Your best option is to use two separate calls to findpeaks with different 'MinPeakHeight' arguments for each. The first one would not have a 'MinPeakHeight' argument at all, and the second would be 0. Then use the setdiff function to retrieve the locations you want.
Example —
locs1 = 1:10; % All Peaks
locs2 = [1:3 7:10]; % Peaks With ‘'MinPeakHeight',0’
locsWanted = setdiff(locs1, locs2); % Desired Peaks
Once you have the ‘locs’, (here ‘locsWanted’)getting the peaks and whatever the independent variable values are for those peaks is just indexing into the various vectors using ‘locsWanted’ as the index. .
