DiffSim-μGUIDE

This project is part of the VIC-HACK 2024 hackathon organised at Cardiff University and is co-lead by Bradley Karat and Maëliss Jallais.

The aim of this project is to integrate simulations from DiffSimGEN into μGUIDE.

If you are using this repository, please cite μGUIDE (see preprint here):

@misc{jallais2023muguide,
      title={$\mu$GUIDE: a framework for microstructure imaging via generalized uncertainty-driven inference using deep learning}, 
      author={Maëliss Jallais and Marco Palombo},
      year={2023},
      eprint={2312.17293},
      archivePrefix={arXiv},
      primaryClass={eess.IV}
}

Installation

Clone the repository with

git clone https://github.com/mjallais/DiffSim-uGUIDE.git

Create a virtual environment with

python -m venv venv_uGUIDE

Activate it with

source venv_uGUIDE/bin/activate

then install the required dependencies with

cd DiffSim-uGUIDE
pip install .

Usage

If installed with pip, the package can be ran with:

diffsimuguide

Run this with the -h flag to get a detailed summary of the toolbox and its flags plus required arguments.

Example Toolbox Call

For a dry-run:

diffsimuguide /path/to/bids/inputs /path/for/outputs participant --model NODDI_watson --SNR 25,50 -np

To actually run the software:

diffsimuguide /path/to/bids/inputs /path/for/outputs participant --model NODDI_watson --SNR 25,50 --cores all

Example File Struture

└── bids
    ├── sub-01
    │ └── dwi
    │     ├── sub-01_brain_mask.nii.gz
    │     ├── sub-01_dwi.bval
    │     ├── sub-01_dwi.bvec
    │     ├── sub-01_dwi.nii.gz
    ├── sub-02
    │ └── dwi
    │     ├── sub-02_brain_mask.nii.gz
    │     ├── sub-02_dwi.bval
    │     ├── sub-02_dwi.bvec
    │     ├── sub-02_dwi.nii.gz

Alternatively, the --path-dwi flag can be used to override BIDS by specifying absolute paths. For example: --path-dwi /path/to/my_data/{subject}/dwi.nii.gz. The other necessary files (.bval, .bvec, and brainmask) must be labelled in a similar fashion (i.e. all have the same prefix).