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Update the Chest Imaging Platform extenstion to support Slicer 5

Key Investigators

  • Rudolf Bumm (KSGR)
  • Raul San Jose Estepar (Brigham)
  • Andras Lasso (PerkLab)
  • Steve Pieper (Kitware)

Project Description

The Chest Imaging Platform (CIP) is an extension to 3D Slicer.

image

It integrates:

  • chest image processing functionality as a toolkit by exposing the CLIs
  • Slicer specific modules to provide user-friendly chest CT quantitative solutions
  • Visualization of scale-space particles and labelmaps
  • Integrated workflows to end-to-end clinical evaluation

In the current preview versions of 3D Slicer (4.13.0) parts of CIP fail to load the following CIP modules because Slicer's "Editor" module has been removed.

CIP_CalciumScoring

CIP_RVLVRatio

CIP_LesionModel

CIP_Calibration

CIP_MIPViewer

CIP_BodyComposition

CIP_ParenchymaSubtypeTrainingLabelling

CIP_ParenchymaAnalysis

CIP_PAARatio

CIP_AVRatio

CIP_InteractiveLobeSegmentation

The CIP extension currently uses legacy editor module, and charts infrastructure (instead of Segment editor, Plots, and Tables modules).

Objective

  • Replace the usage of the "Editor" module in CIP by something different, preferably the SegmentEditor.
  • Replace labelmaps with segmentations
  • Replace outdated fiducial calls (exceptions)
  • Replace the charts infrastructure

Approach and Plan

A fork and branch of SlicerCIP was created at https://github.com/rbumm/SlicerCIP/tree/Branch_CIPCompatSlicer5 to be used as the source base, all changes will later be included in a PR to https://github.com/acil-bwh/SlicerCIP.

Resolve compatibility problems step by step

Deactivate non-working or outdated modules in Slicer 5

Considerations

Progress and Next Steps

01/06/22:

Removing the "Editor" related imports from "Scripted/CIP_/CIP/ui/init.py" results in a complete CIP-startup in Slicer 4.13.0 without initial error messages.

A github search revealed that "Editor" calls are being made from three of the above modules:

  • CIP_Calibration
  • CIP_ParenchymaSubtypeTrainingLabelling
  • CIP_BodyComposition

01/11/22:

  • CIP_Calibration is probably outdated.
  • CIP_ParenchymaSubtypeTrainingLabelling is outdated, probably redundant.
  • CIP_BodyComposition is needed, but probably much better realized with AI segmentation

01/17/22: 12pm Meeting with Raul, Andras, Steve and Rudolf (Discord Red Slice)

  • Incompabilities between 4.13 and CIP seem to be caused by CIPLibrary
  • CIP, it's CLI functions and their history were demonstrated by @Raul
  • CIP_Calibration is not outdated.
  • CIP_ParenchymaSubtypeTrainingLabelling should be kept.
  • CIP_BodyComposition is needed and should be kept
  • CIP Toolkit functions should be included in a future SlicerCIP release
  • A CIPLibrary compatibility branch "4.13" or "5.0" will be created
  • CIP GitHub write access was requested for @Andras to support merging, @Raul agreed
  • As labelmaps are used throughout CIP in nearly every module we will discuss a Slicer-based solution for that problem tomorrow

01/18/22: 12pm Meeting with Raul, Andras, Rudolf (Discord Red Slice)

  • good follow up meeting
  • @rbumm demonstrated the build process
  • a first module (Calibration) has been adapted to 4.13 and now works with the Segment Editor instead of Editor
  • ParenchymaSubtypeTrainingLabelling was demonstrated by Raul
  • we decided to prioritize certain modules during CIP adaptation
  • ParenchymaAnalysis probably the next to go
  • Andras promised to look into CLI modules and letting them use segmentations instead of labelmaps as an input maybe automatically
  • next meeting will be Thursday 11 am Red Slice

Final presentation start here

01/20/22: 11am-12:30pm Meeting with Raul, Andras, Rudolf (Discord Red Slice)

  • The Chest Imaging Platform extension's "Calibrate" module has been finalized for Slicer 5 together with @lassoan and was demonstrated by @rbumm
  • see this SlicerCIP GitHub fork and this commit
  • will serve as a skeleton to adopt the other CIP modules and is now fully functional
  • The "Calibration" widget uses a newly created segmentation for each volume instead of labelmaps
  • the segmentation can be edited in the embedded Segment Editor
  • before pressing "Calibrate" the segmentation is converted to a labelmap for the actual calibration in the logic()
  • in addition, we developed a strategy on how to transform the other CIP modules to Slicer 5
  • non-working modules will be excluded from CMake to provide only those functional to the community
  • @Raul demonstrated new vessel segmentation techniques and answered many questions
  • @Raul agreed on giving @lassoan write access to the SlicerCIP GitHub repository

Illustrations

New Slicer 5 CIP "Calibration" module with embedded "SegmentEditor" instead of the old "Editor":

image

Background and References

https://chestimagingplatform.org/

https://discourse.slicer.org/t/exporting-csv-with-parenchyma-analysis-module/10697/58?u=rbumm