FOOOF/Specparam matlab structure unit of peakfit

lapuUKJ · March 14, 2025, 5:51pm

Hello, I am analizing EEG data using fooof/specparam. I wondered about the unit used for output of peak_fit in matlab. Is it in log(10) or is it in db or what is it, i couldn´t find out yet.
Thank you in advance.

Raymundo.Cassani · March 14, 2025, 10:48pm

None of the above, it does not have units.
It is a ratio of the full spectrum model to the aperiodic fit, at each frequency bin.

github.com/brainstorm-tools/brainstorm3

toolbox/process/functions/process_fooof.m

c113225a8


      
          
                  aperiodic_pars = model(mi).aperiodic_params;
                  peak_pars = model(mi).peak_params;
                  % Return FOOOF results
                  aperiodic_pars(2) = abs(aperiodic_pars(2));
                  fg(chan).aperiodic_params   = aperiodic_pars;
                  fg(chan).peak_params        = peak_pars;
                  fg(chan).peak_types         = func2str(peak_function);
                  fg(chan).ap_fit             = 10.^gen_aperiodic(fs, aperiodic_pars, opt.aperiodic_mode);
                  fg(chan).fooofed_spectrum   = 10.^build_model(fs, aperiodic_pars, opt.aperiodic_mode, peak_pars, peak_function);
                  fg(chan).peak_fit           = fg(chan).fooofed_spectrum ./ fg(chan).ap_fit;
                  fg(chan).error              = model(mi).MSE;
                  fg(chan).r_squared          = model(mi).r_squared;
                  fg(chan).loglik             = model(mi).loglik; % log-likelihood
                  fg(chan).AIC                = model(mi).AIC;
                  fg(chan).BIC                = model(mi).BIC;
                  fg(chan).models             = model;
              end
          catch err
              errMsg = err.message;
          end

The functions gen_aperiodic and fooofed_spectrum return the spectra in Bells, so 10^ just return them to units^2.

That was a tricky question

lapuUKJ · March 28, 2025, 8:37am

I am confused because of you Compare the plots Brainstorm is giving out and the Values Matlab Object, Even after adjusting the log space or linear Space, are Not the Same. In the Tutorial, the Assess the specparam parameters section is Not very detailed. Is it possible to make it more detailed and also Adding the units? Or is it identical with the ones in the normal Fooof Documentation fooof.FOOOF — fooof 1.1.0 documentation Additionally a function in Brainstorm to calculate the aperiod adjusted spectrum would be amazing, if you want a feedback for improvement.
Greetings, Lara

Raymundo.Cassani · March 28, 2025, 12:14pm

Can you be more specific which differences are you finding and how?
You may want to check this simple example on understanding the FOOOF parameters: Understanding FOOOF parameters in Brainstorm · GitHub

The section ** Accessing FOOOF model parameters** does have the units for the FOOOF parameters parameters that do have units. Yes, it is the same as in the FOOOF documentation.
Can you point to the specific information that is missing so we can add it to the tutorial?

This is already in there. Check the code in the function FOOOF_matlab in process_fooof.m
brainstorm3/toolbox/process/functions/process_extract_fooof.m at master · brainstorm-tools/brainstorm3 · GitHub