Automatic placement of `echo` results in BIDS-invalid format

[andrew-yian-sun]

Summary

I'm trying to get the following BIDS-valid output:
sub-0061_echo-1_part-mag_MEGRE.nii.gz Related Github issue at bids-specification: https://github.com/bids-standard/bids-specification/issues/979

However, it seems like echo is automatically generated by HeuDiConv to appear directly before _MEGRE, making it BIDS invalid (echo has to come before part).

The relevant part of my heuristic:
megre_mag = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_part-mag_MEGRE')

I omit echo because it otherwise will generate 2 instances of echo in my output.

Platform details:

Choose one:

• Local environment

• Container: Docker, nipy/heudiconv:latest

• Heudiconv version: 0.9.0

[pvelasco]

Hi @andrew-yian-sun ,
I can work on a fix. However, to test it, would you be able to provide a sample dataset?
Ideally, a very low resolution, just a few echoes, on a phantom.
Thanks,
-Pablo

[andrew-yian-sun]

@pvelasco Yes, I'll try to get that to you tomorrow. Thanks!

[tsalo]

@pvelasco It looks like the keyword you used in #542 didn't auto-close this issue. Now that #542 is merged, can this be closed?

[pvelasco]

I think so.

[tsalo]

Sounds good. I'll close this now, but @andrew-yian-sun if you find that the problems persists, please feel free to follow up here.

[andrew-yian-sun]

@tsalo I recently tried to the recent version of heudiconv, 0.10.0 but echo is still appearing in the wrong place:
it should be sub-001_ses-1_echo-1_part-mag_MEGRE
but I am being given: sub-001_ses-1_part-mag_echo-1_MEGRE

Is this issue still being fixed?

[tsalo]

The issue should be fixed, but the most recent release, 0.10.0, was in October of last year, while the fix was merged in February of this year.

@yarikoptic is it maybe time for 0.11.0?

[pvelasco]

Well, the problem is that I thought the echo entity came last, but I was mistaken 😞 : part is supposed to come after echo (BIDS v1.5.0 and later).

So I would need to fix that, but I'm a little time constrained right now. I'll try to fix it by the end of the week.

[yarikoptic]

Thought to finish #544 before I do 0.11.0 but may be would need to cut it before then. That pr should make order follow bids schema thus guaranteed to be correct