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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

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