1. Image segmentation and morphological analysis
An efficient pipeline from medical images to numerical simulations
Tiziano Passerini, PhD
Department of Mathematics and Computer Science
Emory University
mathcs.emory.edu/~tiziano
Image segmentation and morphological analysis
Left: Magnetic Resonance Angiography of the infrarenal aorta of a healthy male subject; reconstruction of the vessel lumen by means of a level set-based segmentation.
Right: Centerline-based calculation of the angles between the aorta and iliac arteries at the bifurcation point.
Characterize the geometry of vascular structures.
Software: VMTK (
Ongoing project: classify subject-specific morphologies of the infrarenal aorta; relevance of local morphology to the measured flow patterns.
Partners: M.Piccinelli, Dr. J.Oshinski (Emory Radiology); Dr. A. Veneziani (Emory Math&CS); A.Smolensky, Dr. W.R. Taylor (Emory Cardiology).
Aorta-R Iliac
145.5º
Aorta-L Iliac
150º
R Iliac-L Iliac
64.5º
Cost of the computing
resource (in $)
Total runtime (in hours)
Computer simulations
High performance and cloud computing: evaluating the cost-effectiveness of on-demand computing facilities.
Software: LifeV (
Publications:
Slawinski, Passerini, Villa, Veneziani, Sunderam, “Experiences with target-Platform Heterogeneity in Clouds, Grids, and On Premise Resources”, Proc. IPDPS-HCW 2012.
Passerini, Slawinski, Villa, Veneziani, Sunderam, “Experiences with a computational fluid dynamics code on clouds, grids, and on-premise resources”, submitted, JPDC 2012.
Partners:
J.Slawinski, U.Villa, Dr. A.Veneziani,
Dr. V.Sunderam (Emory Math&CS)
Cost vs time of a benchmark CFD simulation on different computing platforms. Puma, Ellipse and Lonestar (traditional computing clusters); EC2 and Rockhopper (on-demand HPC cloud-computing facilities). For each platform we report the number of computing cores yielding the fastest computation. T* is the average computing time across platforms. On demand facilities can be extremely cost-efficient.
Image segmentation
and morphological analysis
Patient data
(medical images, diagnostics…)
Mathematical models & analysis
Computer simulations
Database
Numerical methods
Data mining
knowledge extraction
Hypothesis
Data mining and knowledge extraction
Statistical identification and classification of morphological & fluid-dynamics features
of the arterial system.
Publications:
Passerini, Sangalli, Vantini, Piccinelli, Bacigaluppi, Antiga, Boccardi, Secchi, Veneziani, “An Integrated Statistical Investigation of Internal Carotid Arteries of Patients affected by Cerebral Aneurysms”, CVET, 2012.
Partners:
Dr. S.Vantini, Dr. L.Sangalli, P.Secchi (Politecnico di Milano); M.Piccinelli (Emory Radiology); Dr. A.Veneziani (Emory Math&CS)
The three plots show the values of wall shear stress (WSS), radius (R) and curvature (C) computed in the internal carotid artery of 52 patients, as functions of the spatial location along the artery (s). The features of the curves are statistically associated to the presence, position and rupture status of cerebral aneurysms in the brain.
WSS R C s
(m/s)
Numerical methods
Flow in a cylindrical nozzle with conical collector and sudden expansion. Reynolds number in the throat: 3500.
Direct numerical simulation with second order tetrahedral finite elements. Mesh refinement based on the nozzle diameter.
Verification and validation of the
CFD methodology.
Ongoing project: FDA’s benchmark
(Computational Round Robin #1: Nozzle)
Partners: U.Villa, Dr. A.Veneziani (Emory Math&CS); Dr. A.Quaini, Dr. S.Canic (U Houston)
Mathematical models
Geometrical multiscale models for the
cardiovascular system;
Reduced models for the dynamics of
vascular networks.
Publications:
Alastruey, Passerini, Formaggia, Peiró, “Physical
determinants of the arterial pulse waveform:
theoretical analysis and calculation using the 1-D
formulation”, J Eng Math, 2012.
Passerini, De Luca, Formaggia, Quarteroni, Veneziani, “A 3D/1D geometrical multiscale model of cerebral vasculature”, J Eng Math, 2009.
Partners: Dr. P.Blanco (LNCC, Brazil), Dr. L.Grinberg (Brown University), M.Piccinelli (Emory Radiology), Dr. A.Veneziani (Emory Math&CS).
Pressure dynamics in the human physiological right arm, modeled by means of a 1D blood flow model. Numerical solver based on the LifeV library.
Geometry and model parameters courtesy of Dr. P. Blanco.
Database
Store, classify, query large and complex data sets.
Project:
AneuriskWeb (ecm2.mathcs.emory.edu/aneuriskweb),
a public, free repository of medical images, vascular geometries,
hemodynamics simulations. The database can be browsed or
queried based on geometric and hemodynamic features.
Partners: M.Piccinelli (Emory Radiology), Dr. L.Antiga (Orobix), Dr. A.Veneziani (Emory Math&CS)
Sample data from the database. Velocity streamlines in a giant aneurysm of the internal carotid artery.
In red: the aneurysm neck.
Acknowledgements:
Support from Emory School of Medicine (Dr. W.R.Taylor, Dr. H.Samady)
Support from Emory’s Strategic Initiative “Computational & Life Sciences”
Support from The Brain Aneurysm Foundation (PI: Dr. A.Veneziani)
Testing of hypotheses / Device design
Parametric study on the positioning of the cannula in left ventricular assist device (LVAD) patients, and its effects on blood features.
Partners: Dr. A.Veneziani (Emory Math&CS), M.Piccinelli (Emory Radiology); Dr. D.Gupta (Emory Cardiology)
Velocity streamlines at the systolic peak in baseline conditions and in two different simulated post-surgical scenarios. The flow distribution in the sovra-aortic branches and flow stagnation at the aortic valve are sensitive to the cannula placement.
Partners:
M.Piccinelli (Emory Radiology); M.Corban, Dr. H.Samady (Emory Cardiology); Dr. A.Veneziani (Emory Math&CS); Dr. L.Timmins, Dr. D.Giddens (Georgia Tech)
In patients with left coronary artery disease, arterial segments with endothelial dysfunction (ED) show significantly lower time average wall shear stress (TAWSS) with respect to those with normal endothelial function. A sign of ED is a reduced radius after acetylcholine injection.
Find fluid dynamics parameters that can be predictors of pathological events: study the wall shear stress as a marker of endothelial dysfunction in the coronary circulation.
Post treatment
Pre treatment
Radius (mm)
TAWSS
(dyn/cm2)
OSI (healthy,
simulated amputation
OSI (difference,
Amputation - Baseline
baseline
proximal
distal
Sensitivity analysis of blood flow patterns to local morphological features (angle between bifurcating arteries) and systemic conditions (increased peripheral resistances).
Partners: A.Smolensky, Dr. W.R.Taylor (Emory Cardiology); M.Piccinelli, Dr. J.Oshinski (Emory Radiology); Dr. A.Veneziani (Emory Math&CS)
Oscillatory shear index on the wall of the infrarenal aorta of a healthy subject in baseline conditions and after simulated left above knee amputation (inflation of a pressure cuff at the left thigh). OSI increases on the frontal and left sides of the distal arterial wall, suggesting a possible flow-induced localization of vascular diseases (e.g. aortic abdominal aneurysm).