CAWorks-pipeline-canine heart

From CVRG Wiki

Jump to: navigation, search


Canine Heart Atlas Generation Information

Canine Heart DTI/LDDMM Pipeline

  • Isotropic Preprocessing* - Transform the heart volumes to have the same resolution/spacing in three spatial directions.
  • Landmarker* - Software tool developed at JHU Center for Imaging Science that aligns volumes using sets of corresponding landmarks on the volumes.
  • LDDMM-volume* - Software tool developed at JHU Center for Imaging Science that computes a mapping from one volume to another using large deformation diffeomorphic metric mapping.
  • DTI Atlas* - DTI Volume that is an average of the processed DTI Population Data.

Data Set Description

The data for this pipeline was provided by Drs. Patrick A. Helm and Raimond L. Winslow at the Center for Cardiovascular Bioinformatics and Modeling and Dr. Elliot McVeigh at the National Institute of Health. The data set is eight normal canine hearts. There are two kinds of data: geometry/scalar data and diffusion tensor data. We use the template estimation method [1] developed at CIS to generate a geometry atlas based on geometry data. Then we use LDDMM to map the diffusion tensor data from the subject to the geometry atlas. Finally, the cardiac atlas will have both geometry and diffusion tensor data, which can be used to study shape variation in a population.

Image Acquisition Protocol

Each heart was placed in an acrylic container filled with Fomblin, a perfluoropolyether (Ausimon, Thorofare, NJ). Fomblin has a low dielectric effect and minimal MR signal thereby increasing contrast and eliminating unwanted susceptibility artifacts near the boundaries of the heart. The long axis of the hearts was aligned with the z-axis of the scanner. Images were acquired with a 4-element knee phased array coil on a 1.5 T GE CV/I MRI Scanner (GE, Medical System, Wausheka, WI) using an enhanced gradient system with 40 mT/m maximum gradient amplitude and a 150 T/m/s slew rate.


  1. J. Ma, M. I. Miller, A. Trouve, L. Younes, "Beyesian Template Estimation in Computational Anatomy", Neuroimage, Submitted Y. Cao, M.I. Miller, R.L. Winslow and L. Younes. "Large Deformation Diffeomorphic Metric Mapping of Vector Fields", IEEE Transactions on Medical Imaging, Vol. 24, No. 9, 1216-1230, 2005.
  2. Daniel C. Alexander, Carlo Pierpaoli, Peter J. Basser, James C. Gee. "Spatial Transformations of Diffusion Tensor Magnetic Resonance Images." IEEE Trans. Med. Imaging 20(11): 1131-1139, 2001.
  3. Vincent Arsigny, Pierre Fillard, Xavier Pennec, and Nicholas Ayache. "Log-Euclidean Metrics for Fast and Simple Calculus on Diffusion Tensors." Magnetic Resonance in Medicine, 56(2):411-421, August 2006.
  4. Mirza Faisal Beg, Patrick Helm, Elliot McVeigh, Raimond Winslow and Michael Miller. "Computational Cardiac Anatomy Using Magnetic Resonance Imaging." Magnetic Resonance in Medicine, Volume 52, Issue 5, pages 1176-1174, November 2004.
Personal tools
Project Infrastructures