DBP2:Queens:Roadmap

Back to NA-MIC Internal Collaborations, JHU DBP 2

Johns Hopkins Roadmap Project (Transrectal MRI-guided robotic prostate biopsy)

The transrectal prostate robot visualization inside SLICER.

Objective

We would like to create an end-to-end application within the NA-MIC Kit to enable an existing transrectal prostate biopsy device to perform multi-parametric MRI guided prostate biopsy in closed-bore high-field MRI magnets.

This page describes the technology roadmap for robotic prostate biopsy in the NA-MIC Kit. The basic components necessary for this application are:

• Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work for both supine and prone patients, all imaged with an endorectal coil (ERC).
• Registration: co-registration of MRI datasets taken at different times, in different body positions, and under different imaging parameters
• Prostate Measurement: Measure volume of all segmented structures
• Biopsy Device Parameters: Geometry, kinematics, and calibration/registration of the robot system must be available in some form. This capability is not currently part of the NA-MIC kit. The application will be modular, to enable use of different devices.
• Tutorial: Documentation will be written for a tutorial and sample data sets will be provided to perform simulated biopsies.

Roadmap

The primary goal for the roadmap is to develop an interventional module for Slicer3 for MRI-guided prostate biopsies. This module and the accompanying tutorial will serve as a template for interventional applications with Slicer3. The module will provide the necessary functionality for calibrating the robot to the MR scanner, planning biopsies, computing the necessary robot trajectory to perform each biopsy, and verification via post-biopsy images. We will obtain a biopsy plan from multi-parametric endorectal image volumes, executable with an existing prostate biopsy device. The system will be will be implemented under Slicer3 as an interactive application.

Prostate intervention (biopsy) in closed MR scanner.

Close-up of the transrectal procedure

Transrectal prostate intervention robot assembled.

Workflow

• 1. Calibrate and register robot: Acquire a calibration volume, calibrate/register robotic device to MR coordinate system

Calibrate and register robot markers

Close-up of 3D view

• 2. Segment prostate: Acquire the target planning volume, segment prostate if necessary
  

  Prostate segmentation
• 3. Pick biopsy targets, perform biopsy: Pick targets, and perform biopsy

Biopsy targets picked

Close-up of 3D view

Target selected, and needle trajectory visualized

Close-up of 3D view

Use reformat widget to slice in arbitrary plane

Slice reformated

• 4. Validate target: Acquire validation volume, while needle still in and then provide needle axis to perform validation

Schedule

Data Collection: Done. Initial data available, hand segmented for ground truth.

Segmentation: We plan to use shape-based segmentation methods for the MRI prostate data. Several parts of the procedure have already been implemented with NA-MIC tools such as the conformal flattening procedure. Spherical wavelets for shape analysis are already available in ITK. Despeckling techniques will be used to enhance ultrasound imagery as a pre-processing step for segmentation of the prostate data.

System Implementation: Apart from the one research element (segmentation), the rest of the project is a massive software engineering effort, and will follow these major milestones and schedule:

• 10/15/2007: Application Workflow Development: Define the workflow for the application (David, Csaba, Gabor)

• 10/22/2007: Application Workflow Development: Create GUI templates for the workflow steps only till Calibration step (David)

• 12/15/2007: Device Modeling: Conversion of engineering data into VTK-viewable objects (David)

• 12/15/2007: Data Display: Provide display logic for targets and prostate outlines (David)

• 07/01/2008: Measurement Tools: Semi-automatic identification of fiducials via thresholding & centroids still not integrated inside SLICER (Csaba)

• 07/01/2008: Measurement Tools: Logic for robot registration with fiducials still not integrated inside SLICER (Csaba)

• 07/01/2008: Biopsy Planning/Targeting: Calculations for robot trajectory based on target position still not integrated inside SLICER (Csaba)

• 09/19/2008: Robot positioning: GUI targeting readouts for optical encoders (David, Siddharth)

• 11/10/2008: Robot positioning: Integrate optical encoders with our Slicer module (Siddharth)

• 11/20/2008: Application Workflow Development: Wizard GUI created for Targeting step, and Verification step (Siddharth)

• 11/20/2008: Software architecture compliance of module: Model View Controller pattern reflected in corresponding MRML, GUI, Logic (Siddharth)

• 11/26/2008: Measurement Tools: Integration of semi-automatic identification of fiducials in the SLICER module (Siddharth)

• 01/09/2009: Measurement Tools: Integration of prostate segmentation developed at Georgia Tech by Yi, Tennanbaum during the NAMIC project week in Utah (Siddharth, Yi): prostate segmentation AHM2009

• 02/02/2009: Measurement tools: Integration of Logic for robot marker registration based on segmentation in the SLICER module (Siddharth)

• 02/20/2009: Biopsy Planning/Targeting: Intergrated finding targeting parameters of robot for particular target (Siddharth)

• 03/10/2009: Biopsy Planning/Targeting: Ability to have multiple needles list, with each needle having multiple targets (Siddharth)

• 03/10/2009: Biopsy Planning/Targeting: Targets' list also implemented as fiducials lists for visualization of targets in 2d and 3D viewers (Siddharth)

• 03/20/2009: Software architecture compliance of module: MRML node updated to have all system state parameters ( volume nodes, fiducial lists (targets and markers), targeting parameters for each descriptor..) (Siddharth)

• 04/05/2009: Biopsy Planning/Targeting: On selecting target from the list, bring target to view in all viewers (Siddharth)

• 04/10/2009: Biopsy Planning/Targeting: Needle trajectory visualization (Siddharth)

• 04/15/2009: Application Workflow Development: Verification step GUI and functionality implemented (Siddharth)

• 04/23/2009: Application Workflow Development: Save experiment functionality implemented (Siddharth)

• 05/29/2009: Application Workflow Development: Planning window display (on secondary monitor) implemented (Andras)

• 05/29/2009: Application Workflow Development: 3D display of robot manipulator (with only a simple cylinder model), segmented calibration markers (using VR) implemented (Andras)

• 05/29/2009: Application Workflow Development: Targeting parameter display on planning window implemented (Andras)

• 06/12/2009: Prostate segmentation module development: Created a separate, standalone module for prostate segmentation (ProstateSeg) from the existing algorithm code, which was integrated into the TRProstateBiopsy module (Andras, Yi)

• 06/12/2009: Prostate segmentation module development: Created a separate, standalone module for prostate segmentation (ProstateSeg) from the existing algorithm code, which was integrated into the TRProstateBiopsy module (Andras, Yi)

• 07/15/2009: Multiple devices support: Design proposal created for supporting multiple robotic devices - transrectal and transperineal (Andras)

• 08/15/2009: Coverage area: Implemented robot coverage area display (Andras)

• 10/02/2009: Multiple devices support: Implemented first phase of multiple device support (Andras)

• 11/15/2009: Multiple devices support: Complete implementation of multiple device support

Software

• TRProstateBiopsy module - access online
• Prostate biopsy module with multiple device support - access online
• ProstateSeg module - access online

Tutorial

• Trans-rectal prosate biopsy module: TransRectalProstateBiopsyTutorial
• Trans-rectal prostate biopsy tutorial dataset: TransRectalProstateBiopsyTutorialDataset.zip‎

Publications

• Lasso, A., J. Tokuda, S. Vikal, C. M. Tempany, N. Hata, and G. Fichtinger, "A generic computer assisted intervention plug-in module for 3D Slicer with multiple device support", Medical Image Computing and Computer-Assisted Intervention (MICCAI), London, UK, 2009
• Vikal, S., S. Haker, C. Tempany, and G. Fichtinger, "Prostate contouring in MRI guided biopsy", SPIE Medical Imaging, vol. 7259, 2009.
• Boisvert, J., D. Gobbi, S. Vikal, R. Rohling, G. Fichtinger, and P. Abolmaesumi, "An open-source solution for interactive acquisition, processing and transfer of interventional ultrasound images", Workshop on Systems and Architectures for Computer Assisted Interventions, held in conjunction with the 11th International Conference on Medical Image Computing and Computer Assisted Intervention , 2008.
• Fischer, G., A. Krieger, I. Iordachita, L. Whitcomb, and G. Fichtinger, "MRI Compatibility of Robot Actuation Techniques - A Comparative Study", Medical Image Computing and Computer-Assisted Intervention (MICCAI) Proceedings in Lecture Notes in Computer Science, vol. 5242, pp. 509-517, 2008.
• Gill, S., P. Abolmaesumi, S. Vikal, P. Mousavi, and G. Fichtinger, "Intraoperative Prostate Tracking with Slice-to-Volume Registration in MRI", 20th International Conference of the Society for Medical Innovation and Technology: Society for Medical Innovation and Technology SMIT, pp. 154-158, 08/2008.
• Krieger, A., P. Guion, C. Csoma, I. Iordachita, A. Singh, A. Kaushal, C. Menard, G. Fichtinger, and L. Whitcomb, "Design and Preliminary Clinical Studies of an MRI-Guided Transrectal Prostate Intervention System", International Society of Magnetic Resonance in Medicine (ISMRM), 2008
• Mewes, P., J. Tokuda, S. DiMaio, G. Fischer, C. Csoma, D. Gobbi, C. Tempany, G. Fichtinger, and N. Hata, "Integrated system for robot-assisted in prostate biopsy in closed MRI scanner", Procedings IEEE International Conference on Robotics and Automation ICRA 2008, pp. 2959–2962, 19–23 May, 2008.
• Tokuda, J., S. DiMaio, G. Fischer, C. Csoma, D. Gobbi, G. Fichtinger, N. Hata, and C. Tempany, "Real-time MR Imaging Controlled by Transperineal Needle Placement Device for MRI-guided Prostate Biopsy", 16th Scientific Meeting and Exhibition of International Society of Magnetic Resonance in Medicine, 2008.
• Tokuda, J., G. Fischer, C. Csoma, S. DiMaio, D. Gobbi, G. Fichtinger, C. Tempany, and N. Hata, "Software strategy for robotic transperineal prostate therapy in closed-bore MRI", Medical image computing and computer-assisted intervention (MICCAI), vol. 11, no. Pt 2: Department of Radiology, Brigham, Women's Hospital, Harvard Medical School, 75 Francis St , Boston, MA 02115, USA tokuda@bwh harvard edu, pp. 701–709, 2008.
• Vikal, S., S. Haker, C. Tempany, and G. Fichtinger, "Prostate contouring in MRI guided biopsy", Workshop on Prostate image analysis and computer-assisted intervention, International Conference on Medical Image Computing and Computer Assisted Intervention , 2008.
• Susil, R., C. Menard, A. Krieger, J. Coleman, K. Camphausen, P. Choyke, G. Fichtinger, L. Whitcomb, N. Coleman, and E. Atalar, "Transrectal prostate biopsy and fiducial marker placement in a standard 1 5T magnetic resonance imaging scanner", The Journal of Urology, vol. 175, no. 1, pp. 113–120, Jan, 2006.
• Krieger, A., R. Susil, C. Menard, J. Coleman, G. Fichtinger, E. Atalar, and L. Whitcomb, "Design of a novel MRI compatible manipulator for image guided prostate interventions", IEEE Transactions on Biomedical Engineering, vol. 52, no. 2, pp. 306–313, Feb, 2005

Team and Institutes

• PI: Gabor Fichtinger, Queen’s University (gabor at cs.queensu.ca)
• Co-I: Purang Abolmaesumi, Queen’s University (purang at cs.queensu.ca)
• Software Engineer: Andras Lasso (lasso at cs.queensu.ca), Siddharth Vikal, David Gobbi, Queen’s University
• JHU Software Engineer Support: Csaba Csoma, Johns Hopkins University (csoma at jhu.edu)
• NA-MIC Engineering Contact: Katie Hayes, MSc, Brigham and Women's Hospital (hayes at bwh.harvard.edu)
• NA-MIC Algorithms Contact: Allen Tannenbaum, PhD, GeorgiaTech (tannenba at ece.gatech.edu)
• Host Institutes: Queen's University & Johns Hopkins University