Calling Ideal is Relatively Easy

Ideal Notes

Output = IDEALv3(MultiEchoImage,TEs,[-220,0.75;-244,0.1;-164,0.08;43,0.06],Mode,InitialGuess);

Ray's description/help for IDEALv3 should explain everything, but simply:

MultiEchoImage = X,Y,nEchos
TEs = array of echo times (in ms)
[-220,0.75;-244,0.1;-164,0.08;43,0.06] is the fat profile IDEAL will use
Mode is whether you set an initial phase guess to 0 (Mode = 0), provide an initial guess (Mode = 1) but let IDEAL come to potentially another solution, or 'clamp' to the provided 'initial guess' (Mode = 2)
Initial guess is, as I provide it, the output (X,Y,nEchos) from MRIBackgroundCorrect_new_auto (data_background_r output), when I call it:
[data_corrected_r,data_background_r]=MRIBackgroundCorrect_new_auto(im31/(2*pi*delTE*10^-3),mask,3);
and im31=angle(acq(:,:,3).*conj(acq(:,:,1)));