I ended up using a single ended measurement and using matlab to poll the textronix scope and using the instrument control toolbox:
myScope = oscilloscope
drivers(myScope)
availableResources = getResources(myScope)
availableResources{5}
myScope.Resource = 'TCPIP::xxx.xxx.xxx.xxx::INSTR'
connect(myScope)
get(myScope)
waveformArray = getWaveform(myScope, 'acquisition', true);
figure;plot(waveformArray)
enableChannel(myScope,'CH3');
enableChannel(myScope,'CH4');
Time = linspace(0,myScope.AcquisitionTime,myScope.WaveformLength);
aqs = 1000;
for i = 1:aqs
[w3, w4] = readWaveform(myScope, 'acquisition', true);
pause(0.05);
w3mat{i} = w3;
w4mat{i} = w4;
end
figure;subplot(2,1,1),hold on,legend('D+','D-'),subplot(2,1,2),hold on
for i = 1:aqs
w3 = w3mat{i};
w4 = w4mat{i};
subplot(2,1,1)
plot(Time,w3,'b'),plot(Time,w4,'r')
subplot(2,1,2)
plot(Time,w3-w4,'r')
end
subplot(2,1,1),legend('D+','D-'),ylabel('Volts');
subplot(2,1,2),legend('D+ subtracted from D-'),xlabel('Time'),ylabel('Volts');
subplot(2,1,1)
x = [8.2 21.15 69.93 75.13 69.93 21.15 8.2 ]*1e-9/2;%These come from the USB IF website specs
y = [1.65 2.5 2.5 1.65 0.8 0.8 1.65];
fill(x+1e-7,y,'r')
title('USB Full speed EYE test')
line([1e-7 1.4e-7 ],[-0.9 -0.9])
line([1e-7 1.4e-7 ],[4.4 4.4])