pulseq 1.3.0 compatibility

[KerstinKaspar]

I am working on an application where I will probably need to read and write version 1.3 seq files (or have compatibility for both).

Are you working on the implementation of that compatibility? I am happy to contribute in any case, just wanted to check with you first.

[sravan953]

Hello! Thank you for your comment. I am not actively working on version 1.3. However, it'd be great to collaborate with you and have you as a contributor to the project. If you have already started working on the code by now, please let me know.

[KerstinKaspar]

We will probably work on it, for now we can work around it, I will let you know!

[sravan953]

Hi @KerstinHut! I completely missed out on asking you - were you enquiring about trigger support when you originally asked about Pulseq 1.3.0 compatibility? Trigger support was added to PyPulseq via PR https://github.com/imr-framework/pypulseq/pull/34 and merged in commit 27a281304f6b51c7d3350e3689221f6ca4fd3a1b. The current version of PyPulseq also supports split-gradients.

I plan to start working on incorporating Pulseq 1.3.0 changes into PyPulseq in the coming months. Please let me know if you'd like to collaborate.

[KerstinKaspar]

Hi @sravan953 ,

we don't need the triggers or any of the new 1.3 functionalities, actually, but rather simply needed to readboth v1.2 and v1.3 files (that also don't use any new features). We are working on pypulseq-cest, implementig CEST sequences in cooperation with the Matlab version pulseq-cest, which uses the latest 1.3 files. For compatibility of the sequence files in the simulation tools and to compare for the same outcome on the scanner, it would be preferable to produce the same files with both pulseq and pypulseq. For now, we have implemented a conversion of 1.2 seq files to a pseudo 1.3 and the other way around to allow simulations.

So it's great to hear you're working on PyPulseq 1.3.0. As for me, the next few weeks will hopefully decide whether I will get a PhD position I want and continue working in a related area. In any case I will talk to my colleagues and see if we can collaborate.

[sravan953]

@KerstinHut Thanks for getting back to me! I was not aware of CEST sequences, TIL. I will begin working on transition PyPulseq to match Pulseq 1.3.x shortly; will try to get it done asap.

I'll get back to you here once I update the repo. Best of luck on your PhD decision, whichever way you decide to go! 😄

[sravan953]

Hi @KerstinHut , just as an update. I will be publishing PyPulseq 1.3.1 very soon!

[KerstinKaspar]

That sounds great, thanks for the update!

[sravan953]

Hi! I've just released the latest version. Please take a look and let me know if I can close this issue. :)

[schuenke]

Hey @sravan953,

thanks for your work. We are checking the compatibility of pypulseq 1.3.1 with our code at the moment and found some minor bugs/errors already. What's your favorite way of handling it? Should we create a bug list or should we directly create PRs? If latter, do you prefer a single PR or individual ones for every bug/issue?

[sravan953]

Oh oops, I see! I'd be glad to merge your PRs. If they are multiple but related bugs, please create a single issue and address them in a single PR. If they are unrelated, however, multiple issues/PRs would be cleaner, I suppose. In any case, I am still quite new to all of this, do you have any suggestions as to how these situations are tackled in bigger projects?

[schuenke]

I guess ppl often use kind of big PRs, but I also prefer to keep unrelated things separated. I still have to figure out why some things don't work as expected, but will probably create some PRs soon. As I wrote before, a lot of bugs are just minor like checking for None instead of empty string etc.

[sravan953]

Alright, please open issues. We can split the tasks if there are too many.

[sravan953]

Do let me know if I can close this.

[KerstinKaspar]

Feel free to, thanks!