Installation

Python env

1. Create a Conda Environment with Python 3.11

install anaconda Create conda env with python 3.11

conda create -n mrienv python=3.11

Activate the environment:

conda activate mrienv

Install Dependencies Ensure you are in the project-root directory where the requirements.txt file is located. Install the required Python packages using pip:

pip install -r requirements.txt

Other tools

DHCP registration templates

For the registration step, the dhcp comes with registration atlases which can be downloaded (1Gb).

Docker

To run the skull-stripping and segmentations models, we use their dockerised version.

• Install docker desktop

• Pull the 2 necessary images :

  docker pull cookpa/synthseg:conda-0.1
  docker pull freesurfer/synthstrip:1.6

• The images can also be search within docker desktop using freesurfer/synthstrip:1.6 and cookpa/synthseg:conda-0.1

Freesurfer (optional for now)

Although used in development and tests, it is not currently used in the pipeline since the main parts are run on docker.
Release 7.4.1 is the one used.