Documentation/4.1/Modules/MultiVolumeExplorer

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Home < Documentation < 4.1 < Modules < MultiVolumeExplorer



Introduction and Acknowledgements

This work is supported by NA-MIC, NAC, NCIGT, and the Slicer Community. This work is partially supported by the following grants: P41EB015898, P41RR019703, R01CA111288 and U01CA151261.
Author: Andrey Fedorov, Jean-Cristophe Fillion Robin, Julien Finet, Steve Pieper, Ron Kikinis
Contact: Andrey Fedorov <email>fedorov@bwh.harvard.edu</email>

National Center for Image Guided Therapy (NCIGT)  
National Alliance for Medical Image Computing (NA-MIC)  
Surgical Planning Laboratory (SPL)  
Kitware, Inc.  
Neuroimage Analysis Center (NAC)  


Module Description

This module provides support for exploring multivolume (multiframe) data.

Use Cases

Most frequently used for these scenarios:

  • visualization of a DICOM dataset that contains multiple frames that can be separated based on some tag (e.g., DCE MRI data, where individual temporally resolved frames are identified by Trigger Time tag (0018,1060)
  • visualization of multiple frames defined in the same coordinate frame, saved as individual volumes in NRRD, NIfTI, or any other image format supported by 3D Slicer
  • exploration of the multivolume data (cine mode visualization, plotting, volume rendering)
Screenshot of charts derived from the sample data set. The curves represent average signal intensity in the ROI's with corresponding colors, which were drawn in the editor. Please note the arterial input function in red.

Tutorials


Panels and their use

MultiVolume data is represented in this module using two components:

  • MultiVolume node: this is the node you select when you import the dataset using MultiVolumeImporter module
  • DisplayNode: this is the node responsible for visualization and storage of the actual image data. The name of that latter node is assigned based on the type of data you are importing. For example, if you import "4D DCE" dataset, it will be called "DCEDisplayNode". This is the node you need to choose in slice viewers to see the multivolume dataset.
  • Input: select the MultiVolume node you would like to explore
  • Frame control
    • Current frame number: you can use the slider or spin-box to select the currently shown frame. Play button can be used to activate 'cine' view mode, with the frames being shown in a continuous mode.
    • Current frame copy: you can create and select a conventional scalar volume node in this selector. If Enable current frame copying button is pressed, each time the currently shown frame is updated, it will be copied to the volume selected. This is useful in situations when you want to do processing of an individual frame (e.g., segmentation), or if you want to show volume rendering of the currently active frame.
  • Plotting: there are two modes of plotting that are supported by the module:
    • Static plotting
    • Interactive plotting
Settings panel and interactive plotting chart

Similar Modules

Before multivolume data can be viewed/explored, it has to be loaded using MultVolumeImporter module.

References

Information for Developers


Known issues that won't be resolved

  • bug 1841: multivolumes that contain less than 7 frames will not be saved correctly and the scene containing such objects will not be loaded correctly by Slicer (limitation of the NRRD IO for DWI)

Unresolved issues

  • assign correctly title and points for the X axis
  • review the comments from JC/J2 on github and fix the code
  • bug: repeated loading of a scene that contains a MV node causes crash in onInputChanged()
  • improve error reporting!
  • look into flickering issue of vtkChart
  • improve documentation

Features to be implemented

  • integrate MV importer as a DICOM module plugin
  • allow the user to speed-up or slow-down the playback, and also turn off "loop"
  • report to the user the actual, measured, frame rate
  • add an option to report curves in relative SI change in addition to absolute

Features under consideration

  • can we use chart viewer for interactive plotting? -- Discussed with Jim, speedup is possible, but not a priority right now
  • should use color names for the legend in the chart viewer -- Will be available as general feature of Charts (Jim)
  • interactive update of the active frame based on the point selected in the chart viewer
  • should DWI node be a child under the MV hierarchy?
  • add GUI elements to update the current frame at the exact time intervals specified in multivolume. If the intervals are non-uniform, I am not sure I can use the timer anymore, so this would require some extra thought.
  • import multivolumes from ITK 4d images