DeepMI FastSurfer / FreeSurfer Course 2025

The DeepMI lab is happy to announce the DeepMI FastSurfer / FreeSurfer course, a 2.5-day, hands-on, introductory course on state-of-the-art deep-learning methods for fast and reliable neuroimage analysis.

The goal of the course is to equip participants with working knowledge about fundamental concepts in structural neuroimaging analysis, and enable them to conduct analyses of structural imaging data using the FastSurfer and FreeSurfer software packages.

After completing the course, participants will have gained an understanding of modern methods for the analysis of structural brain images, will have learned how to run both the FastSurfer and FreeSurfer softwares, and will know how to set up an analysis and work with the resulting outputs in the context of their own research projects.

The 2025 course will feature a new session for longitudinal processing and analyses, covering the recent addition of the longitudinal module to the FastSurfer software.

The course consists of lectures, demonstrations, practical exercises, and provides ample opportunities for discussions and informal exchange. A helpdesk will be available during the course to offer individual support for issues related to installing and running the software on your own devices, or any questions you might have about your planned analyses and projects, for example.

The course fee is EUR 250, covering the scientific lectures and practial sessions, course materials and hardware, and catering during the course (lunch, coffee breaks, reception on the first day).

Dates

The course will be held from September 17 to September and 19, 2025 (Wednesday to Friday), starting at 13:30 on Wednesday, and ending on 15:00 on Friday.

Places

The course takes place at the German Center for Neurodegenerative Diseases (DZNE) in Bonn, Germany (directions).
Topics

Topics

• Introduction to structural neuroimaging: an overview of the FastSurfer and FreeSurfer software packages and what they can do
• Advanced deep-learning for image segmentation: fast and reliable anatomical segmentation – the core module of the FastSurfer software
• Surface models: how to create surface models and extract a rich set of anatomical features
• Statistical modeling and inference: how to arrive at conclusions – the evaluation and interpretation of results
• NEW: Longitudinal processing and analysis: taking advantage of longitudinal study designs – and dealing with their challenges and intricacies
• Quality control and edits: how to trust your results – solutions to potential pitfalls and issues
• The FastSurfer ecosystem: specialized applications, add-on modules, and an outlook to future developments

Social events

We will have a small reception with snacks and drinks at the DZNE on the early evening of the first day (Wednesday, until 19:00) as an opportunity for informal exchange and discussion among course participants and with the speakers.

We are planning to conclude the second day of the course (Thursday) at the Waldau restaurant, which is a nice 15 min walk from the DZNE and can also be reached by bus in a few minutes. We will guide one group going by foot, and one group going by bus, right after the course at around 5 pm. For those wanting to join later, the address is “An der Waldau 50”, and the closest bus stop is “Waldau” (served by line 602). Information about the bus schedules is available from the VRS website.

More information including contact and registration by August 31, 2025

This course is organized by the DeepMI Lab (German Center for Neurodegenerative Diseases (DZNE), Martinos Center for Biomedical Imaging, associated to MIT CSAIL) and was originally published here.