Usage

1.Installation

To use LS-MAT, directely clone repository to your local enviroment.

git clone https://github.com/hobacteria/Brain_age_syn.git

2.Dependency & Python pakages

There are several main packages required to run the project pipeline.

We use Python 3.10 in our pipeline and strongly recommend running LS-MAT in a anaconda virtual environment to ensure clear dependency management.

For detialed package requirments, please check here

pip install monai==1.4.0
pip install nibabel
pip install scikit-image
pip install numpy==1.26.4
pip install pandas==2.2.3

Additinally, you need to install some software.

Freesurfer 7.X in https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

Fastsurfer in docker hub from https://github.com/Deep-MI/FastSurfer

Docker 20.10.X in https://docs.docker.com/engine/release-notes/20.10/

pytorch with GPU in https://pytorch.org/get-started/locally/

docker pull deepmi/fastsurfer:latest