Installation Instructions

FSL-MRS can currently be installed using one of two methods.

Option 1: From GitLab

Download or clone from FSL-MRS GitLab. To get FSL-MRS with example data and example Jupyter notebooks, download the full package from gitlab. Git LFS must be installed to download package data.

git clone --recurse-submodules https://git.fmrib.ox.ac.uk/fsl/fsl_mrs.git
cd fsl_mrs
pip install .

Option 2: From Conda

The primary installation method is via conda. After installing conda and creating or activating a suitable you can install FSL-MRS from the FSL conda channel. See our page on setting up a conda enviroment for a step by step guide.

conda install -c conda-forge -c defaults \
              -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ \
              fsl_mrs

Example data with conda

Installation with conda is easy, but you won’t get the packaged example data and notebooks. This can be downloaded separately here: FSL-MRS example data.

Operating systems

FSL-MRS has been tested thoroughly on Mac and Linux operating systems. FSL-MRS dependencies and FSL-MRS is available on native Windows installations, but has not currently been tested. Windows Subsystem for Linux (or WSL2) offers a Linux interface on Windows. FSL-MRS has been tested on WSL.