In OMIQ you can get the MFI (Mean/Median Fluorescent Intensity) by using the Export Statistics Task.
In Step 2, you can create statistics related to a feature, you select the filter for which you want the MFI from, you can select either the Mean or Median in the Measure, and then select the parameter you want the MFI for.
First, select the Filter you wish the statistic to be created for:
Then Select the statistic you wish to use to calculate MFI, either Mean or Median.
You then must select the feature you wish to calculate the MFI for:
Note, at any of these steps it is possible to select more than one option. So, you can simultaneously work out the statistic for Multiple filters or for Multiple features.
Which Units will my Statistic Display in?
In step 6, you can decide whether you want the statistic to report the original "raw" value from your cytometer, or whether you want to report any scaling you have applied in your workflow.
Thoughts on Choice of Mean vs Median

While the Mean might be most useful when used to describe normal distributions and not bimodal or multimodal data, the Median is a nonparametric statistic in that it is a better indicator of the central tendency of your data, regardless of the underlying data distribution.

The Arithmetic Mean is affected by outliers, while the Median is less sensitive to outliers.