MELD classifier

Neural network lesion classifier for the MELD project.

The preprint describing the classifier can be found here:
https://www.medrxiv.org/content/10.1101/2021.12.13.21267721v1

Code Authors : Hannah Spitzer, Mathilde Ripart, Sophie Adler, Konrad Wagstyl

This package comes with a pretrained model that can be used to predict new subjects. It also contains code for training neural network lesion classifiers on new data.

Disclaimer

The MELD surface-based FCD detection algorithm is intended for research purposes only and has not been reviewed or approved by the Medicines and Healthcare products Regulatory Agency (MHRA), European Medicine Agency (EMA) or by any other agency. Any clinical application of the software is at the sole risk of the party engaged in such application. There is no warranty of any kind that the software will produce useful results in any way. Use of the software is at the recipient's own risk.

Installation

Prerequisites

For preprocessing, MELD classifier requires Freesurfer. It is trained on data from versions 6 & v5.3. Please follow instructions on Freesurfer to install FreeSurfer v6.

Conda installation

We use anaconda to manage the environment and dependencies. Please follow instructions on anaconda to install Anaconda.

Install MELD classifier and python dependencies:

# checkout and install the github repo 
git clone https://github.com/MELDProject/meld_classifier.git
# enter the meld_classifier directory
cd meld_classifier
# create the meld classifier environment with all the dependencies 
conda env create -f environment.yml
# activate the environment
conda activate meld_classifier
# install meld_classifier with pip (with `-e`, the development mode, to allow changes in the code to be immediately visible in the installation)
pip install -e .

Set up paths and download model

Before being able to use the classifier on your data, some paths need to be set up and the pretrained model needs to be downloaded. For this, run:

python scripts/prepare_classifier.py

This script will ask you for the location of your MELD data folder and download the pretrained model and test data to a folder inside your MELD data folder. Please provide the path to where you would like to store MRI data to run the classifier on.

Note: You can also skip the downloading of the test data. For this, append the option --skip-download-data to the python call.

FAQs

Please see our FAQ for common installation problems.

Verify installation

We provide a test script to allow you to verify that you have installed all packages, set up paths correctly, and downloaded all data. This script will run the pipeline to predict the lesion classifier on a new patient. It takes approximately 15minutes to run.

cd <path_to_meld_classifier>
conda activate meld_classifier
pytest

Usage

With this package, you can use the provided classifier predict new subjects from existing and new sites. In addition, you can train your own classifier model.
For more details, check out the guides linked below:

• Predict new subjects (existing site)
• Predict new subjects (new site) : COMING SOON
• Train and evaluate models

Contribute

If you'd like to contribute to this code base, have a look at our contribution guide

Manuscript

Please check out our manuscript to learn more.

An overview of the notebooks that we used to create the figures can be found here.

A guide to using the MELD surface-based FCD detection algorithm on a new patient from an existing MELD site is found here.