DBP2:Queens:Roadmap

Back to NA-MIC Internal Collaborations, JHU DBP 2

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

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.

Current Status of System Components

• Segmentation: Semi-automatic segmentation has been implemented by Fichtinger et al. Statistical atlas based segmentation has been prototyped by Tannenbaum et al. Pose-independent segmentation (workable in both supine/prone) is being implemented.
• Registration: contour based registration has been prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
• Prostate Measurement: Prototyped by Fichtinger et al., needs to be re-implemented with native NA-MIC tools.
• Device Modeling: Prototyped by Fichtinger et al, needs to be re-implemented with native NA-MIC tools.
• Biopsy Planning: Clinically functional, needs to be implemented with native NA-MIC tools
• Tutorial: Not yet started. It will be derived from the actual clinically-functional system, with demo data.

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:

Application Workflow Development:

10/15/2007 Define the workflow for the application (David, Gabor, Purang)

10/22/2007 Create GUI templates for the workflow steps (David)

Device Modeling:

11/15/2007 Conversion of engineering data into VTK-viewable objects (David, Gabor)

11/15/2007 Create GUI controls for positioning the virtual device (David)

Data Display:

12/01/2007 Provide display logic for seeds and prostate outlines (David)

Measurement Tools:

01/15/2008 Semi-automatic identification of fiducials via region growing & centroids (new tool) (Siddharth, David)

02/15/2008 Logic for robot registration with fiducials (Siddharth, David)

03/01/2008 Prostate measurement tools (use existing NA-MIC tools) (David, Siddharth)

Biopsy Planning:

03/15/2008 Implement planning tools (display, logic) in Slicer3 (Siddharth, David)

04/01/2008 Verification against pre-existing software and data (Siddharth)

Integration of contour-based prostate registration into Slicer3:

06/01/2008 Create ITK implementation (Siddharth, David, Purang, Gabor)

06/15/2008 Create Slicer3 module, incorporate into workflow (Siddharth)

Integration of prostate segmentation into Slicer3 Siddharth, David)

08/01/2008 Integrate MRI segmentation tools (Siddharth, David, Allen)

08/15/2008 Integrate US segmentation tools (Siddharth, David, Allen)

Verification and testing of integrated system

09/01/2008 Workflow validation (Siddharth, David, Gabor, Purang)

11/15/2008 Complete testing, performance characterization (Siddharth, David)

Tutorial and Documentation

Continuous unit documentation (Siddharth, David)

12/15/2008 Complete tutorial with example data

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 Lead: David Gobbi, Queen’s University (dgobbi at cs.queensu.ca
• Software Engineer Support: Siddharth Vikal, Queen’s University (siddharthvikal at yahoo.com)
• 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