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Hi Mark This does not seem too surprising to me. When you concatenate the two phase-encode datasets, you inevitably will increase the inter-volume variability (due to imperfect distortion correction) and this variability ends up in the denominator of both SNR and CNR calculations. Cheers Saad > On 9 Jul 2019, at 21:10, Mark Pinsk <[log in to unmask]> wrote: > > Hi! > > So I have two identical dMRI scans in opposing directions (AP/PA). > > I concatenate and run eddy (with Jacobian interpolation to keep the output concatenated), then I run eddy_quad, and my SNR/CNR are 17.55/0.90. > > I run eddy on each one individually, and my eddy_quad SNR/CNR for each scan is much higher compared to the concatenated version: > AP scan SNR/CNR: 24.76/1.38 > PA scan SNR/CNR: 22.44/1.40 > > I would expect the concatenated version would give me SNR/CNR that would be roughly average of those two, but it's lower. > > Can someone make sense of that? > > Here are the 3 eddy_quad reports if anyone is interested in taking a look: > https://www.dropbox.com/s/8h5eb23ybohpr9u/EddyQuad-comparison.zip?dl=0 > > Thanks! > Mark > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1