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Update @itk-wasm/dicom for new SEG pipeline #653

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merged 4 commits into from
Oct 8, 2024
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@PaulHax PaulHax commented Sep 25, 2024

  • Deal with overlapping segments coming out as multi-component images. Short putt: turn mergeSegments option to true, pull first output file/component for use as segment group, and pop a warning.
  • Stash segment label and color tags in a store on load. Then create new segments with colors when converting SEG volume to segment group.

image

closes #639

Suggest we just put these in an issue and not do in this PR:

  • Fix thumbnail for big SEG here: Incorrect rendering of DICOM SEG #639
  • Loading indicator. Like a spinner on the image in the image browser.
  • When loading SEG volume without "background" volume, apply approate color map, surface segment group colors and labels to GUI.
  • Handle overlaping segments.

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@PaulHax PaulHax marked this pull request as draft September 25, 2024 19:49
@PaulHax PaulHax force-pushed the wasm-seg branch 2 times, most recently from 34acfe9 to 650b9d2 Compare October 2, 2024 17:52
@PaulHax PaulHax force-pushed the wasm-seg branch 2 times, most recently from a752baf to e555bee Compare October 3, 2024 15:07
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fedorov commented Oct 3, 2024

Short putt: turn mergeSegments option to true and expect one component image as output.

Just to make sure there is no misunderstanding here. mergeSegments option will merge non-overlapping segments into minimal number of files. So if SEG does not have any overlapping segments, unless there is a bug, you should get only one file when mergeSegments is on. But if some segments overlap, they will be saved into separate files with mergeSegments on. TotalSegmentator should not produce overlapping segments. But you can look at the NSCLC-Radiomics or QIN-Prostate-Repeatability collections that contains overlapping segments:

@jadh4v - one of the above would be a good sample to include in testing in InsightSoftwareConsortium/ITK-Wasm#1208.

As always, to download the images in the above example, you can use StudyInstanceUID available in the URL and idc-index package:

$ pip install idc-index --upgrade
$ idc download 1.3.6.1.4.1.14519.5.2.1.3671.4754.121472087445374646718121301133

Note that to see overlapping segments in the above I used OHIF v2. The current OHIF v3 cannot display overlapping segments as of yet, see OHIF/Viewers#3496.

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PaulHax commented Oct 4, 2024

I did misunderstood. Thanks for the clarification and files.

Changed to do the wrong thing better. That is: just using the first output file and popping a warning.

@floryst floryst added this pull request to the merge queue Oct 8, 2024
Merged via the queue into Kitware:main with commit d193233 Oct 8, 2024
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@PaulHax PaulHax deleted the wasm-seg branch October 8, 2024 15:53
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Incorrect rendering of DICOM SEG
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