DeepMI FastSurfer / FreeSurfer course


The DeepMI lab is happy to announce a two-day, hands-on, introductory FastSurfer/FreeSurfer course focussing on the analysis of structural brain MRI data. The course consists of lectures, demonstrations, and practical exercises and will cover a range of topics, such as:

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.


The course will be held on September 28 and 29 (Thursday and Friday) between 9:15 am and 4:30 pm.


The course takes place at the German Center for Neurodegenerative Diseases (DZNE), Venusberg Campus, Bonn.

Room: B.1.119/120. Non-DZNE participants will be picked-up at 9:10 am each day at the reception in the DZNE main building.


Thursday, September 28:

09:15 - 09:30Welcome
09:30 - 10:30FastSurfer / FreeSurfer overview
10:30 - 10:45Break
10:45 - 12:30Analyzing individual cases 1: segmentations
12:30 - 13:30Lunch break
13:30 - 14:30Analyzing individual cases 2: surfaces (part 1)
14:30 - 14:45Break
14:45 - 15:45Analyzing individual cases 2: surfaces (part 2)
15:45 - 16:30Questions and answers
17:00 - 19:00Social event (optional)

Friday, September 29:

09:15 - 11:00Group analysis 1: preparations and modeling
11:00 - 11:15Break
11:15 - 12:30Group analysis 2: inference
12:30 - 13:30Lunch break
13:30 - 15:00QC, troubleshooting, edits, and caveats
15:00 - 15:15Break
15:15 - 16:00FastSurfer ecosystem and outlook
16:00 - 16:30Questions and answers

All sessions will contain lectures and demos as well as practical and interactive parts.


The intended audience for this course is the DZNE and UKB neuroimaging community, as well as external guests.

There is a maximum capacity of 20 participants and no course fee.

Registration is now closed.


Participants should have initial experience in working with MRI data.

During the course, participants will be provided with workstations, software, and materials for the lectures and practical exercises.

We can neither provide support for personal devices nor individual datasets.


The German Center for Neurodegenerative Diseases (Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE) is located at the Venusberg campus of the university hospital, its address is “Building 99, Venusberg-Campus 1”. The most convenient way to get from Bonn main ststion to the DZNE is by bus. From Bonn main station, cross the street towards the city center to get to the bus station. At the bus station, take line 601 towards the direction “Venusberg / Uniklinikum” until its final stop “Uniklinikum Süd”; don’t take the 601 bus towards “Tannenbusch” (which is the opposite direction). The bus towards “Venusberg / Uniklinikum” typically leaves at platform A1, roughly every 10 mins.

When arriving at the “Uniklinikum Süd” bus stop, follow the road until the roundabout, then turn left. The DZNE is located approximately 100m from the bus stop, and it’s a huge black building with colorful windows.


Deep Medical Imaging Lab
German Center for Neurodegenerative Diseases (DZNE)
Venusberg Campus 1/99
Bonn, Germany