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
>
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