Unexplained flip of the PE direction under some unknown circumstances

[oesteban]

Using @mgxd's dataset in the debugging of the fMRIPrep + SDCFlows integration, we seem to have hit a difficult bug for which I haven't found the failure point (and hence the fix).

In order to permit progress on nipreps/fmriprep#2392, I'm separating this problem that seems to do with some idiosyncratic parameter (likely related to orientation headers) that makes the problem apparent.

[effigies]

I vaguely recall FSL making strong assumptions about an image being left or right handed in some context. Could be related?

[oesteban]

The flip is A/P so I'm afraid this is genuinely an SDCFlows problem. It also occurs that correction is correctly performed on the reference (i.e., a combination of EPI scans that were fed into topup) but then incorrectly applied on the target bold.

Registration of the bold target and the EPI reference seems okay (no gross error there), and I've checked the implementation a few times not.

[effigies]

Is it possible that we have, e.g., an LPS file that we're reorienting to RAS without flipping the PhaseEncodingDirection polarity?

[oesteban]

It is very possible, probably top 1 suspect. The alternative is also true: we have an LPS file and we are flipping two times.

[effigies]

Well, ds003130 has A/P and P/A bold series, sbrefs and EPI fieldmaps. Everything's in LAS. Should be a good test dataset.