placenta-flattening

version 1.0.0 (331 KB) by Mazy Abulnaga
An algorithm to parameterize volumetric shapes of the placenta represented as tetrahedral meshes to a flattened template.

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Updated 30 Jun 2022

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placenta-flattening

A MATLAB algorithm for volumetric mesh parameterization. Developed for mapping a placenta segmentation derived from an MRI image to a flattened template for visualization. The code can work on NIFTI images or MATLAB matrices containing imaging information.

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Requirements

Add the MATLAB packages to the working path.

Usage

main(grayImage, segImage): input a grayscale MRI image and the corresponding binary segmentation, where voxels labeled '1' correspond to the placenta. The inputs grayImage, segImage can either be full path locations of NIFTI image files, or image matrices. The grayImage input can be a 3D MRI volume, or a 4D series of MRI volumes. The script outputs the flattened meshes and images containing the mapped intensities.

Development

Please contact Mazdak Abulnaga, abulnaga@mit.edu.

Citing and Paper

If you use this method or some parts of the code, please consider citing one of our papers.

Our journal paper develops additional template models and provides extensions to improve robustness, an expanded evaluation on a significantly larger dataset, and experiments demonstrating utility for clinical research. eprint arXiV:2111.07900

@ARTICLE{abulnaga2022placenta,
  author={Abulnaga, S. Mazdak and Abaci Turk, Esra and Bessmeltsev, Mikhail and Grant, P. Ellen and Solomon, Justin and Golland, Polina},
  journal={IEEE Transactions on Medical Imaging}, 
  title={Volumetric Parameterization of the Placenta to a Flattened Template}, 
  year={2022},
  volume={41},
  number={4},
  pages={925-936},
  doi={10.1109/TMI.2021.3128743}}

The MICCAI conference paper develops the parallel planes template and validates on a smaller dataset. eprint arXiV:1903.05044

@inproceedings{abulnaga2019placenta,
title={Placental Flattening via Volumetric Parameterization},
author={Abulnaga, S. Mazdak and Abaci Turk, Esra and Bessmeltsev, Mikhail and Grant, P. Ellen and Solomon, Justin and Golland, Polina},
booktitle={Medical Image Computing and Computer Assisted Intervention -- MICCAI 2019},
year={2019},
pages={39--47},
}

Cite As

Abulnaga, S. Mazdak, et al. “Volumetric Parameterization of the Placenta to a Flattened Template.” IEEE Transactions on Medical Imaging, vol. 41, no. 4, Institute of Electrical and Electronics Engineers (IEEE), Apr. 2022, pp. 925–36, doi:10.1109/tmi.2021.3128743.

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MATLAB Release Compatibility
Created with R2022a
Compatible with R2016b to R2022a
Platform Compatibility
Windows macOS Linux

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To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.