Difference between revisions of "Modules:ProstateNav-Documentation-3.6"

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{|
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|[[Image:ProstateModule-3.4.jpg|thumb|280px|ProstateNav module in Calibration Phase.]]
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|[[Image:ProstateModule-3.6.jpg|thumb|360px|ProstateNav in clinical MRI-guided prostate biopsy.]]
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|[[Image:ProstateNav-3.6_Transrectal.png|thumb|360px|ProstateNav for MRI-guided transrectal biospy]]
 
|}
 
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===Module Description===
 
===Module Description===
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The ProstateNav module is designed to add an integrated user interface (UI) for MRI-guided prostate intervention (e.g. needle biopsy and brachytherapy) to 3D Slicer. In version 3.6, the module provides user interfaces for the following devices:
+
The ProstateNav module is designed to add an integrated user interface (UI) for MRI-guided prostate intervention (e.g. needle biopsy and brachytherapy) to 3D Slicer. Like all of Slicer it is not FDA approved and only intended for research. In version 3.6, the module provides user interfaces for the following devices:
 
*MRI-compatible pneumatic needle placement robot for transperineal prostate biopsy and brachytherapy (Johns Hopkins University + Brigham and Women's Hospital + Queen's Univeristy)
 
*MRI-compatible pneumatic needle placement robot for transperineal prostate biopsy and brachytherapy (Johns Hopkins University + Brigham and Women's Hospital + Queen's Univeristy)
 
*MRI-compatible transrectal needle biopsy device (Queen's University + Johns Hopkins University)
 
*MRI-compatible transrectal needle biopsy device (Queen's University + Johns Hopkins University)
 
*Template-based needle guiding system for MRI-guided prostate biopsy and brachy therapy (Queen's University + Brigham and Women's Hospital)
 
*Template-based needle guiding system for MRI-guided prostate biopsy and brachy therapy (Queen's University + Brigham and Women's Hospital)
  
 +
The module has wizard-style interface, which helps an operator follow the clinical procedure step by step. It supports target planning and management, patient-device registration, and verification. The module can also communicate with some of the devices listed above using [http://www.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink protocol].
  
−
The module has Wizard-style interface, which provides the operators the step-by-step navigation to follow the clinical procedure of the clinical prostate intervention. The module also provides several functionalities to follow the procedure, including calibration of the robot using fiducial-based registration, target management, and communication with devices (MRI-compatible robot and MR scanner) using [[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLink]].
+
== Usage ==
 +
===Tutorials===
 +
The ProstateNav switches its user interface based on the device type selected by the user. This section describes step-by-step instruction.
 +
 
 +
===Template-based needle guiding system for MRI-guided prostate biopsy and brachy therapy===
 +
====Step 1: Create a manager node and select a device type====
 +
First, create a manager node by choosing '''Create New ProstateNavManager''' from a node selector menu in '''Active configuration'''.
 +
Then click '''Create New TransperinealProstateTemplate''' from '''Robot''' node selector.
 +
 
 +
<center>
 +
{|
 +
|[[Image:Slicer3_ProstateNav_SelectManager.png|thumb|center|240px|]]
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|[[Image:Slicer3_ProstateNav_SelectDevice.png|thumb|center|240px|]]
 +
|}
 +
</center>
 +
 
 +
 
 +
====Step 2: Calibration====
 +
Press '''Cliabration''' button in the workphase tab to open '''2/4 Calibration''' page.
 +
[[Image:Slicer3_ProstateNav_OpenCalibration.png|thumb|center|240px|]]
 +
 
 +
First, we load a multi-slice Z-frame image to register the device coordinate system to the image coordinate system. Choose "File->Add Volume..." menu to open the file selection dialog box.
 +
 
 +
[[Image:Slicer3_ProstateNav_LoadZFrameImage.png|thumb|center|400px|]]
 +
 
 +
To display a model of Z-frame fiducial frame in the 3D viewer, click '''Show Z-frame''' check box.
 +
 
 +
[[Image:Slicer3_ProstateNav_ShowZFrameModel.png|thumb|center|400px|]]
  
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====Wizard interface====
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Before run automatic Z-frame registration, scroll the all slices in the multi-slice Z-frame image to identify the range of slices that show clear Z-frame images. If you want to adjust the slice range, input the start and end slice index in the text box.
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The interface consists of six pages, corresponding six phases in the procedure:
 
  
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*'''START-UP.''' Software and hardware systems are initialized in this workphase. The 3D Slicer reads a configuration file that defines data stream among the components. Meanwhile, the robot is set up by connecting the pneumatic system to pressurized air, connecting the device to the control unit, and attaching sterilized needle driver kit and needle to the robot. The needle is adjusted to a pre-defined home position of the robot. The imaging coil is attached to the patient, who is then positioned in the scanner.
+
[[Image:Slicer3_ProstateNav_CheckZFrameSliceRange.png|thumb|center|400px|]]
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*'''PLANNING.''' Pre-procedure 3D images, including T1- and T2-weighted images, are acquired and loaded into the 3D Slicer. Target points for needle insertions are interactively defined on the pre-operative images.
 
−
*'''CALIBRATION.''' The transformation that registers robot coordinates to patient coordinates is calculated by acquiring images of the Z-shape fiducial frame. The calibration procedure is performed for every intervention by the operator. Once the robot coordinate system is registered, the robot control unit and the 3D Slicer exchange target positions and the current position of the needle using the image (i.e., patient) coordinate system. Details of the Z-shape fiducial will be described in the following section.
 
−
*'''TARGETING.''' A current target is selected from the targets defined in the PLANNING workphase, and sent to the robot control unit. The robot moves the needle to the target while transmitting its current position in real time. After the needle guide is maneuvered to the desired position, the needle is manually inserted along an encoded guide to the target lesion. The insertion process is monitored through semi real-time 2D image, automatically aligned to the plane along the needle axis.
 
−
*'''MANUAL.''' The operator can directly control the robot position remotely from the 3D Slicer. The system enters this workphase when the needle position needs to be adjusted manually.
 
−
*'''EMERGENCY.''' All robot motion is halted for safety reasons, as soon as the system enters the EMERGENCY workphase. The actuators are locked in this state to prevent unwanted motion and allow manual needle retraction.
 
  
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The unique feature in this wizard interface is a set of "jump buttons" placed above the wizard. The buttons not only allow the users to jump from one phase to another, but restrict certain critical phase transitions by disabling the buttons. For example, jumping from START-UP phase to TARGETING should not happen, because it is risky to control the robot before the calibration. Therefore, the button to jump to the TARGETING phase is disable, while the module is in the START-UP phase.
+
To start automatic Z-frame registration, press '''Perform Calibration''' button. It takes a few seconds or more depending on the environment and number of slices. Once the Z-frame is registered to the image coordinate system, the z-frame model is overlaid to the Z-frame image in the 3D view.
  
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====Fiducial-based registration====
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[[Image:Slicer3_ProstateNav_ZFrameRegistration.png|thumb|center|400px|]]
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To transform a position from the image coordinate system to the robot coordinate system, or vice versa, a calibration is performed by registering the Z-shape fiducial frame attached to the robot in the image coordinate system. The Z-shape fiducial frame is designed to be localized from a single 2D image intersecting the frame. The position and orientation of the Z-shape fiducial frame provide the transformation between the image and robot coordinate systems. Once the transformation is calculated, the needle position and orientation measured by the encoders of the robot can be transformed to image coordinates. The rigid structure of the fiducial frame is made up of seven rigid glass tubes with 3 mm inner diameters that are filled with contrast agent (MR Spots, Beekley, Bristol, CT) and placed on three faces of a 60 mm cube. The ProstateNav module can load 2D sectional image of the Z-frame in DICOM format and calculate its orientation and location in the image space. The image should have field of view (FOV) of 160mm and matrix size of 256 by 256.
+
 
 +
 
 +
====Step 3: Targeting====
 +
 
 +
To start targeting, open '''Targeting''' button in '''Workphase''' panel or '''Next''' button in the '''Calibration''' Page.
 +
 
 +
[[Image:Slicer3_ProstateNav_Targeting.png|thumb|center|400px|]]
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 +
By clicking '''Needle''' and '''Template''' check buttons, models of the needle and the template can be displayed in 3D viewer.
 +
 
 +
[[Image:Slicer3_ProstateNav_ShowNeedleAndTemplate.png|thumb|center|400px|]]
 +
 
 +
 
 +
For the needle placement planning, load a target volume from '''File->Add Volume...''' menu.
 +
 
 +
<center>
 +
{|
 +
|[[Image:Slicer3_ProstateNav_LoadTargetVolumeMenu.png|thumb|center|200px|]]
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|[[Image:Slicer3_ProstateNav_LoadTargetVolumeDialog.png|thumb|center|400px|]]
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|}
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</center>
 +
 
 +
To place a target point, simply click at the point on the axial image. Make sure '''Add Target by Image Click''' check box before you click the image.
 +
 
 +
[[Image:Slicer3_ProstateNav_Planning.png|thumb|center|400px|]]
  
−
== Usage ==
 
  
−
===Examples, Use Cases & Tutorials===
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To choose a template hole for needle insertion, choose a target point from the list and press '''Move''' button at the bottom of the module's user interface. The index of the hole shows up on the panel.
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The module is designed for NIH-funded Biomedical Research Partnership project: Enabling Technologies for MRI-Guided Prostate Interventions (NIH 1R01CA111288, PI: Clare Tempany, MD). The focus of this research project is to develop an MRI-guided robotic intervention technology. The detailed description of the system and clinical use-case scenario are described in the papers listed below in this page.
 
  
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===Quick Tour of Features and Use===
 
−
List all the panels in your interface, their features, what they mean, and how to use them. For instance:
 
  
−
* '''Input panel:'''
+
[[Image:Slicer3_ProstateNav_TargetSelection.png|thumb|center|400px|]]
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* '''Parameters panel:'''
 
−
* '''Output panel:'''
 
−
* '''Viewing panel:'''
 
  
 
== Development ==
 
== Development ==
  
 
===Dependencies===
 
===Dependencies===
−
[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]]
+
[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]]
  
 
===Known bugs===
 
===Known bugs===

Latest revision as of 14:59, 10 February 2011

Home < Modules:ProstateNav-Documentation-3.6

Return to Slicer 3.6 Documentation

Gallery of New Features

Module Name

ProstateNav

ProstateNav in clinical MRI-guided prostate biopsy.
ProstateNav for MRI-guided transrectal biospy

General Information

Module Type & Category

Type: Interactive
Category: IGT

Authors, Collaborators & Contact

  • Junichi Tokuda, BWH
  • Andras Lasso, Queen's University (New GUI interface)
  • Simon DiMaio, Intuitive Surgical Inc. (System design, Z-frame registration)
  • Gregory Fischer, WPI (System design, Robot Software)
  • David Gobbi (Wizard Interface)
  • Csaba Csoma, JHU (System design, Robot Software)
  • Haiying Liu, BWH (Software packaging)
  • Philip Mewes (Initial version)
  • Gabor Fitchinger, Queen's University
  • Nobuhiko Hata, BWH
  • Clare Tempany, BWH

Module Description

The ProstateNav module is designed to add an integrated user interface (UI) for MRI-guided prostate intervention (e.g. needle biopsy and brachytherapy) to 3D Slicer. Like all of Slicer it is not FDA approved and only intended for research. In version 3.6, the module provides user interfaces for the following devices:

  • MRI-compatible pneumatic needle placement robot for transperineal prostate biopsy and brachytherapy (Johns Hopkins University + Brigham and Women's Hospital + Queen's Univeristy)
  • MRI-compatible transrectal needle biopsy device (Queen's University + Johns Hopkins University)
  • Template-based needle guiding system for MRI-guided prostate biopsy and brachy therapy (Queen's University + Brigham and Women's Hospital)

The module has wizard-style interface, which helps an operator follow the clinical procedure step by step. It supports target planning and management, patient-device registration, and verification. The module can also communicate with some of the devices listed above using OpenIGTLink protocol.

Usage

Tutorials

The ProstateNav switches its user interface based on the device type selected by the user. This section describes step-by-step instruction.

Template-based needle guiding system for MRI-guided prostate biopsy and brachy therapy

Step 1: Create a manager node and select a device type

First, create a manager node by choosing Create New ProstateNavManager from a node selector menu in Active configuration. Then click Create New TransperinealProstateTemplate from Robot node selector.

Slicer3 ProstateNav SelectManager.png
Slicer3 ProstateNav SelectDevice.png


Step 2: Calibration

Press Cliabration button in the workphase tab to open 2/4 Calibration page.

Slicer3 ProstateNav OpenCalibration.png

First, we load a multi-slice Z-frame image to register the device coordinate system to the image coordinate system. Choose "File->Add Volume..." menu to open the file selection dialog box.

Slicer3 ProstateNav LoadZFrameImage.png

To display a model of Z-frame fiducial frame in the 3D viewer, click Show Z-frame check box.

Slicer3 ProstateNav ShowZFrameModel.png

Before run automatic Z-frame registration, scroll the all slices in the multi-slice Z-frame image to identify the range of slices that show clear Z-frame images. If you want to adjust the slice range, input the start and end slice index in the text box.

Slicer3 ProstateNav CheckZFrameSliceRange.png

To start automatic Z-frame registration, press Perform Calibration button. It takes a few seconds or more depending on the environment and number of slices. Once the Z-frame is registered to the image coordinate system, the z-frame model is overlaid to the Z-frame image in the 3D view.

Slicer3 ProstateNav ZFrameRegistration.png


Step 3: Targeting

To start targeting, open Targeting button in Workphase panel or Next button in the Calibration Page.

Slicer3 ProstateNav Targeting.png

By clicking Needle and Template check buttons, models of the needle and the template can be displayed in 3D viewer.

Slicer3 ProstateNav ShowNeedleAndTemplate.png


For the needle placement planning, load a target volume from File->Add Volume... menu.

Slicer3 ProstateNav LoadTargetVolumeMenu.png
Slicer3 ProstateNav LoadTargetVolumeDialog.png

To place a target point, simply click at the point on the axial image. Make sure Add Target by Image Click check box before you click the image.

Slicer3 ProstateNav Planning.png


To choose a template hole for needle insertion, choose a target point from the list and press Move button at the bottom of the module's user interface. The index of the hole shows up on the panel.


Slicer3 ProstateNav TargetSelection.png

Development

Dependencies

OpenIGTLinkIF Module

Known bugs

Follow this link to the Slicer3 bug tracker.


Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.


Source code & documentation

See ViweCV page for the source code.

Links to documentation generated by doxygen.

More Information

Acknowledgment

This work is supported by 1R01CA111288, 5U41RR019703, 5P01CA067165, 1R01CA124377, 5P41RR013218, 5U54EB005149, 5R01CA109246 from NIH. This study was also in part supported by NSF 9731748, CIMIT, Intelligent Surgical Instruments Project of METI (Japan).

References

  • Fischer GS, Iordachita I, Csoma C, Tokuda J, DiMaio SP, Tempany CM, Hata N and Fichtinger G. MRI-Compatible Pneumatic Robot for Transperineal Prostate Needle Placement. IEEE/ASME Trans Mechatronics 2008; 13(3):295-305 [1]
  • Tokuda J, Fischer GS, Csoma C, DiMaio SP, Gobbi DG, Fichtinger G, Tempany CM, Hata N. Software Strategy for Robotic Transperineal Prostate Therapy in Closed-Bore MRI. In: Proc. 11th International Conference on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2008; 9/6/2008-9/10/2008; New York, NY ;2008. p. 701-709. [2]
  • DiMaio S, Samset E, Fischer G, Iordachita I, Fichtinger G, Jolesz F, Tempany C. Dynamic MRI Scan Plane Control for Passive Tracking of Instruments and Devices. Int Conf Med Image Comput Comput Assist Interv. 2007;10(Pt 2):50-58. [3]
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