Schedule

The initial session, Welcome & Setup Clinic, is dedicated to ensuring a smooth technical start for all participants. The primary goals are to complete administrative onboarding (including badge collection and venue information) and to ensure every participant's laptop is properly configured for the practical sessions. This involves running the provided check_setup.sh script to verify that all necessary software (following the prerequisite installation attempt) is correctly installed and configured. Instructors will provide direct, one-on-one technical support to resolve any last-minute errors and software conflicts (e.g., between conda, virtualenv, or Docker), and confirm that the participant's hardware specifications are adequate, allowing everyone to start the workshop without technical issues.

This session aims to establish a common vocabulary for neuroimaging data by covering three primary representations: voxels for volumetric data (e.g., T1w, fMRI, DWI), vertices and faces forming meshes for surface-based data (e.g., cortical surfaces from FreeSurfer), and streamlines (polylines) for tractography results. It also introduces the hierarchy of linear spatial transformations—translation (3 parameters), rigid-body (6 parameters), and affine (9 parameters)—used for image alignment. Finally, it explores reference spaces, including strides, voxel order, and different conventions (e.g., VOX, VOXMM, RASMM, LPSMM) across software and file formats.

This session provides a theoretical review of the core principles necessary for interpreting diffusion-weighted images (DWI). The lecture will explain how the diffusion MRI signal relates to the water molecule displacement and how diffusion weighting creates contrast. Key concepts covered include the b-value, which defines the degree of diffusion weighting, and b-vectors, which specify the direction of observation. The session emphasizes that restricted and hindered diffusion of water molecules by organized tissue like white matter is the physical basis for anisotropic diffusion. Anisotropic diffusion is presented as the fundamental contrast mechanism that allows researchers to map white matter fiber orientation.

This session provides a high-level neuroanatomical overview of the brain's major white matter pathways, effectively bridging the gap between dMRI physics and the biological structures being imaged. The goal is to introduce the concept of "connectional anatomy," which forms the foundation for tractography and connectomics. The lecture categorizes the major white matter systems into three groups: Commissural fibers (connecting hemispheres, e.g., Corpus Callosum), Association fibers (connecting cortical regions within a hemisphere, e.g., Arcuate Fasciculus), and Projection fibers (connecting the cortex to subcortical structures and the spinal cord). Participants will gain a mental atlas of these macroscale pathways, preparing them to accurately visualize and reconstruct these structures in later tractography sessions.