Specify "direction" for bipolar correction

[georg-brunner]

Hi Korbinian,

I'm using your implementation of Romeo and MCPC3DS.
These are two great algorithms! Thank you so much for providing/maintaining these!

I have the following (possibly odd) use-case:
I have multi-echo gradient-echo acquisitions with bipolar readout.
I use MCPC3DS and ROMEO to estimate coil-specific phase offsets, as well as a field map.
My goal is to then use these in a type of model-based reconstruction, ie. later I try to iteratively fit a complex-valued model to the whole data.
In order to be able to validate the fit, I decided to "leave out" some echo times during fitting.
I can then use the fitted model to predict and compute an error on unseen samples.

However now I am in the situation, where my data has a rather weird (& unrealistic) readout pattern.
Let's say originally we had alternating even (E) and odd (O) echos: "O-E-O-E-O-E".
Now if I keep the third echo time for validation, the new pattern is: "O-E-E-O-E".
I believe this leads to an issue with the bipolar correction & gives worse results.

Here is my question:
Do you think it is possible, to add an argument, such that one can provide the specific readout pattern?
Would this make sense even? Or am I missing something?

Thanks again & best wishes,
Georg

[korbinian90]

Hi Georg,

Interesting use case!
Estimating the bipolar correction is a bit tricky with a different pattern. The first three echo times are used for the estimation of the bipolar artifact and need to be O-E-O (see https://doi.org/10.34726/hss.2021.43447, page 53, 3.1.3 Bipolar Corrections). It might be possible for a general OE pattern... but I don't see it quickly.

You can try to go for a workaround solution:

1. Add a dummy echo to fix the pattern by copying another echo (with its echo time) to that location*
2. Run mcpc3ds
3. Remove the dummy echo
4. Run romeo

• I think the first three echoes need different echo times, so using the first as a dummy at the third location might go wrong.

I hope this helps!
Best,
Korbinian