MYKingma / AMR3D-NMRI

Accelerated high-resolution and motion-robust 3D volume reconstruction for neonatal MRI

AMR3D-NMRI

Accelerated high-resolution and motion-robust 3D volume reconstruction for neonatal MRI

This repository contains the code used in the thesis project of Maurice Kingma, titled "Accelerated high-resolution and motion-robust 3D volume reconstruction for neonatal MRI". Used to obtain a reconstructed volume with high isotropic resolution of the neonatal brain.

Link to published thesis will be posted when available

Requirements

This repoistiry makes use of the Bart toolbox and MRecon with MRSense from Gyrotools to preprocess the raw MRI data. The MRIDC toolbox is used for implementing the motion-robust reconstrucion model. The Slice-to-Volume Reconstruction ToolKit is used for transforming anisotropic slice stacks isotropic resolution.

Installation

It is recommended to use a virtual environment to install the required packages. The following commands will create a virtual environment and install the required packages:

conda create -n AMR3D-NMRI python=3.11
conda activate AMR3D-NMRI
pip install -r requirements.txt

To enable the import of utilities, add the project root directory to the PYTHONPATH environment variable:

export PYTHONPATH=$PYTHONPATH:/path/to/AMR3D-NMRI/code

Or, if you are using a Windows machine:

set PYTHONPATH=%PYTHONPATH%;C:\path\to\AMR3D-NMRI\code

When using a supported IDE, such as Visual Studio Code, you can also add the python path to the integrated terminal settings:

.vscode/settings.json

{
  "terminal.integrated.env.windows": {
    "PYTHONPATH": "C:\\path\\to\\AMR3D-NMRI\\code"
  },
  "terminal.integrated.env.linux": {
    "PYTHONPATH": "/path/to/AMR3D-NMRI/code"
  },
  "terminal.integrated.env.osx": {
    "PYTHONPATH": "/path/to/AMR3D-NMRI/code"
  }
}