How did you set your pwelch's options? If you set them correctly, then you should obtain a very accurate plot. For instance:
h1=spectrum.welch;
set(h1,'Windowname','Hann');
Fs=1000;
set(h1,'OverlapPercent',66.7);
set(h1,'SegmentLength',512);
The lines above make the necessary settings for your pwelch function.
myPsd=psd(h1,X(:,1)-mean(X(:,1)),'Fs',Fs)
semilogx(myPsd.Frequencies,myPsd.Data);grid on
Imagine that your data is X, if you run the two lines above, then you should obtain the same result in a better way.
Please enter OverlapPercent and SegmentLength carefully, according to your data. Hope this helps.
