Brainhack Western France

Open science hackathon

November 14-15, 2019

An event of BrainHack Global

Keynote speakers

Feedback from a routine care imaging study in depression - the LONGIDEP cohort
Jean-Marie Batail, November 14, 13:30

Reversible Networks for Brain MRI Synthesis
François Rousseau, November 14, 14:00

Expert Aided CNNs: improving fracture classification with curriculum learning
Diana Mateus, November 15, 13:30

Source localisation: from the room to the brain
Nancy Bertin, November 15, 14:00

Registration (before November 5)

Submit a Project!


Brainhack events convenes engineers, researchers and clinicians to work together on projects related to neuroscience. Are you are interested in sciences and neurosciences? Come and learn about existing tools or bring your own projects and find passionate people to join.

There is a lot of open data available (e.g. 101 nights, FC 1000, OASIS, etc.), waiting to be analysed ! Are you looking for contributors on an existing software? Would you like to meet new collaborators? Do you have open questions in your research? Come and discuss with us during these 2 days.
Brainhack Rennes will feature presentations from key researchers in our community as well as video links to the global community. Visit BrainHack Global 2019 to learn more about events worldwide.


  • Camille Maumet (Program committee)
  • Emmanuel Caruyer (Program committee)
  • Julie Coloigner (Program committee)
  • Raphaël Truffet (Program committee)
  • Édith Blin (Local Organising Committee)
  • Armelle Mozziconacci (Local Organising Committee)


The conference will be held in Rennes, at INRIA Rennes-Bretagne-Atlantique / IRISA, on the university campus (called “Campus de Beaulieu”), in the east of Rennes.

To reach Inria from the city center, you can

  • walk (about 30 minutes),
  • take a bus (more information: Star – public transportation service – only in French) or
  • rent a bike (more information: Velo Star).

This map explains how to reach INRIA from the bus Station “Tournebride” : Map from bus stop

If you need informations about accomodations, please contact us !

More information here.

IRISA/Inria Rennes
Campus de Beaulieu
35000 Rennes, France

Share ideas

Build Projects

Meet the community

Learn Tools

Keynote speakers

Feedback from a routine care imaging study in depression - the LONGIDEP cohort
Jean-Marie Batail , CHGR, Rennes.

Actually, research in the field of depression encounter challenges such as the need of biomarker which could help physicians in identifying subtypes of depressed patients who will have a pejorative outcome or need specific therapeutics. LONGIDEP cohort was a prospective study conducted in routine care. 180 patients suffering from a mood depressive episode benefited from a clinical, neuropsychological and brain imaging. They were assessed at 6, 12 months, 2 and 3 years. Brain imaging protocols composed anatomical (T1, DTI), and perfusion sequences (ASL). The aim of this work was to study anxiety and apathy in depression. These clinical factors and its imaging correlates were tested in prediction of outcome at 6-months follow-up. Our study has shown that 1) apathy in depression was associated with specific clinical and pathophysiological patterns, 2) categorical and phenotypic approaches identified different white matter abnormalities in depression, 3) trait anxiety, cognitive patterns of visuospatial memory were predictive of pejorative outcome. Structural abnormalities in key regions involved in emotion regulation were associated with pejorative outcome of depression. Only anxiety was involved in prognosis. Further works should study the link between anxiety and motivation using multimodal imaging protocol such as anatomical and functional connectivity with methodological supports such as machine learning, or graph theory. These challenges will be conducted in PHRCi project DEPREDICT.

Reversible Networks for Brain MRI Synthesis
François Rousseau, IMT Atlantique, Brest.

Image synthesis in medical imaging is an emerging research area and the main applications are data normalization, cross modality synthesis, super-resolution, validation of algorithms (segmentation, registration). In this talk, we will tackle the problem of image synthesis as a regression problem, formulated in a deep learning framework. More specifically, we will explore the use of deep reversible networks for brain MRI synthesis.

Expert Aided CNNs: improving fracture classification with curriculum learning
Diana Mateus, Ecole Centrale Nantes.

We target the problem of fracture classification from clinical X-Ray images towards the development of an effective Computer Aided Diagnosis (CAD) system. The fracture classification problem is difficult as confirmed by low intra- and inter-expert agreement rates of our in-house study and also in the previous literature. The talk will show the design and application of different deep learning techniques towards identifying, localizing and finally classifying proximal femur fractures. In particular, a recently proposed curriculum learning approach which takes expert knowledge into account to guide the CNN weight optimization.

Source localisation: from the room to the brain
Nancy Bertin, Univ Rennes, Inria, CNRS, IRISA UMR 6074, Rennes.


Current projects

Develop interfaces and workflows for Anima in Nipype

Nipype and Anima

Nipype looks like a great framework to define small processing bricks and automatically assemble them to form pipelines. At last year brainhack, we had time to define interfaces for the Anima open-source software. The idea this time is to go all the way to define a pipeline based on Anima interfaces and try to run it on a cluster on some toy data.

Contact: Olivier Commowick

BULLE (cereBral vascULar bifurcation LabElling)

Intracranial aneurysm

Context and issues ⮟

ICAN is a french multi-center study aimed at bridging clinical observations, genomic markers as well as quantitative imaging biomarkers to better understand the formation, the development and the possible rupture of intracranial aneurysms. Saccular aneurysms are generally localized at vessel bifurcations and several studies have identified the anatomical localization of saccular aneurysms as an important risk factor for rupture. One of the outcomes of ICAN is a large imaging biobank resulting from routine medical imaging exams (ToF MRIs, CTs, or DSAs) provided by the 34 french participating academic hospitals. This data can be accessed for further analysis through the Shanoir database. However the analysis of the geometrical features of the bifurcation that carry the IA is hampered by the lack of anatomical labelling. Determining to which artery belongs a bifurcation carrying a saccular aneurysms is a time-consuming task and requires expertise in brain anatomy.

Objectives and expected outcomes

BULLE aims to design and implement an atlas-based neuroimaging processing workflow for automatic labelling of the cerebrovascular trunk, also known as the circle of Willis. These approaches, known as atlas-based segmentation, are based on the registration between an anatomical atlas and the patient images, and the subsequent transfer of annotations from the atlas to the images. We expect to gather experts in 3D MRI registration and vascular imaging. Based on their expertise we will collaboratively develop a reusable Jupyter notebook dedicated to the automatic annotation of cerebral vessels.

Contact: Alban Gaignard Perrine Paul Gilloteaux Vincent L’Allinec Romain Bourcier

Improve EEG-fMRI neurofeedback prediction using EEG signal only : Signal processing, graph and optimisation

Neurofeedback prediction

A new kind of data is available : EEG-fMRI Neurofeedback scores. Neurofeedback approaches (NF) provide real-time feedback to a subject about its brain activity and help him or her perform a given task. Brain activity features are extracted, online, from non-invasive modalities such as EEG or fMRI for example. Here, EEG and fMRI signals were acquired simultameously, and subjects recieved, in real time, NF informations extracted from EEG and fMRI. The goal of this project, is to learn EEG patterns in order to predict NF scores coming from fMRI using EEG signals only, as the use of fMRI is expensive and time consuming.

Contact: Claire Cury

fNIRS: A "light" approach for brain studies


Functional Near InfraRed Spectroscopy (fNIRS) is a novel technique that allows brain mapping and hemodynamic response registration in a rather cheap and portable manner. The idea of this project is to go through the basics of data acquisition and processing for different kinds of motor and cognitive tasks, with the help of a recently bought NIRx device and software developed in Matlab and LabView.

Contact: Héctor García

Diminished Reality

Diminished Reality

With the ever accelerating development of augmented reality and artifical intelligence technologies, we might be tempted to think that matrix like scenarios - where everything we feel and know is simulated - could become a reality.

This conceivable future might be attracting to some people, yet it is easy to see the risks and limits of such paradigm.

Numerous intelectuals (Alain Damasio, Eric Sadin, ...) question progress and technology and propose to collectively redefine the goals and trajectory of human development.

From this perspective, Diminished Reality aims at utilizing advanced technologies in a subversive fashion to promote alternative and low-tech experiences.

The project consists in a virtual reality headset coupled with a stereo-vision camera and basic image processing algorithms designed to immerge the user in an quantized, voxel based reality.

Contact: Arthur Masson

An R Package for the Statistical Analysis of Tractography Data


Structural connectivity can be assessed using diffusion MRI. It relies on the idea that water trapped within axons or glial cells undergo restricted diffusion patterns that can be modelled, estimated and used to provide a mathematical representation of the brain microstructure, ultimately leading to a mapping of the structural connections in the brain. Lots of tools are available nowadays to perform this task, which is known as tractography. However, there is very little in the community about open-source softwares that allow users to perform sound statistical analyses of tractography data.

This project is an attempt to create such an open-source software from scratch. Given that the ultimate goal is to perform statistical analysis and data visualisation, it seems natural to lean towards R, which a programming language dedicated to statistical computing ( The objective of the project will be:

1. To build the state of the art about already existing R packages for tractography data; 2. To brainstorm our new R package API, including the definition of relevant object classes and related methods for later uniform integration of statistical methods; 3. To start the package, including package creation, website for promoting it, GitHub repository, description, logo creation and so on; 4. To start implementing existing statistical methods for tractography data.

Contact: Aymeric Stamm

Code for a reproducible analysis in task-based fMRI


With the ever accelerating development of augmented reality and artifical intelligence technologies, we might be tempted to think that matrix like scenarios - where everything we feel and know is simulated - could become a reality.

The goal of the project is to examine, edit and organize the code and content of a study on analytic variability in task-based fMRI, to describe the data structures, high-level functions, and to display the results in a Jupyter Notebook, in order to facilitate its reproducibility.

In this study, we try to highlight the existing analytic variability in task-based fMRI pipelines, by comparing groups of subjects data from the Human Connectome Project which we have preprocessed and analyzed with different pipelines.

Contact: Xavier Rolland

Develop a workflow to automatically extract white matter tracts bundles from diffusion MRI.


Diffusion tensor imaging (DTI) allows for the estimation and quantitative analysis of white matter tracts properties, for instance fiber tracts integrity. DTI has been used, for example, to characterize cerebrospinal tract (CST) properties from diffusion MRI in stroke patients, and identify biomarkers of motor recovery based on CST properties. In the case of stroke, a challenge is to robustly take in account the lesion when estimating fibers tracts.

In this project, we are interested in developing a workflow to automatically extract white matter bundles from diffusion MRI exploring a range of tools (ANIMA, WMQL, Freesurfer in order to robustly estimate CST properties. We will first design and test the workflow on healthy subject data, and eventually apply it to stroke patients’ images to verify how the lesion affects automatic CST estimation.

Contact: Giulia Lioi

Further Information

Brainhack Western France 2019. This 2-day workshop will be held November 14-15th at IRISA / Inria, Rennes, France, and is part of BrainHack Global 2019, where a constellation of such events happen simultaneously around the globe. Brainhack events convenes researchers from a myriad of disciplines to work together on projects related to neuroscience. Similar to hackathons in the tech sector, much of the schedule is left open for attendees to work together on projects of their choosing. We also include “unconference” sessions where talks are chosen by the attendees based on their interests as they evolve throughout the meeting. Brainhacks are not “coding sprints” or exclusive to programmers, but rather are open to brain scientists from all backgrounds.

Hacking: The core of Brainhack are “open hacking” sessions during which attendees collaborate together on projects of their choosing. Attendees who have specific project ideas or data that they would like to explore are encouraged to submit their project below prior to the event. At the opening of the Brainhack event, typically after the ice breaker, attendees pitch their ideas and afterwards mingle with others to organize a project team. Teams work together throughout the remainder of Brainhack and are given the opportunity to present their progress during the wrap-up session at the end of the event.

“Hackathons are based on collaboration, not competition”

Unconference: Sessions for attendees to present their research or other topics of current interest. Immediately prior to these sessions, the agenda is determined on-site. Attendees who are willing to present add their name to a sign-up sheet.

Working papers on the outcomes from Brainhack Western France can appear in the Gigascience Brainhack Thematic Series, and shorter project reports from the event are eligible for the annual Brainhack Proceedings.

Thanks to generous support from Inria, registration is free, and includes 2 lunches and all coffee breaks. Registration will be open shortly.

Brainhack Western France is generously supported by:


Brainhack Western France is hosted by:


Get In Touch!

Contact us for information or with your ideas.

Join us on Slack #bhg19-rennes

Code of Conduct

Brainhack is dedicated to providing a harassment-free conference experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion. We do not tolerate harassment of conference participants in any form. Sexual language and imagery is not appropriate for any conference venue, including talks. Conference participants violating these rules may be sanctioned or expelled from the conference without a refund at the discretion of the conference organizers.

Harassment includes, but is not limited to:

  • Verbal comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion.
  • Sexual images in public spaces
  • Deliberate intimidation, stalking, or following
  • Harassing photography or recording
  • Sustained disruption of talks or other events
  • Inappropriate physical contact
  • Unwelcome sexual attention
  • Advocating for, or encouraging, any of the above behaviour


Participants asked to stop any harassing behavior are expected to comply immediately.

Organizers and presenters are also subject to the anti-harassment policy. In particular, they should not use sexualized images, activities, or other material.

If a participant engages in harassing behaviour, event organisers retain the right to take any actions to keep the event a welcoming environment for all participants. This includes warning the offender, expulsion from the conference with no refund or not being allowed to participate in future events.

Event organisers may take action to redress anything designed to, or with the clear impact of, disrupting the event or making the environment hostile for any participants.

We expect participants to follow these rules at all event venues and event-related social activities. We think people should follow these rules outside event activities too!


If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible. You can report to Camille or Julie. Harassment and other code of conduct violations reduce the value of our event for everyone. We want you to be happy at our event. People like you make our event a better place.

You can make a report either with your personal email or using an anonymous email.

Past Editions