Published on May 2, 2008
A Dynamic Data Driven Grid System for Intra-operative Image Guided Neurosurgery: A Dynamic Data Driven Grid System for Intra-operative Image Guided Neurosurgery A Majumdar1, A Birnbaum1, D Choi1, A Trivedi2, S. K. Warfield3, K. Baldridge1, and Petr Krysl2 1 San Diego Supercomputer Center University of California San Diego 2 Structural Engineering Dept University of California San Diego 3 Computational Radiology Lab Brigham and Women’s Hospital Harvard Medical School Grants: NSF: ITR 0427183,0426558; NIH:P41 RR13218, P01 CA67165, LM0078651, I3 grant (IBM) TALK SECTIONS: TALK SECTIONS PROBLEM DESCRIPTION AND DDDAS GRID ARCHITECTURE ADVANCED BIOMECHANICAL MODEL PARALLEL AND END-to-END TIMING SUMMARY 1. PROBLEM DESCRIPTION AND DDDAS: 1. PROBLEM DESCRIPTION AND DDDAS Neurosurgery Challenge: Neurosurgery Challenge Challenges : Remove as much tumor tissue as possible Minimize the removal of healthy tissue Avoid the disruption of critical anatomical structures Know when to stop the resection process Compounded by the intra-operative brain shape deformation that happens as a result of the surgical process – preoperative plan diminishes Important to be able to quantify and correct for these deformations while surgery is in progress by dynamically updating pre-operative images in a way that allows surgeons to react to these changing conditions The simulation pipeline must meet the real-time constraints of neurosurgery – provide images approx. once/hour within few minutes during surgery lasting 6 to 8 hours Intraoperative MRI Scanner at BWH: Intraoperative MRI Scanner at BWH Brain Shape Deformation: Brain Shape Deformation Before surgery After surgery Overall Process: Overall Process Before image guided neurosurgery During image guided neurosurgery Timing During Surgery: Timing During Surgery Time (min) Before surgery During surgery 0 10 20 30 40 Preop segmentation Intraop MRI Segmentation Registration Surface displacement Biomechanical simulation Visualization Surgical progress Current Prototype DDDAS Inside Hospital: Current Prototype DDDAS Inside Hospital Current Prototype DDDAS System: Current Prototype DDDAS System Receives 3-D MRI from operating room once/hour or so Uses displacement of known surface points as BC to solve a crude linear elastic biomechanical FEM material model on compute system located at BWH This crude inaccurate model is solvable within the time constraint of few minutes once an hour on local computers at BWH Dynamically updates pre-op images with biomechanical volumetric simulation based intra-op images Time critical updates shown to surgeons for intra-op surgical navigation Two Research Aspects: Two Research Aspects Grid Architecture – grid scheduling, on demand remote access to multi-teraflop machines, data transfer Data transfer from BWH to SDSC, solution of detail advanced biomechanical model, transfer of results back to BWH for visualization need to be performed in a few minutes Development of detailed advanced non-linear scalable viscoelastic biomechanical model To capture detail intraoperative brain deformation Example of visualization: Intra-op Brain Tumor with Pre-op fMRI: Example of visualization: Intra-op Brain Tumor with Pre-op fMRI 2. GRID ARCHITECTURE: 2. GRID ARCHITECTURE Queue Delay Experiment on TeraGrid Cluster: Queue Delay Experiment on TeraGrid Cluster TeraGrid is a NSF funded grid infrastructure across multiple research and academic sites Queue delays at SDSC and NCSA TG were measured over 3 days for 5 mins wall clock time on 2 to 64 CPUs Single job submitted at a time If job didn’t start within 10 mins, job terminated, next one processed What is the likelihood of job running 313 jobs to NCSA TG cluster and 332 to SDSC TG cluster – 50 to 56 jobs of each size on each cluster % of submitted tasks that run, as a fn of CPUs requested: % of submitted tasks that run, as a fn of CPUs requested Average queue delay for tasks that began running within10 mins: Average queue delay for tasks that began running within10 mins Queue Delay Test Conclusion: Queue Delay Test Conclusion There appears to be a direct relationship between the size of request and the length of the queue delay Two clusters exhibit different performance profiles This behavior of queue systems clearly merits further study More rigorous statistical characterization ongoig on much larger data sets Data Transfer: Data Transfer We are investigating grid based data transfer mechanisms such as globus-url-copy, SRB All hospitals have firewalls for security and patient data privacy – single port of entry to internal machines Transfer time in seconds for 20 MB file 3. ADVANCED BIOMECHANICAL MODEL: 3. ADVANCED BIOMECHANICAL MODEL Mesh Model with Brain Segmentation: Mesh Model with Brain Segmentation Current and New Biomechanical Model: Current and New Biomechanical Model Current linear elastic material model – RTBM Advanced model under development - FAMULS Advanced model is based on conforming adaptive refinement method – FAMULS package (AMR) Inspired by the theory of wavelets this refinement produces globally compatible meshes by construction First task is to replicate the linear elastic result produced by the RTBM code using FAMULS FEM Mesh : FAMULS & RTBM: FEM Mesh : FAMULS & RTBM RTBM (Uniform) FAMULS (AMR) Deformation Simulation After Cut: Deformation Simulation After Cut No – AMR FAMULS 3 level AMR FAMULS RTBM Advanced Biomechanical Model: Advanced Biomechanical Model The current solver is based on small strain isotropic elastic principle The new biomechanical model will be inhomogeneous scalable non-linear viscoelastic model with AMR We also want to increase resolution close to the level of MRI voxels i.e. millions of FEM meshes Since this complex model still has to meet the real time constraint of neurosurgery it requires fast access to remote multi-tflop systems 4. PARALLEL AND END-to-END TIMING : 4. PARALLEL AND END-to-END TIMING Parallel Registration Performance: Parallel Registration Performance Parallel Rendering Performance: Parallel Rendering Performance Parallel RTBM Performance: Parallel RTBM Performance (43584 meshes, 214035 tetrahedral elements) - 10.00 20.00 30.00 40.00 50.00 60.00 1 2 4 8 16 32 # of CPUs Elapsed Time (sec) IBM Power3 IA64 TeraGrid IBM Power4 End to End (BWH SDSCBWH) Timing : End to End (BWH SDSCBWH) Timing RTBM – not during surgery Rendering - during Surgery Slide30: End-to-end Timing of RTBM Timing of transferring ~20 MB files from BWH to SDSC, running simulations on 16 nodes (32 procs), transferring files back to BWH = 9* + (60** + 7***) + 50* = 124 sec. This shows that the grid infrastructure can provide biomechanical brain deformation simulation solutions (using the linear elastic model) to surgery rooms at BWH within ~ 2 mins using TG machines This satisfies the tight time constraint set by the neurosurgeons End-to-end Timing of Rendering : End-to-end Timing of Rendering MRI data from BWH was transferred to SDSC during a surgery Parallel rendering was performed at SDSC Rendered viz was sent back to BWH (but not shown to surgeons) Total time (for two sets of data) in sec = 2*53 (BWH to SDSC) + 2* 7.4 (render on 32 procs) + 0.2 (overlapping viz) + 13.7 (SDSC to BWH) = 148.4 sec 5. SUMMARY: 5. SUMMARY Ongoing and Future DDDAS Research: Ongoing and Future DDDAS Research Continuing research and development in grid architecture, on demand computing, data transfer Continuing development of advanced biomechanical model and parallel algorithm Moving towards near-continuous DDDAS instead of once an hour or so 3-D MRI based DDDAS Scanner at BWH can provide one 2-D slice every 3 sec or three orthogonal 2-D slices every 6 sec Near-continuous DDDAS architecture Requires major research, development and implementation work in the biomechanical application domain Requires research in the closed loop system of dynamic image driven continuous biomechanical simulation and 3-D volumetric FEM results based surgical navigation and steering
A Dynamic Data Driven Grid System for Intra-operative Image Guided Neurosurgery A Majumdar1, A Birnbaum1, ... majumdar_iccs05. Author: UCSD Physics.
Publications. Reports and Papers; ... Amit Majumdar, Phillip Papadopoulos, Wayne Pfeiffer, Robert S. Sinkovits ... APGAC05 as part of ICCS05, ...