Ingress of Synb0-DISCO corrected data into qsiprep

[cookpa]

I know there's plans to integrate Synb0 into qsiprep (#546), but I'm not sure what the timeline is on that, so I'm considering alternative approaches.

Option 1: Run Synb0 and topup, and then run qsiprep with the anat and topup-corrected dwi data, and --hmc-model eddy. This involves an extra interpolation of the DWI data.

Option 2: Run Synb0 and get the undistorted b0. Copy this to fmap/ with a sidecar json that is identical to the dwi except:

• PhaseEncodeDirection="j" (opposite to the dwi)
• TotalReadOutTime=0.0000001
• EffectiveEchoSpacing = 0.0 (BIDS requires TotalReadOutTime > EffectiveEchoSpacing)

I'm trying out option 2 right now. Does this seem reasonable?

Thanks for any suggestions! The use case is mostly b=1000 retrospective data (no field maps) and a bit of ABCD-style data (field maps incorrectly acquired and unusable)

[mattcieslak]

Hi Phil, option 2 will definitely work! It has a couple other nice advantages like eddy will be able to incorporate the fieldmap into its motion correction. Have you tried this out yet?

[cookpa]

You're right, it chose the synb0 image - results look pretty decent though

[mattcieslak]

this is great news!

[cookpa]

The report uses the first volume in imain returned by get_best_b0_topup_inputs_from.

One way to deal with this would be for that function to look for the largest TotalReadOutTime and return that one explicitly as the "before" image. PR?

[mattcieslak]

I was thinking about doing what we currently do for drbuddi, which is to make one visual report for plus and one for minus. but I like your idea as a way to get better reports right now

[cookpa]

Update: user error, the code is fine. It checks that the chosen "before" image matches distortion parameters with the dwi series. It is looking good now