Monai training of an MS lesion segmentation model

[plbenveniste]

This PR details the work to build a model using monai to automatically segment MS lesions in the SC.

It contains the following files:

• 1_create_msd_data.py : to create an MSD dataset, from the multiple MS lesion dataset, usable by monai
• config.yml : the config YAML file used to configure the parameters of the model and the training
• losses.py : where we define the losses used during model training
• requirements.txt : where we list the libraries to install using pip
• train_monai_unet_lightning_multichannel_input.py : the main script to train a model with multiple input channel (image and SC seg) and one output (lesion seg)
• train_monai_unet_lightning_multichannel_output.py : the main script to train a model with one input (the image) and multiple outputs (SC seg and lesion seg)
• train_monai_unet_lightning.py : the main script to train a model with one input (image) and one output (lesion seg)
• utils.py : a file which contains other useful function for model training

This is a work in progress.