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Participant Onboarding

To make the most of our time together and create a collaborative, engaging learning experience, it’s important that everyone starts with a common baseline of knowledge and a fully functional technical setup. In this section, you’ll find information about the target audience, the knowledge that will help you get the most out of the course, and step-by-step instructions for installing the necessary software.

Target audience

This winter school is designed especially for:

  • PhD students, postdoctoral researchers, and clinical scientists who are new to the practical aspects of dMRI data and tractography processing.

  • Researchers with a theoretical understanding of dMRI who wish to develop the hands-on skills necessary to conduct their own tractography analysis.

  • Individuals from related fields (e.g., neuroscience, psychology, radiology) seeking to incorporate dMRI methods into their research programs.

Required knowledge

We recommend that participants already have a working knowledge of several key areas before the start of the workshop. This ensures that session time is focused on new, advanced material rather than remedial instruction.

Conceptual:

  • A general understanding of MRI physics, including concepts like relaxation times (T1​, T2​), signal excitation, and image contrast.

  • A foundational understanding of dMRI principles, including the purpose of diffusion weighting, the concept of the b-value, and how diffusion anisotropy arises in biological tissues.4

Mathematical:

  • Familiarity with fundamental vector and matrix operations, including dot products, matrix multiplication, and the concepts of eigenvalues and eigenvectors, which are central to the Diffusion Tensor Imaging (DTI) model.

Technical:

  • Proficiency with basic command-line operations in a Unix-like environment (Bash). This includes navigating the filesystem (cd, ls, pwd), creating directories (mkdir), and managing files (cp, mv, rm).

  • A basic understanding of shell scripting, particularly the ability to write and execute simple for loops, is highly recommended for automating tasks.

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/)

Installation Options

To optimize the time dedicated to understanding concepts and the various tools, we hope to minimize potential obstacles from software installation and development environment configuration issues.

You have two ways to prepare your environment. We recommend the Megadocker solution for a consistent experience.

1. Megadocker Solution

This approach guarantees an identical, functional software stack regardless of your operating system.

2. Manual Installation

  • Linux/macOS: Install via package managers or source (see table below).

  • Windows: You should use Windows Subsystem for Linux (WSL) to facilitate the installation of these neuroimaging tools.
    Experienced users can manually install the software on any OS. Windows users should use Windows Subsystem for Linux (WSL) to facilitate installation of tools.

Verification

Once your environment is set up, you should verify that all tools are available. First, download the verification script here. The expected output is shown at the last page of this document.

If using the Megadocker:

Launch the container and run the verification script directly with this command:

docker run --rm -v "/path/to/verification/script":/winter_school frheault/ist_winter_school_2026 bash /winter_school/check_installation.sh

/path/to/verification/script must be modified to point where you downloaded the script.

If using a Manual Installation:

  1. Open your terminal (or WSL terminal on Windows).

  2. Navigate to your download folder (e.g., cd ~/Downloads).

Run the script using: bash check_installation.sh
(Note: If you are on Windows using WSL, your C: drive is usually located at /mnt/c/Users/[YourUser]/Downloads).