Software & system requirements

A standardized software environment is critical for the success of the hands-on sessions. Participants are required to install a suite of open-source neuroimaging tools before their arrival. The provision of a pre-configured containerized environment is strongly recommended to minimize installation-related issues (see below).

Table 2: Required software stack

MRtrix3 - Advanced dMRI analysis, modeling, tractography, and visualization. (https://www.mrtrix.org/download/)

FSL - General neuroimaging analysis, including brain extraction (bet) and distortion correction (topup, eddy). (https://web.mit.edu/fsl_v5.0/fsl/doc/wiki/FslInstallation.html)

FreeSurfer - Structural MRI analysis, surface reconstruction, and anatomical segmentation. (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)

ANTs - Advanced image registration and segmentation tools. (https://github.com/ANTsX/ANTs?tab=readme-ov-file#installation)

Scilpy - A library of Python scripts for dMRI processing, often used for pipeline development and analysis. (https://github.com/scilus/scilpy?tab=readme-ov-file#scilpy)
(either venv or anaconda)

dcm2niix - Industry-standard tool for converting DICOM images to the NIfTI format. (https://github.com/rordenlab/dcm2niix#install)

MI-Brain - A visualization and analysis tool particularly useful for tractography and ROI manipulation. (https://github.com/imeka/mi-brain#mi-brain)

ExploreDTI - Processing, analysis and visualization for diffusion MRI and fiber tractography (https://www.exploredti.com/)

The megadocker solution

To circumvent common installation problems related to operating system differences, library dependencies, and PATH environment variables, a megadocker image will be provided. This Docker container includes all the necessary software pre-installed and pre-configured in a stable Linux environment. This approach guarantees that every participant has an identical, functional software stack, regardless of their host operating system (Windows, macOS, or Linux). This is the recommended and most robust method for workshop preparation.

You are expected to install Docker (LINK TO BE ADDED SHORTLY) and test it…

The manual installation

Experienced users can manually install the software on any OS. Windows users should use Windows Subsystem for Linux (WSL) to facilitate installation of tools. Linux and macOS users can install software via package managers or by compiling from source (see table above), and then verify dependencies and environment variables are correctly configured.

Pre-Workshop setup verification

All participants, whether using the megadocker or a manual installation, must run a provided verification script (check_setup.sh) before arriving at the winter school. This script will execute a simple command from each required software package (e.g., mrinfo -version, bet -help) and report whether each tool is correctly installed and accessible from the command line. This is done to identify and resolve setup issues beforehand, an online ‘help desk’ will be available a month before the workshop.