Volumetric parameterization of the placenta to a flattened template

Last update: Mar 14, 2022

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Overview

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.

Requirements

MATLAB
GPU with CUDA compute capability
MATLAB Packages:
- iso2mesh: mesh generating toolbox
- geometry processing toolbox
- medical imaging MATLAB toolbox (only needed if working with NIFTI files)

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, [email protected].

Citing and Paper

Please consider citing our paper

@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},
}

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Comments

Is it possible to provide public input data?

Hello, I am a master student majoring in computer science. I am very interested in your work and hope to reproduce the results, but because there is no MRI scan data, I cannot successfully run the program to observe the effect. If you can provide the program input data, I will really appreciate.

opened by yuemos 3
4d

Now accepts 4D input grayscale images as input. Implemented by adding a loop when mapping the MRI images to the flattened space. I've tested with 4D nifti input, but not 4D image matrices.

opened by PaddySlator 0

Releases(v1.0.0)

v1.0.0(Jun 30, 2022)

IEEE TMI paper version release
Source code(tar.gz)
Source code(zip)

Volumetric parameterization of the placenta to a flattened template

Related tags

Overview

placenta-flattening

Requirements

Usage

Development

Citing and Paper

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Comments

Is it possible to provide public input data?

4d

Releases(v1.0.0)

v1.0.0(Jun 30, 2022)

Owner

Mazdak Abulnaga

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