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Queens Roadmap Project (Transrectal MRI-guided robotic prostate biopsy)

The transrectal prostate robot visualization inside SLICER.


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.


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.
Transrectal prostate intervention robot assembled.


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:

  • 2007-10: Application Workflow Development (Define the workflow for the application; create GUI templates for Calibration step - David, Csaba, Gabor)
  • 2007-12: Device Modeling & Data Display (Conversion of engineering data into VTK-viewable objects, provide display logic for targets and prostate outlines - David)
  • 2008-07: Measurement Tools: Semi-automatic identification of fiducials via thresholding & centroids, logic for robot registration with fiducials, calculations for robot trajectory based on target position - Csaba)
  • 2008-11: Robot positioning & Application Workflow Development (GUI targeting readouts for optical encoders; Wizard GUI for Targeting and Verification step - David, Siddharth)
  • 2009-03: Measurement Tools & Biopsy Planning/Targeting (Integration of prostate segmentation developed at Georgia Tech by Yi, Tennanbaum during the NAMIC project week in Utah; integration of semi-automatic identification of fiducials in the SLICER module; finding targeting parameters of robot for particular target; Targets' list implemented as fiducials lists for visualization of targets in 2d and 3D viewers - Siddharth, Yi)
  • 2009-05: Application Workflow Development (On selecting target from the list, bring target to view in all viewers, Needle trajectory visualization; Verification step GUI and functionality, Save experiment functionality; planning window display (on secondary monitor), 3D display of robot manipulator and segmented calibration markers (using VR) - Siddharth, Andras)
  • 2009-10: Prostate segmentation module development & Coverage area display & Multiple devices support (create a separate, standalone module for prostate segmentation (ProstateSeg) from the existing algorithm code, design proposal for supporting multiple robotic devices - transrectal and transperineal; Implement robot coverage area display - Andras, Yi)
  • 2010-03: Multiple devices support & fixes (implementation of multiple device support for transrectal (APT-MRI) and transperineal (BRP) device and transrectal template; Test and fix robot calibration method; multiple fixes and enhancements in the 3D Slicer core - Andras, Junichi)
  • 2010-06: Fixes of ProstateNav module; Packaging of ProstateSeg module (fix usability and other potential problems in ProstateNav in the Slicer3-3.6 branch; package prosate segmentation module as an extension module for Slicer3-3.6)


  • Prostate biopsy module with multiple device support:
    • Latest stable version is available in Slicer3-3.6
    • Latest development version source code is available in SVN
  • ProstateSeg module source code is available in SVN



Screenshots of the Slicer-based software

Targets, targeting parameters and robot coverage area display
3D view and targeting parameters display on a secondary (procedure room) monitor
Target verification, slicer reformatted to be aligned with the planned needle trajectory
Visualization of patient motion between targeting and verification image
Calibrate and register robot markers
Prostate segmentation

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; Junichi Tokuda, Brigham and Women's Hospital; Csaba Csoma, Johns Hopkins University
  • 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


  • Gao, Y., Sandhu, R., Fichtinger, G., Tannenbaum, A. “A coupled global registration and segmentation framework with application to magnetic resonance prostate imagery,” IEEE Transactions on Medical Imaging, vol. 29, no. 10, pp. 1781–1795, 2010.
  • 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.S., Krieger A., Iordachita I., Csoma C., Whitcomb L., Fichtinger G. MRI Compatibility of Robot Actuation Techniques - A Comparative Study. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 2):509-517.
  • Gill S., Abolmaesumi P., Vikal S., Mousavi P., Fichtinger G. Intraoperative Prostate Tracking with Slice-to-Volume Registration in MRI. Proceedings of the 20th International Conference of the Society for Medical Innovation and Technology 2008; 154-158.
  • 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., Tokuda J., DiMaio S.P., Fischer G., Csoma C., Gobbi D., Tempany C.M., Fichtinger G., Hata N. Integrated System for Robot-Assisted in Prostate Biopsy in Closed MRI Scanner. Proceedings of the IEEE International Conference on Robotics and Automation 2008; 2959-2962.
  • 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., Fischer G.S., Csoma C., DiMaio S.P., Gobbi D.G., Fichtinger G., Tempany C.M., Hata N. Software Strategy for Robotic Transperineal Prostate Therapy in Closed-Bore MRI. Int Conf Med Image Comput Comput Assist Interv. 2008;11(Pt 2):701-709.
  • 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., Menard C., Krieger A., Coleman J., Camphausen K., Choyke P., Fichtinger G., Whitcomb L., Coleman N., Atalar E., Transrectal prostate biopsy and fiducial marker placement in a standard 1.5T magnetic resonance imaging scanner. J Urol. 2006 Jan;175(1):113-20.
  • 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 2005;52(2):306–313.