous regressor (my independent variable of interest). However, some subjects have a missing value for this regressor, so I added NaN. This makes me run into the following error. When I replace the NaN values by random numbers in the FSGD, it all runs fine.
M = [ ... 1.00000 0.99577 0.70711 0.98278 0.97547 -0.97111 nan 0.99577 1.00000 0.70628 0.97775 0.97819 -0.95833 nan 0.70711 0.70628 1.00000 0.68252 0.70488 -0.70032 nan 0.98278 0.97775 0.68252 1.00000 0.95399 -0.96466 nan 0.97547 0.97819 0.70488 0.95399 1.00000 -0.92863 nan -0.97111 -0.95833 -0.70032 -0.96466 -0.92863 1.00000 nan nan nan nan nan nan nan nan ] Normalized matrix condition is 1e+08 Design matrix ------------------ <design matrix> 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.
I made sure that my FSGD file does not have any weird characters, so i applied the cat fsgd.txt | sed 's/\r/\n/g' > new.fsgd.txt, but this also didn't help.
Thank you for your help, Julie