NaN will not work for this. You can't do incomplete designs with an FSGD. You
can create your own design matrix and pass it with --X, otherwise you'll have
to exclude those subjects or put some reasonable (eg, imputed) value
On 1/12/2021 6:35 PM, Julie Ottoy wrote:
External Email - Use Caution
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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