It seems the transmission and reflection curves you simulated (bottom figure) are similar to the publication (up figure). Usually it is better to check the reflection instead of transmission since the latter has a dip. You will need to find the point of 3dB level for FWHM.
There are different methods to calculate Q.
The low Q analysis group calculates the fft of the fields and computes the FWHM. Please check the script and make sure they work fine.
You can try to use findresonance: findresonances - Script command
You could also fit the result near the resonate wavelength
In addition, you may also try the high-Q analysis group.
The discrepancy appears when the resonance peak is not a Lorentizian shape.
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