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feat: rename BIDS files for multi-orientation series. #788
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feat: rename BIDS files for multi-orientation series. #788
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #788 +/- ##
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+ Coverage 82.13% 82.22% +0.08%
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Files 42 43 +1
Lines 4226 4275 +49
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+ Hits 3471 3515 +44
- Misses 755 760 +5 ☔ View full report in Codecov by Sentry. |
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Overall - makes sense, thanks! Left some recommendations/comments.
My main concern is that we would do that "all the time" and unconditionally to anything else , i.e. may be there is some other entity for which we would already separate by and thus this orientation would not be needed?
what I mean -- what other (if any) scans other than localizer/scouts could have multiple ImageOrientationPatientDICOM
?
Co-authored-by: Yaroslav Halchenko <[email protected]>
Thanks @bpinsard . But could you add anything about that concern of "all the time"? ;-) |
For now, multi-orient series cause heudiconv to crash unless the overwrite flag is used, but in that case only one nifti (the last) is kept. So the only hypothetical case where we would add the The only series other than localizers that could maybe result in multiple ImageOrientationPatientDICOM that I could think of would be non-product sequences:
However, depending on how the dicoms contain that dynamic orientation, they might not be converted to separate nifti by dcm2niix. I doubt that all the possible cases of fancy custom WIP/C2P can be planned, as it seems there is room for developers to decide how dicoms are formatted. (sorry for the lengthy response) |
Retrieved some of this fancy multi-FoV sequence dicoms, and the IOP is indeed different for the 2 resulting niftis (brain, cspine), and would likely be both labelled as |
I will move it to draft until we decide on the way forward (correct me if I am mistaken and it is all clear) |
Thanks for the follow-up! |
(rebase of #441 , many years later I know slightly more what I am doing.)
The purpose of that PR is to rename files adding
acq-orient
when there are multiple files with varying orientation generated by dcm2niix (...._i00000[0-9].json/nii.gz
) . Otherwise heudiconv want to rename the separate files to the same BIDS name and crash.The obvious main use-case would be 3-plane localizers.
You're gonna tell me: why do you want to bidsify localizers?
Well, why not? Also, we started exporting the localizers combined+uncombined as a potential way to QA the head-coil elements. And I would like to have that future tool running on clean BIDS, not on messy dicoms.