Friedrich-Alexander-Universität
Friedrich-Alexander-Universität
Stanford Radiology

Heart Model

Conrad Cardiac Model v1.0

  • Overview

    We present an open-source 3D+t statistical shape model of the heart developed as numerical phantom for cone-beam CT simulation. The training set consists of surface meshes from 20 ten-phase-CT angiography data sets extracted using automatic registration-based segmentation. Incorporating 90% of the training set variation, the model exhibits a generalization ability of 5.00+/-0.93mm and specificity of 7.30+/-0.97mm. The model is implemented in CONRAD, an open-source simulation and reconstruction framework. We provide all algorithms and high resolution projection data.

    The model is integrated into our in-house open-source simulation and reconstruction framework Conrad, that can be obtained here: conrad.stanford.edu. The framework includes all methods used to generate the forward projections, including the 3D+t statistical shape model of the heart. Additionally, there are classes available that allow the user to export the meshes (vertices plus connectivity) in the legacy .vtk polydata format, that can then be read by e.g. VTK (Paraview) or ITK.

    To the best of our knowledge, this is the first open-source 3D+t statistical shape model of the heart.

    For questions please refer to: Opens external link in new windowhttps://www5.cs.fau.de/~unberath

    If you use any of the provided material please cite: 

     

    Unberath, MathiasMaier, Andreas; Fleischmann, Dominik; Hornegger, Joachim; Fahrig, Rebecca

    Proceedings of the ISBI (Biomedical Imaging, 2015 IEEE 12th International Symposium on), Brooklyn, NY, 16-19.4.2015, pp. 739-742, 2015

  • Surface rendering with cutplane

Projection imaging

Surface renderings and forward projections of the dynamic statistical shape model at representative phases throughout the cardiac cycle (end-diastole: right, end-systole: second from the left) with a contrasted left ventricle.

Variation

Shape changes induced by variation of the three largest Eigenmodes in descending order at end-diastole (left) and end-systole (right), respectively. The mean shape is shown in the middle row, the top and bottom row are obtained using minus (top row) and plus (bottom row) one half of the respective variance.

Projection data: Info

Sample projection data using the Conrad Cardiac Model v1.0 can be found below.

For use with CONRAD:
Use the .xml files provided below as configuration for the reconstruction. The geometry will automatically be set correctly. In order to guarantee correct alignment of ConradCardiacModel meshes and reconstruction, the meshes need to be rotated and translated according to the transformation given in the Transformation file (found below).

Else:
Download the .xml files. The projection matrices and detector setup (number of pixel, spacing, axis orientation) can be found in the file. Meshes of the cardiac model are included with CONRAD. When used, they must be transformed using the rigid transform described in the file in order to guarantee alignment of the meshes and a reconstruction.

 

To come:

- forward projections using real scanner geometry
- remaining predifined models 
- pathologic cases

Data for 4D SSM phantom

  • 4D SSM model filesIf you would like to use the 4D statistical shape model heart phantom, just download the archive and unpack all the files into your "CONRAD/data" directory.

Projection data and Configuration files for CONRAD

  • Conrad Configuration for 133 projectionsConrad Configuration .xml containing the geometry and detector for the short scan with 133 projections and 9 heart beats.
  • Conrad Configuration for 381 projectionsConrad Configuration .xml containing the geometry and detector for the long scan with 381 projections and 26 heart beats
  • File containing the rigid transformation Contains rotation and translation used to transform the cardiac model in world coordinates prior to forward projection.
  • Mean Heart Dataset, 52% Ejection fractionAcquisition with 133 projections at 00% phase (diastole, static) and with 9 heart beats (120bpm at 4.5s acquisition), and a long acquisition featuring 381 projections with 26 heart beats (120bpm, 13s). The corresponding configuration files can be found above.
  • Male, 56 years, 56% Ejection fractionAcquisition with 133 projections at 00% phase (diastole, static) and a long acquisition featuring 381 projections with 26 heart beats (120bpm, 13s). The corresponding configuration files can be found above.
  • Female, 81 years, 62% Ejection fractionAcquisition with 133 projections at 00% phase (diastole, static) and a long acquisition featuring 381 projections with 26 heart beats (120bpm, 13s). The corresponding configuration files can be found above.