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Print your Brain

Leader: Dr. Timo Torsten Schmidt, Center for Cognitive Neuroscience Berlin, Freie Universität Berlin; institutional connection: Fachbereich Erziehungswissenschaft und Psychologie, Center for Cognitive Neuroscience Berlin (CCNB), Freie Universität Berlin

Period of sponsorship: April 2021 – March 2022

Print Your Brain began at the start of 2021 as a team of students working online to develop an Open Source data processing pipeline by which MRI brain scans of individual brains could be 3D printed. You can find a summary and video about what has been achieved by now on the following webpage:


Within Print Your Brain, several focus groups were formed in order to ensure that each student could best contribute their individual skills, expertise, and passion to the project: (1) Infrastructure (2) Data Processing (3) Open Science (4) 3D Printer (5) Product Design & Public Relations The overall structure of the research group implements organization and management similar to small businesses or start-ups to explore how such efficient structures and project management can be applied and adapted to the academic world and to practice teamwork beyond the classical academic environment.

Learning outcomes: Students will have the knowledge how structural MRI images are acquired according to current research standards. Students are able to process structural MRI images with different state-of-the art software packages (e.g. SPM, FSL, Freesurfer). Students will have gained experience in working in a virtual team and working with classic and agile project management. Students will gain experience in 3D printing and at the end of the course, they will hold a 3D print of their own brain in their hands. 

Tasks in the winter term 2021: (1) Data Processing optimization: Optimize scripts for 3D-reconstruction i.e. optimization of artifact corrections in 3D image processing, automatizing and combination of scripts to batch scripts, optimization of printable models in Meshlab. (2) Tutorial/Documentation: Providing detailed instructions of the necessary data processing steps in the spirit of Open Science on a Github website and publication of scripts. (3) Product Design: Create a printable stand and connectors for the 3D models parts. (4) Optimize printer settings and try different 3D-print post processing, like smoothing, painting etc. (5) Establish multi-color printing.

We look specifically for students with some of the following background skills: 

(1) Experience with Github (2) Experience with bash (unix shell) command syntax (3) Experience with Meshlab and 3D modelling (4) Experience in 3D-printing / post processing of 3D-printed objects

Format: Virtual team via Discord server

Language: Englisch

Target group: Masterstudents with background in Neuroscience and a basic understanding of neuroimaging data, programming experience in Matlab or Python, high motivation for teamwork

Beginn: October 28, 2021

Termin: Thursday, 11 a.m. – 12 p.m.

Kontakt: timo.t.schmidt@fu-berlin.de