Documentation/4.3/Modules/PortPlacement - Revision history

Luist: Updating documentation for latest version

2013-11-13T16:49:18Z

Updating documentation for latest version

UpdateBot: Nightly -> 4.3

2013-09-05T03:43:50Z

Nightly -> 4.3

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Extension: [[Documentation/{{documentation/version}}/Extensions/PortPlacement|PortPlacement]] <br>
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.<br>
Author: Andinet Enquobahrie (Kitware), Luis G. Torres (UNC-Chapel Hill)<br>
Contact: Andinet Enquobahrie, <email>andinet.enqu@kitware.com</email> and Luis G. Torres, <email>lgtorres42@gmail.com</email><br>
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{{documentation/{{documentation/version}}/module-section|Module Description}}
The PortPlacement module assists in the planning of surgical port placement in a laparoscopic procedure. Users can specify ports using fiducial markers and the module will automatically visualize simulated surgical tools at the port locations. Users can freely pivot the simulated surgical tools about the ports, as well as automatically orient all surgical tools toward a specified surgical target. Simulated tools are represented by cylinders whose lengths and radii can be varied from tool to tool.


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== Ports ==
There are two ways to add surgical ports to be visualized:
* Individually
# Place a fiducial marker at a desired surgical port location.
# Select that fiducial in the box labeled "Surgical Port".
# Click the "Add Port" button.
* From a List
# Select the Annotations module.
# Click the "Create a new hierarchy" button.
# (Optional) Rename the new hierarchy to something meaningful like "My Surgical Ports".
# Add fiducial markers to the scene where surgical ports are desired.
# Select the Port Placement module.
# Select your annotation hierarchy in the box labeled "List of Surgical Ports".
# Click the "Add Ports from List" button.

Once you've added your ports, the module will automatically visualize surgical tools at each port at some default (and likely useless) orientation.

You can remove a port by selecting the fiducial used to specify it in the ports table and then clicking the "Remove Port" button.

== Tools ==
Once you've added some ports, you can re-orient the surgical tools in two ways:
* Target-oriented
# Place a fiducial marker in the scene that you want your surgical tools to point at. Think of this as your surgical target.
# Select that fiducial marker 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 select it by clicking on it.
# Use the Tool Orientation sliders to re-orient the 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.

== Notes ==
Each port added to the scene is tied directly to the fiducial marker used to specify it; this means the user can move the fiducial marker around and the port/tool will follow automatically. This also means that if the user deletes a fiducial marker associated with the port, the port will also be removed from the scene.









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*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)





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@@ Line 31: / Line 31: @@
 == Ports ==
-There are two ways to add surgical ports to be visualized:
+You can use Markups fiducials to add surgical ports for visualization:
-* Individually
+# Select the Markups module.
-# Place a fiducial marker at a desired surgical port location.
+# Click the combo box labeled "Select a MarkupsFiducial".
-# Select that fiducial in the box labeled "Surgical Port".
+# Select "Create and rename new MarkupsFiducial" and give your MarkupsFiducial list a meaningful name like "surgical ports".
-# Click the "Add Port" button.
+# Begin placing fiducial markers in the scene where surgical ports are desired.
-* From a List
+# Select the Port Placement Module (under the IGT category).
-# Select the Annotations module.
+# Select your MarkupsFiducial list using the combo box labeled "Markups node of surgical ports"
-# Click the "Create a new hierarchy" button.
+# Click "Set Port Markups Node" to associate the selected MarkupsFiducial list with the Port Placement module.
-Once you've added your ports, the module will automatically visualize surgical tools at each port at some default (and likely useless) orientation.
+The module will automatically visualize surgical tools centered at each fiducial marker at some default (and likely useless) orientation.
-You can remove a port by selecting the fiducial used to specify it in the ports table and then clicking the "Remove Port" button.
+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".
 == Tools ==
 Once you've added some ports, you can re-orient the surgical tools in two ways:
 * Target-oriented
-# Place a fiducial marker in the scene that you want your surgical tools to point at. Think of this as your surgical target.
+# Select the Markups module.
-# Select that fiducial marker in the box labeled "Surgical Target Fiducial".
+# Click the combo box labeled "List" and then click "Create and rename new MarkupsFiducial". Rename this MarkupsFiducial to something meaningful like "surgical target".
 # 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 select it by clicking on it.
+# 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 tool about the port location.
+# 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.
-== Notes ==
+Finally, you can toggle the visibility of individual tools by clicking "Visible" checkboxes at each row of the ports table.
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