Repository navigation
Soft delays #185
Description
When reading in a seq file using Sequence.import_file an optional parameter soft_delays: Optional[dict[str, float]] = None can be provided.
I could not find any documentation what soft_delays should look like. I would also suggest that if set to None, it should simply default to 0 for all soft_delays. This would be consistent with the behaviour of previous versions. Currently soft_delays = None leads to the following error for sequences containing soft delays:
ValueError: pulseq-rs parse error: Failed to convert parsed file into sequence: Referenced extension with id 6 does not exist
Metadata
Metadata
Assignees
Labels
No labels
Activity
J-Endres commentedon Jul 28, 2026
Thank you for the feedback. Does that mean that loading sequences with soft delays works as expected when specifying all of them? So it's only a matter of defaults + documentation? Will fix these two soon
J-Endres commentedon Jul 28, 2026
I released version 1.0.5, which adds documentation and defaults soft delays to 0.
Please let me know if this fixed your issues.
ckolbPTB commentedon Aug 10, 2026
Thank you for looking into this. I am struggling to get the correct pulseq-rs version installed with mrzerocore.
Even when I install mrzerocore==1.0.5 in a clean environment, I still seem to get the old pulseq-rs version because I get the same error message as above but in pulseq-rs==0.2.2 this error message was removed.
I have never jused Cargo.toml. Is there a way of verifying the pulseq-rs version?
J-Endres commentedon Aug 24, 2026
The exact commit of pulseq-rs used in the build of MR-zero core is noted here (it is the latest commit):
MRzero-Core/Cargo.lock
Lines 137 to 140 in 639dced
However, the error you originally reported points to something else: Some block references an extension that was not found in the list of extensions, raised here in the code:
https://github.com/pulseq-frame/pulseq-rs/blob/5e81c1ba3f7a099d4aa26a80f903d07435d75fa7/src/seq/convert/mod.rs#L367-L370
It is absolutely possible that there is an error in how extensions are parsed; I assume that your file is written with (py-)pulseq and writes blocks and extensions correctly.
ckolbPTB commentedon Aug 26, 2026
Yes, you were right - sorry for the confusion. It seems that the error occurs depending on the pulseq version.
I am using pypulseq and when I save the seq file in v1.4.1 compatibility modus (https://github.com/pulseq/pypulseq/blob/805c76f9427d536a63bb0a7aa405fa9403e4d08a/src/pypulseq/Sequence/write_seq.py#L282) then I get the above error. If I save it in the latest v1.5 format, then it works. Officially soft delays are only supported from v1.5.0 onwards so I guess this issue can be closed.
One suggestion for improvement: Currently
trig_delaydefaults to 0 in MRZero if nothing else is defined. Maybe it would be better to default to thedefault_durationspecified for the soft delay object (https://github.com/pulseq/pypulseq/blob/805c76f9427d536a63bb0a7aa405fa9403e4d08a/src/pypulseq/make_soft_delay.py#L41)J-Endres commentedon Aug 26, 2026
Thank you for the investigation. In this case we could make the error message more clear and tell the user that the extension is not supported in the pulseq version of the file. Alternatively the soft_delay (and other) extensions could be backported to be supported with earlier pulseq versions (But that violates the specification; would have to look into how much effort that is).
About
trig_delay: This can be considered a bug and should definitely be fixed.J-Endres commentedon Oct 19, 2026
I finally got around to fix this: in the new version 1.1.3, the soft delay default value will be taken from the block duration (if no value was set). This should fix the issue - if it doesn't please reopen.
See #199