Slicer Wiki - User contributions [en]

Documentation/Nightly/Modules/AutoPortPlacement

2014-04-14T15:17:13Z

Luist:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PortPlacement|PortPlacement]] 
This work is supported by NA-MIC and the 3DSlicer community. This work was partially supported by NSF GRFP Grant No. DGE-1144081 and NIH/NIBIB Grant No. 1R43EB014074-01. 
Authors: Andinet Enquobahrie (Kitware), Hamidreza Azimian (Hospital for Sick Children), Luis G. Torres (UNC-Chapel Hill) 
Contact: Andinet Enquobahrie, <email>andinet.enqu@kitware.com</email> and Luis G. Torres, <email>lgtorres42@gmail.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
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{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The AutoPortPlacement module assists in the planning of surgical port placement in a robotic laparoscopic procedure. Users can specify surgical task frames of interest, potential positions for surgical ports, and potential placements of the surgical robot's base, and the automated port placement algorithm will select a set of surgical ports and visualize a simulated Davinci surgical robot with its tools positioned at the selected ports.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
[[File:Automated port placement surgical plan.png|640px]]


{{documentation/{{documentation/version}}/module-section|Tutorials}}

The automated port placement module requires three pieces of information in order to select a set of surgical ports for a robotic laparoscopic procedure:

# A Fiducial node representing a set of points of surgical interest, or ''task frames'';
# A Fiducial node consisting of two points representing a curve of potential positions for surgical ports;
# A region of interest (ROI) representing the potential positions of the surgical robot's base.

== Surgical task frames ==

Surgical task frames describe positions of interest for the surgical robot's tools to be able to reach. You can use the Markups module to add surgical task frames:
# Select the Markups module.
# Click the combo box labeled "Select a MarkupsFiducial".
# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical task frames".
# Begin placing fiducial markers in the scene where surgical task frames are desired.

=== Optional: Setting orientations of surgical task frames ===

In the current version of Slicer, fiducial markers can only specify positions. However, useful surgical task frames typically require specification of both their position and the angle of approach for the tool to reach the frame. If you use the AutoPortPlacement module with the current version of Slicer, the angle of approach for each fiducial marker will default to the Superior direction, or "straight up".

The functionality for specifying fiducial orientation is not yet complete, but you're free to preview it by checking out [https://github.com/giogadi/PortPlacement/tree/add-auto-pp-module this fork of Slicer]. You can adjust fiducial markers' orientations in the following way:

# Select the Markups module.
# Use the combo box labeled "List" to select the MarkupsFiducial list whose orientations you want to edit.
# Right-click the Fiducial list table and select "Toggle position/orientation mode"
# Now all fiducial markers of that list will be in orientation mode. Each marker will be composed of a large sphere centered at the marker's position, and smaller sphere pointed in the direction of that fiducial's orientation. You can alter the fiducial's direction by clicking and dragging the smaller sphere. The small sphere denotes the direction from the surgical tool should approach this task frame.

== Port Curve ==

The port curve describes the potential positions on the body to place surgical ports for passing through surgical instruments. Currently, the automated port placement module can only handle potential port positions along a straight line segment defined by two endpoints, where the endpoints are represented as fiducial markers. Here's how you can define a port curve:

# Select the Markups module.
# Click the combo box labeled "Select a MarkupsFiducial".
# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical port curve".
# Place two fiducial markers to mark the endpoints of the line segment of potential port positions for the automated port placement algorithm to consider.

== Robot Base ROI ==

The Robot Base ROI (region of interest) describes the potential positions in the environment to place the surgical robot relative to the patient. It helps to specify a set of positions because in some cases a slight adjustment of the robot's base can allow the robot to reach the surgical task frames more safely. You can specify the robot base ROI with the following procedure:

# In the top toolbar, there is an icon with a red dot and a blue arrow pointing upward. Immediately to the right of this icon, there is a dropdown arrow; click this arrow and select "ROI".
# Click two points in Slicer's 3D view that roughly correspond to your desired region's bounds, and a region of interest will appear in the scene.
# Use the colored anchors to adjust the region's position and size.
# If you like, select the Annotations module, right-click your newly created ROI, and click "Rename" to give it a more meaningful name like "Robot base ROI".

== Automated Port Placement ==

Once you've created a set of surgical task frames, a port curve, and a robot base ROI, you are ready to specify these to the automated port placement module for automated surgical planning with the following procedure:

# Select the AutoPortPlacement module.
# Click the combo box labeled "Markups List of Task Frames" and specify the Markups node you previously created for the surgical task frames.
# Click the combo box labeled "Port Curve Endpoints" and specify the Markups node you previously created for the endpoints of the surgical port curve.
# Click the combo box labeled "Robot Base ROI" and specify the ROI node you previously created for the robot base ROI.
# Click "Find Surgical Plan".

It might take a minute or two, but after some you will see that the robot's arms have automatically moved. If the automated port placement was successful, the arms will be situated such that they reach points on the port curve. We note that there is still lots of room for improvement on the optimization algorithm that drives the automated port placement procedure, so the result may not always make much sense.

== Robot Arm Configuration ==

The user is also welcome to manually move the simulated surgical robot's arms around in order to explore the robot's reachable workspace, as well as make adjustments to surgical plans returned by the automated port placement procedure. The user may do this by selecting which joint she wishes to move with the combo boxes labeled "Passive Joints (Left)" and "Passive Joints (Right)". The user may then rotate the selected joint by dragging the slider immediately to the right of the selected combo box. This will cause the visualized robot's arms to interactively update their configuration to reflect the user's changes. The user can also reset the robot's arms to their initial configuration by clicking the "Reset Robot Configuration" button.









{{documentation/{{documentation/version}}/module-section|Source Code}}
[https://github.com/giogadi/PortPlacement/tree/add-auto-pp-module/AutoPortPlacement Github]


{{documentation/{{documentation/version}}/module-section|References}}
* Luis G. Torres, Hamidreza Azimian, Andinet Enquobahrie. [http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1849104 A user-friendly automated port placement planning system for laparoscopic robotic surgery], SPIE, Mar. 2014.

*[http://www.na-mic.org/publications/item/view/1266 SPL Abdominal Atlas] (used in examples)





{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/AutoPortPlacement

2014-04-14T15:07:42Z

Luist:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PortPlacement|PortPlacement]] 
This work is supported by NA-MIC and the 3DSlicer community. This work was partially supported by NSF GRFP Grant No. DGE-1144081 and NIH/NIBIB Grant No. 1R43EB014074-01. 
Authors: Andinet Enquobahrie (Kitware), Hamidreza Azimian (Hospital for Sick Children), Luis G. Torres (UNC-Chapel Hill) 
Contact: Andinet Enquobahrie, <email>andinet.enqu@kitware.com</email> and Luis G. Torres, <email>lgtorres42@gmail.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
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|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The AutoPortPlacement module assists in the planning of surgical port placement in a robotic laparoscopic procedure. Users can specify surgical task frames of interest, potential positions for surgical ports, and potential placements of the surgical robot's base, and the automated port placement algorithm will select a set of surgical ports and visualize a simulated Davinci surgical robot with its tools positioned at the selected ports.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
[[File:Automated port placement surgical plan.png|640px]]


{{documentation/{{documentation/version}}/module-section|Tutorials}}

The automated port placement module requires three pieces of information in order to select a set of surgical ports for a robotic laparoscopic procedure:

# A Fiducial node representing a set of points of surgical interest, or ''task frames'';
# A Fiducial node consisting of two points representing a curve of potential positions for surgical ports;
# A region of interest (ROI) representing the potential positions of the surgical robot's base.

== Surgical task frames ==

Surgical task frames describe positions of interest for the surgical robot's tools to be able to reach. You can use the Markups module to add surgical task frames:
# Select the Markups module.
# Click the combo box labeled "Select a MarkupsFiducial".
# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical task frames".
# Begin placing fiducial markers in the scene where surgical task frames are desired.

=== Optional: Setting orientations of surgical task frames ===

In the current version of Slicer, fiducial markers can only specify positions. However, useful surgical task frames typically require specification of both their position and the angle of approach for the tool to reach the frame. If you use the AutoPortPlacement module with the current version of Slicer, the angle of approach for each fiducial marker will default to the Superior direction, or "straight up".

The functionality for specifying fiducial orientation is not yet complete, but you're free to preview it by checking out [https://github.com/giogadi/PortPlacement/tree/add-auto-pp-module this fork of Slicer]. You can adjust fiducial markers' orientations in the following way:

# Select the Markups module.
# Use the combo box labeled "List" to select the MarkupsFiducial list whose orientations you want to edit.
# Right-click the Fiducial list table and select "Toggle position/orientation mode"
# Now all fiducial markers of that list will be in orientation mode. Each marker will be composed of a large sphere centered at the marker's position, and smaller sphere pointed in the direction of that fiducial's orientation. You can alter the fiducial's direction by clicking and dragging the smaller sphere. The small sphere denotes the direction from the surgical tool should approach this task frame.

== Port Curve ==

The port curve describes the potential positions on the body to place surgical ports for passing through surgical instruments. Currently, the automated port placement module can only handle potential port positions along a straight line segment defined by two endpoints, where the endpoints are represented as fiducial markers. Here's how you can define a port curve:

# Select the Markups module.
# Click the combo box labeled "Select a MarkupsFiducial".
# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical port curve".
# Place two fiducial markers to mark the endpoints of the line segment of potential port positions for the automated port placement algorithm to consider.

== Robot Base ROI ==

The Robot Base ROI (region of interest) describes the potential positions in the environment to place the surgical robot relative to the patient. It helps to specify a set of positions because in some cases a slight adjustment of the robot's base can allow the robot to reach the surgical task frames more safely. You can specify the robot base ROI with the following procedure:

# In the top toolbar, there is an icon with a red dot and a blue arrow pointing upward. Immediately to the right of this icon, there is a dropdown arrow; click this arrow and select "ROI".
# Click two points in Slicer's 3D view that roughly correspond to your desired region's bounds, and a region of interest will appear in the scene.
# Use the colored anchors to adjust the region's position and size.
# If you like, select the Annotations module, right-click your newly created ROI, and click "Rename" to give it a more meaningful name like "Robot base ROI".

== Automated Port Placement ==

Once you've created a set of surgical task frames, a port curve, and a robot base ROI, you are ready to specify these to the automated port placement module for automated surgical planning with the following procedure:

# Select the AutoPortPlacement module.
# Click the combo box labeled "Markups List of Task Frames" and specify the Markups node you previously created for the surgical task frames.
# Click the combo box labeled "Port Curve Endpoints" and specify the Markups node you previously created for the endpoints of the surgical port curve.
# Click the combo box labeled "Robot Base ROI" and specify the ROI node you previously created for the robot base ROI.
# Click "Find Surgical Plan".

It might take a minute or two, but after some you will see that the robot's arms have automatically moved. If the automated port placement was successful, the arms will be situated such that they reach points on the port curve. We note that there is still lots of room for improvement on the optimization algorithm that drives the automated port placement procedure, so the result may not always make much sense.

== Robot Arm Configuration ==

The user is also welcome to manually move the simulated surgical robot's arms around in order to explore the robot's reachable workspace, as well as make adjustments to surgical plans returned by the automated port placement procedure. The user may do this by selecting which joint she wishes to move with the combo boxes labeled "Passive Joints (Left)" and "Passive Joints (Right)". The user may then rotate the selected joint by dragging the slider immediately to the right of the selected combo box. This will cause the visualized robot's arms to interactively update their configuration to reflect the user's changes. The user can also reset the robot's arms to their initial configuration by clicking the "Reset Robot Configuration" button.









{{documentation/{{documentation/version}}/module-section|References}}
* Luis G. Torres, Hamidreza Azimian, Andinet Enquobahrie. [http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1849104 A user-friendly automated port placement planning system for laparoscopic robotic surgery], SPIE, Mar. 2014.

*[http://www.na-mic.org/publications/item/view/1266 SPL Abdominal Atlas] (used in examples)





{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/AutoPortPlacement

2014-04-13T20:14:07Z

Luist:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PortPlacement|PortPlacement]] 
This work is supported by NA-MIC and the 3DSlicer community. This work was partially supported by NSF GRFP Grant No. DGE-1144081 and NIH/NIBIB Grant No. 1R43EB014074-01. 
Authors: Andinet Enquobahrie (Kitware), Hamidreza Azimian (Hospital for Sick Children), Luis G. Torres (UNC-Chapel Hill) 
Contact: Andinet Enquobahrie, <email>andinet.enqu@kitware.com</email> and Luis G. Torres, <email>lgtorres42@gmail.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The AutoPortPlacement module assists in the planning of surgical port placement in a robotic laparoscopic procedure. Users can specify surgical task frames of interest, potential positions for surgical ports, and potential placements of the surgical robot's base, and the automated port placement algorithm will select a set of surgical ports and visualize a simulated Davinci surgical robot with its tools positioned at the selected ports.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
[[File:Automated port placement surgical plan.png|640px]]


{{documentation/{{documentation/version}}/module-section|Tutorials}}

The automated port placement module requires three pieces of information in order to select a set of surgical ports for a robotic laparoscopic procedure:

# A Fiducial node representing a set of points of surgical interest, or ''task frames'';
# A Fiducial node consisting of two points representing a curve of potential positions for surgical ports;
# A region of interest (ROI) representing the potential positions of the surgical robot's base.

== Surgical task frames ==

Surgical task frames describe positions of interest for the surgical robot's tools to be able to reach. You can use the Markups module to add surgical task frames:
# Select the Markups module.
# Click the combo box labeled "Select a MarkupsFiducial".
# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical task frames".
# Begin placing fiducial markers in the scene where surgical task frames are desired.

=== Optional: Setting orientations of surgical task frames ===

In the current version of Slicer, fiducial markers can only specify positions. However, useful surgical task frames typically require specification of both their position and the angle of approach for the tool to reach the frame. If you use the AutoPortPlacement module with the current version of Slicer, the angle of approach for each fiducial marker will default to the Superior direction, or "straight up".

The functionality for specifying fiducial orientation is not yet complete, but you're free to preview it by checking out [https://github.com/giogadi/PortPlacement/tree/add-auto-pp-module this fork of Slicer]. You can adjust fiducial markers' orientations in the following way:

# Select the Markups module.
# Use the combo box labeled "List" to select the MarkupsFiducial list whose orientations you want to edit.
# Right-click the Fiducial list table and select "Toggle position/orientation mode"
# Now all fiducial markers of that list will be in orientation mode. Each marker will be composed of a large sphere centered at the marker's position, and smaller sphere pointed in the direction of that fiducial's orientation. You can alter the fiducial's direction by clicking and dragging the smaller sphere. The small sphere denotes the direction from the surgical tool should approach this task frame.

== Port Curve ==

The port curve describes the potential positions on the body to place surgical ports for passing through surgical instruments. Currently, the automated port placement module can only handle potential port positions along a straight line segment defined by two endpoints, where the endpoints are represented as fiducial markers. Here's how you can define a port curve:

# Select the Markups module.
# Click the combo box labeled "Select a MarkupsFiducial".
# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical port curve".
# Place two fiducial markers to mark the endpoints of the line segment of potential port positions for the automated port placement algorithm to consider.

== Robot Base ROI ==

The Robot Base ROI (region of interest) describes the potential positions in the environment to place the surgical robot relative to the patient. It helps to specify a set of positions because in some cases a slight adjustment of the robot's base can allow the robot to reach the surgical task frames more safely. You can specify the robot base ROI with the following procedure:

# In the top toolbar, there is an icon with a red dot and a blue arrow pointing upward. Immediately to the right of this icon, there is a dropdown arrow; click this arrow and select "ROI".
# Click two points in Slicer's 3D view that roughly correspond to your desired region's bounds, and a region of interest will appear in the scene.
# Use the colored anchors to adjust the region's position and size.
# If you like, select the Annotations module, right-click your newly created ROI, and click "Rename" to give it a more meaningful name like "Robot base ROI".

== Automated Port Placement ==

Once you've created a set of surgical task frames, a port curve, and a robot base ROI, you are ready to specify these to the automated port placement module for automated surgical planning with the following procedure:

# Select the AutoPortPlacement module.
# Click the combo box labeled "Markups List of Task Frames" and specify the Markups node you previously created for the surgical task frames.
# Click the combo box labeled "Port Curve Endpoints" and specify the Markups node you previously created for the endpoints of the surgical port curve.
# Click the combo box labeled "Robot Base ROI" and specify the ROI node you previously created for the robot base ROI.
# Click "Find Surgical Plan".

It might take a minute or two, but after some you will see that the robot's arms have automatically moved. If the automated port placement was successful, the arms will be situated such that they reach points on the port curve. We note that there is still lots of room for improvement on the optimization algorithm that drives the automated port placement procedure, so the result may not always make much sense.

== Robot Arm Configuration ==

The user is also welcome to manually move the simulated surgical robot's arms around in order to explore the robot's reachable workspace, as well as make adjustments to surgical plans returned by the automated port placement procedure. The user may do this by selecting which joint she wishes to move with the combo boxes labeled "Passive Joints (Left)" and "Passive Joints (Right)". The user may then rotate the selected joint by dragging the slider immediately to the right of the selected combo box. This will cause the visualized robot's arms to interactively update their configuration to reflect the user's changes. The user can also reset the robot's arms to their initial configuration by clicking the "Reset Robot Configuration" button.









{{documentation/{{documentation/version}}/module-section|References}}
*Andinet Enquobahrie, Vikas Shivaprabhu, Stephen Aylward, Julien Finet, Kevin Cleary, and Ron Alterovitz. [http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1668860 Patient-specific port placement for laparoscopic surgery using atlas-based registration], SPIE, Mar. 2013.

*[http://www.na-mic.org/publications/item/view/1266 SPL Abdominal Atlas] (used in examples)





{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/AutoPortPlacement

2014-04-13T19:44:41Z

Luist:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/PortPlacement|PortPlacement]] 
This work is supported by NA-MIC and the 3DSlicer community. This work was partially supported by NSF GRFP Grant No. DGE-1144081 and NIH/NIBIB Grant No. 1R43EB014074-01. 
Authors: Andinet Enquobahrie (Kitware), Hamidreza Azimian (Hospital for Sick Children), Luis G. Torres (UNC-Chapel Hill) 
Contact: Andinet Enquobahrie, <email>andinet.enqu@kitware.com</email> and Luis G. Torres, <email>lgtorres42@gmail.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The AutoPortPlacement module assists in the planning of surgical port placement in a robotic laparoscopic procedure. Users can specify surgical task frames of interest, potential positions for surgical ports, and potential placements of the surgical robot's base, and the automated port placement algorithm will select a set of surgical ports and visualize a simulated Davinci surgical robot with its tools positioned at the selected ports.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
[[File:Automated port placement surgical plan.png|640px]]


{{documentation/{{documentation/version}}/module-section|Tutorials}}

The automated port placement module requires three pieces of information in order to select a set of surgical ports for a robotic laparoscopic procedure:

# A Fiducial node representing a set of points of surgical interest, or ''task frames'';
# A Fiducial node consisting of two points representing a curve of potential positions for surgical ports;
# A region of interest (ROI) representing the potential positions of the surgical robot's base.

== Surgical task frames ==

Surgical task frames describe positions of interest for the surgical robot's tools to be able to reach. You can use the Markups module to add surgical task frames:
# Select the Markups module.
# Click the combo box labeled "Select a MarkupsFiducial".
# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical task frames".
# Begin placing fiducial markers in the scene where surgical task frames are desired.

=== Optional: Setting orientations of surgical task frames ===

In the current version of Slicer, fiducial markers can only specify positions. However, useful surgical task frames typically require specification of both their position and the angle of approach for the tool to reach the frame. If you use the AutoPortPlacement module with the current version of Slicer, the angle of approach for each fiducial marker will default to the Superior direction, or "straight up".

The functionality for specifying fiducial orientation is not yet complete, but you're free to preview it by checking out [https://github.com/giogadi/PortPlacement/tree/add-auto-pp-module this fork of Slicer]. You can adjust fiducial markers' orientations in the following way:

# Select the Markups module.
# Use the combo box labeled "List" to select the MarkupsFiducial list whose orientations you want to edit.
# Right-click the Fiducial list table and select "Toggle position/orientation mode"
# Now all fiducial markers of that list will be in orientation mode. Each marker will be composed of a large sphere centered at the marker's position, and smaller sphere pointed in the direction of that fiducial's orientation. You can alter the fiducial's direction by clicking and dragging the smaller sphere. The small sphere denotes the direction from the surgical tool should approach this task frame.

== Ports ==
You can use Markups fiducials to add surgical ports for visualization:
# Select the Markups module.
# Click the combo box labeled "Select a MarkupsFiducial".
# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical ports".
# Begin placing fiducial markers in the scene where surgical ports are desired.
# Select the Port Placement Module (under the IGT category).
# Select your MarkupsFiducial list using the combo box labeled "Markups node of surgical ports"
# Click "Set Port Markups Node" to associate the selected MarkupsFiducial list with the Port Placement module.

The module will automatically visualize surgical tools centered at each fiducial marker at some default (and likely useless) orientation.

You can always remove a port by either deleting its associated fiducial marker or by highlighting the port in the module's ports table and clicking "Remove Selected Port".

You can also continue to add fiducial markers to the associated MarkupsFiducial list and the module will automatically add the new markers as ports.

Lastly, you can move a markups fiducial around the scene and the port will interactively follow the fiducial.

== Tools ==
Once you've added some ports, you can re-orient the surgical tools in two ways:
* Target-oriented
# Select the Markups module.
# Click the combo box labeled "List" and then click "Create and rename new MarkupsFiducial". Rename this MarkupsFiducial to something meaningful like "surgical target".
# With the new MarkupsFiducial enabled, place a fiducial marker in the scene that you want your surgical tools to point at. Think of this as your surgical target.
# In the Port Placement module, select your new MarkupsFiducial in the box labeled "Surgical Target Fiducial".
# Click the "Aim Tools at Target" button to automatically orient all surgical tools toward your selected target.
* Manual Orientation
# In order to manually orient an individual tool, look in the port table for the fiducial corresponding to that tool's port and click on it.
# Use the Tool Orientation sliders to re-orient the selected tool about the port location.

You can also vary the length and radius of individual tools by selecting them in the table and adjusting the "Tool radius" and "Tool length" spinboxes.

Finally, you can toggle the visibility of individual tools by clicking "Visible" checkboxes at each row of the ports table.









{{documentation/{{documentation/version}}/module-section|References}}
*Andinet Enquobahrie, Vikas Shivaprabhu, Stephen Aylward, Julien Finet, Kevin Cleary, and Ron Alterovitz. [http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=1668860 Patient-specific port placement for laparoscopic surgery using atlas-based registration], SPIE, Mar. 2013.

*[http://www.na-mic.org/publications/item/view/1266 SPL Abdominal Atlas] (used in examples)





{{documentation/{{documentation/version}}/module-footer}}

File:Automated port placement surgical plan.png

2014-04-13T18:49:51Z

Luist: Visualization of a surgical plan found by the AutoPortPlacement module

Visualization of a surgical plan found by the AutoPortPlacement module

Documentation/Nightly/Modules/AutoPortPlacement

2014-04-13T18:47:51Z

Luist:

Documentation/Nightly/Modules/AutoPortPlacement

2014-04-13T18:46:09Z

Luist: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'

Documentation/4.3/Modules/PortPlacement

2013-11-13T16:49:18Z

Luist: Updating documentation for latest version

Documentation/4.3/Extensions/PortPlacement

2013-11-13T16:47:49Z

Luist: Ensuring that 4.3 wiki points to 4.3 version of PortPlacement documentation

#REDIRECT [[Documentation/4.3/Modules/PortPlacement]]

Documentation/Nightly/Modules/PortPlacement

2013-11-11T14:59:14Z

Luist: Removing warning about this module only working on 4.2

Documentation/Nightly/Modules/PortPlacement

2013-11-11T14:58:34Z

Luist: /* Notes */

Documentation/Nightly/Modules/PortPlacement

2013-11-11T14:58:11Z

Luist: /* Ports */ Adding documentation on movement of fiducials

Documentation/Nightly/Modules/PortPlacement

2013-11-11T14:56:54Z

Luist: /* Tools */ Updating tools documentation for new markups-enabled module.

Documentation/Nightly/Modules/PortPlacement

2013-11-11T14:51:27Z

Luist: /* Ports */ Updating ports documentation for new Markups-enabled module

Documentation/4.2/Extensions

2013-11-11T14:38:24Z

Luist: /* Cat 2 */ Adding Port Placement documentation link

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>{{:{{FULLPAGENAME}}/Description}}

__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|CARMA]] (Alan Morris)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
** [[Documentation/{{documentation/version}}/Extensions/LabelToDICOMSEGImport|LabelToDICOMSEGConverter]]
** [[Documentation/{{documentation/version}}/Extensions/DICOMSEGImport|DICOM SEG Import]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Deformation field visualizer]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|IGyne]] (Guillaume Pernelle, Xiaojun Chen, Yi Gao, Jan Egger)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylaward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]] (Sunil Kumar, Dan Marcus, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)

Documentation/4.2/Extensions/PortPlacement

2013-11-11T14:36:40Z

Luist:

Documentation/4.2/Extensions/PortPlacement

2013-11-11T14:36:08Z

Luist: Porting the current out-dated "nightly" port placement documentation to 4.2 where it belongs

Documentation/Nightly/Modules/PortPlacement

2013-11-06T20:06:10Z

Luist: added note that this module does not work yet on Slicer 4.3.

Documentation/Nightly/Modules/PortPlacement

2013-07-11T13:59:19Z

Luist: Fixed acknowledgements

Documentation/Nightly/Extensions

2013-07-10T14:53:35Z

Luist: Added Port Placement extension documentation link to category 2

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
** [[Documentation/{{documentation/version}}/Modules/PatientHierarchy|Patient hierarchy]]
** [[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Deformation field visualizer]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*** [[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] [[image:UnderConstruction.png|tumb|10px]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/PathPlanner|PathPlanner]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VisuaLine|VisuaLine]] (Laurent Chauvin)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Andinet Enquobahrie, Luis G. Torres)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)

<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

Documentation/Nightly/Modules/PortPlacement

2013-07-09T15:47:47Z

Luist: Added references

Documentation/Nightly/Modules/PortPlacement

2013-07-09T15:36:50Z

Luist: Updated contact info

Documentation/Nightly/Extensions/PortPlacement

2013-07-01T16:45:02Z

Luist: Redirected page to Documentation/Nightly/Modules/PortPlacement

#REDIRECT [[Documentation/Nightly/Modules/PortPlacement]]

File:Portplacement icon.png

2013-07-01T16:36:45Z

Luist:

Documentation/Nightly/Modules/PortPlacement

2013-06-20T17:41:14Z

Luist:

Documentation/Nightly/Modules/PortPlacement

2013-06-20T17:31:35Z

Luist:

Documentation/Nightly/Modules/PortPlacement

2013-06-20T17:08:51Z

Luist:

File:Portplacement.png

2013-06-20T17:06:44Z

Luist: Screenshot of example usage of PortPlacement module

Screenshot of example usage of PortPlacement module

Documentation/Nightly/Modules/PortPlacement

2013-06-20T17:05:47Z

Luist:

Documentation/Nightly/Modules/PortPlacement

2013-06-20T15:31:52Z

Luist:

Documentation/Nightly/Modules/PortPlacement

2013-06-20T15:24:20Z

Luist: Creating new PortPlacement module page from template

Documentation/Nightly/Extensions/PortPlacement

2013-06-20T15:23:21Z

Luist: Adding redirect to (soon-to-exist) PortPlacement module page

<noinclude>{{documentation/versioncheck}}</noinclude>
#REDIRECT [[Documentation/Nightly/Modules/PortPlacement]]