2014 Winter Project Week:SubjectHierarchy

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  Projects List

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  Screenshot of Subject Hierachy module

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  Huntington's longitudinal data in Sibject Hierarchy

Key Investigators

• Queen's: Csaba Pinter, Andras Lasso
• Isomics: Steve Pieper
• Kitware: Jean-Cristophe Fillion-Robin

Project Description

Objective

• Review the current state of Subject Hierarchy
• Discuss features to develop and things to change
• Create roadmap for the integration

Approach, Plan

• Breakout session
  • Slides
  • Detailed class diagram

Progress

• Subject hierarchy enhanced to better support handling Huntington's longitudinal data, video
  • Volumes subject hierarchy plugin handles labelmap and proper show/hide of volumes in the slice viewers
• Subject hierarchy module and mechanism presented in the breakot session, a lot of valuable feedback was given (see below)

Received feedback

• DICOM back into SH? Derived vtkMRMLDICOMSubjectHierarchyNode class? For tags, UID, maybe levels?
• DICOM connections
  • "All DICOM all the time" (@QIICR) means for import/export on disc, not in memory
  • Tree vs DAG: Support DAGs? How to display them? "Infinite trees"?
  • Update referenced UIDs and references when reparenting and the connections are known (plugins reparent method)
  • Look at BioImageSuite (by Xenios) - User manual chapter 15 (page 193)
    • Connector lines in the tree are colored (indicate status of registration?)
• Export
  • Override the selection made by the user to the most sensible one (if they select a contour, the RTSS is also selected)
  • Determine mandatory tags for export
    • Stored in the plugins?
      • Maybe in XML or JSON templates that are read by the plugins?
      • Collect tags from plugin dependencies
  • Use DICOM header widget with some changes (ctkDICOMObjectModel + ListWidget)
  • Similar modalities to export (legacy, multiframe, enhanced) - separate plugins?
  • Explicit representation of DICOM tags in Slicer in separate class?
  • Ask for mandatory DICOM tags and connections (e.g. after conversion, resample, manual plugin selection)
• Use cases
  • Neuro
    • Multiple modalities (different MR types)
    • Display tractography
    • Register volumes and indicate the registration status in the tree (in the icons)
  • Data probe custom readout (e.g. dose)
  • DICOM slice offset into the slice views
  • Displayable manager customizable behavior
    • Scalar volume types e.g. multi-component vector volumes
    • Volume rendering transfer functions
• UIDs
  • "2.25.hash" DICOM UIDs will be generated as new UIDs (perhaps even instead of MRML IDs in the future)
  • What happens to the UIDs if we modify a node?
    • Create new SH node and move the data there?
  • MIDAS url should be a SH storage node property? (Julien)
• Plugins
  • Give confidence value of -1 if the node cannot be handled for sure?
  • Per-structure labelmaps
  • More abstraction: Qt, JavaScript etc. -> presentation managers
  • Icon could be in the MRML node as a resource (string)
  • Move core plugins into their corresponding modules after integration (Volumes, Transforms, Markups, etc.)
• Create dummy parents for loaded node if there is no parent (Study, Patient too)
• 'Unclaimed' section on the bottom of the tree instead of potential list? (Jim)
• Drag&drop would be difficult if there is a lot of nodes in the tree already
• Generate thumbnails as icons for volumes
• vtkSubjectHierarchyConstants -> vtkMRMLSubjectHierarchyConstants?
• qMRMLSortFilterPotentialSubjectHierarchyProxyModel be merged into qMRMLSortFilterSubjectHierarhcyProxyModel?
• Maybe a Q_PROPERTY controls their different behavior?
• Propagating / Overwriting attributes
• In the model, for example for "height" of an item
• Select and drag&drop multiple nodes from the potential list

Reference

• Summer Project Week page