Abstract
Purpose
This paper presents CardIAc, an open-source application designed as an alternative to commercial software for left ventricle myocardial strain quantification in short-axis cardiac magnetic resonance images. The aim is to provide a useful extension for myocardial strain analysis that can be easily adapted to incorporate different strategies of motion tracking to improve the strain accuracy. In this way, users with programming skills can easily modify the code and adjust the program’s performance according to their own scientific or clinical requirements. The software is intended for research and clinical use is not advised.
Methods
CardIAc was developed as a 3D Slicer extension for an easy installation and usability. The main contribution of this article is to provide a general workflow, going from data and segmentation loading, 3D heart modeling, analysis and several options for visualization of the myocardial strain.
Results
CardIAc strain feature was evaluated on a public dataset (Cardiac Motion Analysis Challenge—STACOM 2011) of 15 volunteers, and a synthetic one generated from this real dataset. Results on the real dataset show that cardIAc achieves suitable accuracy for myocardial motion estimation with a median error of 3.66 mm. In particular, global strain curves show strong correlation with the bibliography for healthy patients and similar approaches. On the other hand, results on the synthetic dataset show a mean global error of 4.07%, 7.76% and 8.18% for circumferential, radial and longitudinal strain.
Conclusion
This paper introduces a new open-source application for strain analysis distributed under a BSD-style open-source license. Results demonstrate the capability and merits of the proposed application for strain analysis.
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Code availability
The code is distributed by contacting the corresponding author; however, in next versions it will be included in the 3D Slicer extension manager for an even more easy installation and distribution. The code is distributed under a BSD-style open-source license.
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Acknowledgements
This work was partially supported by Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Comisión Nacional de Energía Atómica (CNEA). German Mato acknowledges CONICET for the Grant PIP 112 201301 00256.
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Appendix A
Appendix A
Load Volumes button opens up a dialog that allows the user to select the MR-C volume files of the sequence. Then, it prompts a text input popup where the user must choose a name for the sequence. Load Segmentation button is used to load the myocardial segmentation. Furthermore, if a single file is loaded, the software recognizes it as an ED segmentation or at least close to ED, the extension will not work properly if the segmentation is close to ES. Whereas if the numbers of files selected is equal to the number of volumes in the sequence, it recognizes it as a tracking sequence. Save segmentation button saves the current segmentation files of the sequence to the disk drive. Load deformation button lets the user load a previously calculated displacement field. Save deformation button lets the user choose a directory where the displacement field will be saved. Save Strain button saves a NumPy array of shape (d, t, 17) where d represents the dimension of the registration method, i.e., 2 if 3D Tracking is unchecked or 3 otherwise (see Fig. 1a), t represents the total time intervals over the cardiac cycle, and 17 is the number of segments proposed in the AHA model. Load strain button lets the user choose a NumPy array file from the disk drive to input as strain. Save AHA button lets the user save the AHA regions and the local coordinate systems to a directory. Load AHA button lets the user choose a directory to find AHA regions and local coordinate systems to load into the workflow.
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Curiale, A.H., Bernardo, A., Cárdenas, R. et al. CardIAc: an open-source application for myocardial strain analysis. Int J CARS 16, 65–79 (2021). https://doi.org/10.1007/s11548-020-02291-z
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DOI: https://doi.org/10.1007/s11548-020-02291-z