Difference between revisions of "Documentation/Nightly/Modules/PlusRemote"

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<br>
 
<br>
 
Author: Franklin King (PerkLab, Queen's University)<br>
 
Author: Franklin King (PerkLab, Queen's University)<br>
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Contributor: Tamas Ungi (PerkLab, Queen's University)<br>
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Contributors: Tamas Ungi (PerkLab, Queen's University), Andras Lasso (PerkLab, Queen's University), Amélie Meyer (Télécom Physique Strasbourg, Université de Strasbourg)<br>
 
Contact: Tamas Ungi, <email>ungi@cs.queensu.ca</email><br>
 
Contact: Tamas Ungi, <email>ungi@cs.queensu.ca</email><br>
 
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Convenience module for sending commands through OpenIGTLink Remote to PLUS. Requires OpenIGTLink Remote module available in the SlicerIGT extension
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Convenience module for sending commands through OpenIGTLink Remote to PLUS. Requires OpenIGTLink Remote module available in the SlicerIGT extension. See PLUS [https://plustoolkit.github.io/usersguide user guide] and [http://perk-software.cs.queensu.ca/plus/doc/nightly/user/PlusServerCommands.html manual] for more information about PLUS server commands.
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'''Demo video:''' https://youtu.be/lfZeXabDjMg
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The module provides the following features:
 +
 
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*Recording of 2D tracked ultrasound frames
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*Volume reconstruction of recorded frames
 +
*Live ultrasound volume reconstruction using scout scanning
 +
*Sending Transform Update command to PLUS server
  
 
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{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
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* Sending Recording and Transform Update commands to PLUS server
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Some ultrasound-guided interventions require a general view of an entire area followed by more detailed images of a specific region. One example is spinal injection procedures. The problem is that, for elderly patients, the epidural area is not directly visible in ultrasound images because the intervertebral space is often compressed or deformed. In this case, physicians use four vertebrae landmarks to estimate the position of the target. Visualization can be improved using reconstructed 3D ultrasound volumes, but often there is not enough time for high resolution reconstruction of a large area during interventions.
 +
 
 +
The live ultrasound volume reconstruction workflow using scout scanning is then adapted for these procedures. The two-step method allows user to perform quick low resolution scout scan followed by high resolution volume reconstruction of a selected region of interest, in real-time. Low resolution scout scanning offers visualization of the global area and selection of the region of interest, and then high resolution reconstruction provides a good image quality of the targeted region.
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<gallery widths="250px" heights="200px" perrow="3">
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Image:VolRec_Workflow.jpg|Workflow for live ultrasound volume reconstruction using scout scanning<br>
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Image:PlusRemote_phantom_scan.jpg|Completed scout scan (left-side image), live update of reconstruction (middle) and final live reconstructed volume (right) of a spine phantom<br>
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Image:PlusRemote_volunteer_scan.jpg|Scout scan (left) and live reconstruction (right) of an adult spine<br>
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</gallery>
  
 
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The SlicerIGT [http://www.slicerigt.org/wp/user-tutorial/ website] provides a [https://onedrive.live.com/view.aspx?cid=7230D4DEC6058018&resid=7230D4DEC6058018%213992&app=PowerPoint&authkey=%21AGQkSCZOwjVYXw8 tutorial] for ultrasound volume reconstruction in Slicer using Plus Remote (U35).
  
 
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
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[[File:PlusRemote_panel.png|500px|thumb|right|Plus Remote panel]]
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[[File:PlusRemote_AdvancedOptions.png|500px|thumb|right|Plus Remote panel with advanced parameters]]
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*'''Parameters sets:''' saving of all parameters
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**Create a new parameter set to save your parameters
 +
**Select previously saved ones
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**Default parameter set is selected when entering the module
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 +
This is useful when user knows optimal parameters for a specific procedure. The parameters set is saved when saving the scene and is reloaded when opening a saved scene.
 +
 
 +
 
 +
*'''Parameters:''' parameters for communication with PLUS server, recording and reconstruction
 +
**OpenIGTLinkConnector
 +
**Capture Device ID
 +
**Volume Reconstructor ID
 +
 
 +
These parameters are essential. Therefore all commands are disabled when these parameters are not set. List of available OpenIGTLinkConnector is available once you created connections in [[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLinkIF]] module. When a connector is selected, capture device ID and volume reconstruction ID lists are automatically filled.
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 +
 
 +
*'''Recording:'''
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**Start and stop recording
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**Advanced parameters:
 +
***Modify default output filename "Recording.mha"
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***Add timestamp (YYYYMMDD_HHMMSS) to filename
 +
 
 +
 
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*'''Offline reconstruction of recorded volume:'''
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**Offline reconstruction
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**Advanced parameters:
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***Spacing (default value is 3mm)
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***Output volume device name
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***Volume to reconstruct filename (automatically filled when user record a file, but user can also edit this line and reconstruct previously saved files)
 +
***Show results on completion (display reconstructed volume in the green, yellow and 3D views)
 +
 
 +
 
 +
*'''Scout scan and live reconstruction:'''
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**Start and stop scout scan
 +
**Advanced parameters:
 +
***Spacing (default value is 3mm as we expect a low resolution scout scan)
 +
***Modify default output filename "ScoutScanRecording.mha"
 +
***Add timestamp (YYYYMMDD_HHMMSS) to filename
 +
***Show results on completion (display reconstructed volume in the green, yellow and 3D views)
 +
 
 +
Scout scan button record a file and automatically performs the volume reconstruction once the recording is over. The result of scout scan volume reconstruction is saved in "scoutFile.mha"
 +
 
 +
**Start and stop live volume reconstruction:
 +
**Display and modify ROI using eye icon (initialized to fit scout scan volume)
 +
**Spacing (default value is 1mm for high resolution reconstruction)
 +
**Advanced parameters:
 +
***Output volume device name (read only)
 +
***Modify default output filename "LiveReconstructedVolume.mha"
 +
***Add timestamp (YYYYMMDD_HHMMSS) to filename
 +
***Display volume extent values (updated when clicking on scout scan or live reconstruction command buttons)
 +
***Display snapshots during live volume reconstruction (if 0, no snapshots)
 +
***Show results on completion (display reconstructed volume in the green, yellow and 3D views)
 +
 
 +
 
 +
*Transform Update: Update transform from what is set in the PLUS config file; Requires name of transform node to match an existing transform in the PLUS config file
 +
*Reply: Feedback message from PLUS server (also visible when moving the mouse on blue information icons)
  
 
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*[http://perk-software.cs.queensu.ca/plus/doc/nightly/user/PlusServerCommands.html PlusServer commands]
  
 
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
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Latest revision as of 02:42, 27 November 2019

Home < Documentation < Nightly < Modules < PlusRemote


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements


Author: Franklin King (PerkLab, Queen's University)
Contributors: Tamas Ungi (PerkLab, Queen's University), Andras Lasso (PerkLab, Queen's University), Amélie Meyer (Télécom Physique Strasbourg, Université de Strasbourg)
Contact: Tamas Ungi, <email>ungi@cs.queensu.ca</email>

Cancer Care Ontario  

Module Description

Convenience module for sending commands through OpenIGTLink Remote to PLUS. Requires OpenIGTLink Remote module available in the SlicerIGT extension. See PLUS user guide and manual for more information about PLUS server commands.

Demo video: https://youtu.be/lfZeXabDjMg

The module provides the following features:

  • Recording of 2D tracked ultrasound frames
  • Volume reconstruction of recorded frames
  • Live ultrasound volume reconstruction using scout scanning
  • Sending Transform Update command to PLUS server

Use Cases

Some ultrasound-guided interventions require a general view of an entire area followed by more detailed images of a specific region. One example is spinal injection procedures. The problem is that, for elderly patients, the epidural area is not directly visible in ultrasound images because the intervertebral space is often compressed or deformed. In this case, physicians use four vertebrae landmarks to estimate the position of the target. Visualization can be improved using reconstructed 3D ultrasound volumes, but often there is not enough time for high resolution reconstruction of a large area during interventions.

The live ultrasound volume reconstruction workflow using scout scanning is then adapted for these procedures. The two-step method allows user to perform quick low resolution scout scan followed by high resolution volume reconstruction of a selected region of interest, in real-time. Low resolution scout scanning offers visualization of the global area and selection of the region of interest, and then high resolution reconstruction provides a good image quality of the targeted region.

  • Workflow for live ultrasound volume reconstruction using scout scanning

  • Completed scout scan (left-side image), live update of reconstruction (middle) and final live reconstructed volume (right) of a spine phantom

  • Scout scan (left) and live reconstruction (right) of an adult spine

Tutorials

The SlicerIGT website provides a tutorial for ultrasound volume reconstruction in Slicer using Plus Remote (U35).

Panels and their use

Plus Remote panel
Plus Remote panel with advanced parameters
  • Parameters sets: saving of all parameters
    • Create a new parameter set to save your parameters
    • Select previously saved ones
    • Default parameter set is selected when entering the module

This is useful when user knows optimal parameters for a specific procedure. The parameters set is saved when saving the scene and is reloaded when opening a saved scene.


  • Parameters: parameters for communication with PLUS server, recording and reconstruction
    • OpenIGTLinkConnector
    • Capture Device ID
    • Volume Reconstructor ID

These parameters are essential. Therefore all commands are disabled when these parameters are not set. List of available OpenIGTLinkConnector is available once you created connections in OpenIGTLinkIF module. When a connector is selected, capture device ID and volume reconstruction ID lists are automatically filled.


  • Recording:
    • Start and stop recording
    • Advanced parameters:
      • Modify default output filename "Recording.mha"
      • Add timestamp (YYYYMMDD_HHMMSS) to filename


  • Offline reconstruction of recorded volume:
    • Offline reconstruction
    • Advanced parameters:
      • Spacing (default value is 3mm)
      • Output volume device name
      • Volume to reconstruct filename (automatically filled when user record a file, but user can also edit this line and reconstruct previously saved files)
      • Show results on completion (display reconstructed volume in the green, yellow and 3D views)


  • Scout scan and live reconstruction:
    • Start and stop scout scan
    • Advanced parameters:
      • Spacing (default value is 3mm as we expect a low resolution scout scan)
      • Modify default output filename "ScoutScanRecording.mha"
      • Add timestamp (YYYYMMDD_HHMMSS) to filename
      • Show results on completion (display reconstructed volume in the green, yellow and 3D views)

Scout scan button record a file and automatically performs the volume reconstruction once the recording is over. The result of scout scan volume reconstruction is saved in "scoutFile.mha"

    • Start and stop live volume reconstruction:
    • Display and modify ROI using eye icon (initialized to fit scout scan volume)
    • Spacing (default value is 1mm for high resolution reconstruction)
    • Advanced parameters:
      • Output volume device name (read only)
      • Modify default output filename "LiveReconstructedVolume.mha"
      • Add timestamp (YYYYMMDD_HHMMSS) to filename
      • Display volume extent values (updated when clicking on scout scan or live reconstruction command buttons)
      • Display snapshots during live volume reconstruction (if 0, no snapshots)
      • Show results on completion (display reconstructed volume in the green, yellow and 3D views)


  • Transform Update: Update transform from what is set in the PLUS config file; Requires name of transform node to match an existing transform in the PLUS config file
  • Reply: Feedback message from PLUS server (also visible when moving the mouse on blue information icons)

Similar Modules

N/A

References

Information for Developers


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