# Improving computational reproducibility or how-to share your research code

Camille Maumet

► To cite this version:

Camille Maumet. Improving computational reproducibility or how-to share your research code. Basel ReproducibiliTea 2025, Oct 2025, Online (Basel), Switzerland. hal-05385162

HAL Id: hal-05385162

https://inria.hal.science/hal-05385162v1

Submitted on 27 Nov 2025

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archive for the deposit and dissemination of sci-
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lished or not. The documents may come from
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abroad, or from public or private research centers.

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scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
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publics ou privés.

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Distributed under a Creative Commons Attribution 4.0 International License
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# Improving computational reproducibility or **how-to share** *your* research code

Camille Maumet

Inria, Univ Rennes, Inserm, CNRS, IRISA

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Inserm

Institut national
de la santé et de la recherche médicale

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Université
de Rennes

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An MRI study

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Acquisition

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Preprocessing

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Derived date

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Statistics

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An MRI study

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Acquisition

<figure><img src="image_15.png" /></figure>

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Preprocessing

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Derived data

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Statistics

<figure><img src="image_19.png" /></figure>

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An MRI study

<figure><img src="image_21.png" /></figure>

Acquisition

<figure><img src="image_22.png" /></figure>

<figure><img src="image_23.png" /></figure>

Preprocessing

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Derived data

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Statistics

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An MRI study

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Acquisition

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Preprocessing

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Derived data

<figure><img src="image_33.png" /></figure>

Statistics

<figure><img src="image_34.png" /></figure>

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# An MRI study

<figure><img src="image_36.png" /></figure>

Acquisition

<figure><img src="image_37.png" /></figure>

<figure><img src="image_38.png" /></figure>

Preprocessing

<figure><img src="image_39.png" /></figure>

Derived data

<figure><img src="image_40.png" /></figure>

Statistics

<figure><img src="image_41.png" /></figure>

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Credits: MRI by Flowicon [Noun Project](CC BY), process by Konkapp [Noun Project](CC-BY), analysis by Siti Solekah [Noun Project](CC-BY), Parcel [PublicDomainPictures](CC0), Git [Wikimedia](CC0)
# An MRI study

<figure><img src="image_43.png" /></figure>

Credits: MRI by Flowicon [Noun Project](CC BY), process by Konkapp [Noun Project](CC-BY), analysis by Siti Solekah [Noun Project](CC-BY), Parcel [PublicDomainPictures](CC0), Git [Wikimedia](CC0)
An MRI study

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An MRI study

<figure><img src="image_45.png" /></figure>

Humm... I can't
reproduce the
published results...
# An MRI study

<figure><img src="image_46.png" /></figure>

<figure><img src="image_47.png" /></figure>

Which version of
the SPM software
was used?

Which registration
algorithm?

How was the brain
mask computed?

Humm... I can't
reproduce the
published results...
# An MRI study

<figure><img src="image_48.png" /></figure>

Humm... I can't
reproduce the
published results...

<figure><img src="image_49.png" /></figure>

Did I understand
correctly the
method that was
used?

Which version of
the SPM software
was used?

Which registration
algorithm?

How was the brain
mask computed?

... is this due to my
(different) data?

... or is this due to
my (different)
computing
resources?

... or even
something
else?
# An MRI study

<figure><img src="image_50.png" /></figure>

Humm... I can't
reproduce the
published results...

<figure><img src="image_51.png" /></figure>

Which version of
the SPM software
was used?

Which registration
algorithm?

How was the brain
mask computed?

Is this due to my
different) data?

Is this due to
(different)
computing
resources?

... or even
something
else?
# Towards reproducible research

<figure><img src="image_52.png" /></figure>

Acquisition

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Pré-traitements

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Données dérivées

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Statistiques

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# Towards reproducible research

<figure><img src="image_59.png" /></figure>

Acquisition

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Pré-traitements

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Données dérivées

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Statistiques

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Open access

(pre-prints, diamond open access, etc.)

<figure><img src="image_66.png" /></figure>
# Towards reproducible research

<figure><img src="image_67.png" /></figure>

Acquisition

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Pré-traitements

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Données dérivées

<figure><img src="image_71.png" /></figure>

Statistiques

<figure><img src="image_72.png" /></figure>

<figure><img src="image_73.png" /></figure>

Open access

(pre-prints, diamond open access, etc.)

<figure><img src="image_74.png" /></figure>

<figure><img src="image_75.png" /></figure>

Credits: MRI by Flowicon [Noun Project](CC BY), process by Konkapp [Noun Project](CC-BY), analysis by Siti Solekah [Noun Project](CC-BY), Parcel [PublicDomainPictures](CC0), Git [Wikimedia](CC0)
# Towards reproducible research

<figure><img src="image_76.png" /></figure>

Acquisition

<figure><img src="image_77.png" /></figure>

Open data
(FAIR principles)

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<figure><img src="image_79.png" /></figure>

OpenNEURO

Radboud Data
Repository

Public-nEUro

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LORIS

shancir

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Pré-traitements

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Données dérivées

<figure><img src="image_83.png" /></figure>

Statistiques

<figure><img src="image_84.png" /></figure>

Open access
(pre-prints, diamond open access, etc.)

<figure><img src="image_85.png" /></figure>

<figure><img src="image_86.png" /></figure>
# Towards reproducible research

<figure><img src="image_87.png" /></figure>

Acquisition

<figure><img src="image_88.png" /></figure>

<figure><img src="image_89.png" /></figure>

Pré-traitements

<figure><img src="image_90.png" /></figure>

Données dérivées

<figure><img src="image_91.png" /></figure>

Statistiques

<figure><img src="image_92.png" /></figure>

<figure><img src="image_93.png" /></figure>

Open data
(FAIR principles)

<figure><img src="image_94.png" /></figure>

OpenNEURO

<figure><img src="image_95.png" /></figure>

LORIS

Radboud Data
Repository

Public-nEUro

shancir

<figure><img src="image_96.png" /></figure>

Open access
(pre-prints, diamond open access, etc.)

<figure><img src="image_97.png" /></figure>
# Towards reproducible research

<figure><img src="image_98.png" /></figure>

Acquisition

<figure><img src="image_99.png" /></figure>

<figure><img src="image_100.png" /></figure>

Pré-traitements

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Données dérivées

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Statistiques

<figure><img src="image_103.png" /></figure>

CODE

<figure><img src="image_104.png" /></figure>

<figure><img src="image_105.png" /></figure>

Open data

(FAIR principles)

<figure><img src="image_106.png" /></figure>

OpenNEURO

<figure><img src="image_107.png" /></figure>

LORIS

Radboud Data
Repository

Public-nEUro

shancir

Open access

(pre-prints, diamond open access, etc.)

<figure><img src="image_108.png" /></figure>
# Towards reproducible research

<figure><img src="image_109.png" /></figure>

Acquisition

<figure><img src="image_110.png" /></figure>

<figure><img src="image_111.png" /></figure>

Pré-traitements

<figure><img src="image_112.png" /></figure>

Données dérivées

<figure><img src="image_113.png" /></figure>

Statistiques

<figure><img src="image_114.png" /></figure>

CODE

<figure><img src="image_115.png" /></figure>

<figure><img src="image_116.png" /></figure>

Open data

(FAIR principles)

<figure><img src="image_117.png" /></figure>

OpenNEURO

Radboud Data
Repository

Public-nEUro

<figure><img src="image_118.png" /></figure>

LORIS

shancir

Open codes?

<figure><img src="image_119.png" /></figure>

Open access

(pre-prints, diamond open access, etc.)

<figure><img src="image_120.png" /></figure>
# Towards reproducible research

**Computational reproducibility**

Ability to reproduce **exactly the same results** using the **same data** and **same code**.

**Replicability**

Ability to reach the **same scientific findings** using
**similar data** and a **similar method**.
# Towards reproducible research

**Computational reproducibility**

Ability to reproduce exactly the same results using the
same data and same code.

**Replicability**

Ability to reach the **same scientific findings** using
**similar data** and a **similar method**.
# Open codes

<figure><img src="image_121.png" /></figure>

## Open source
Transparency

* With an open source licence and accessible in a public forge.

Guide

OPEN SCIENCE

SOURCE CODE
AND SOFTWARE

<figure><img src="image_122.png" /></figure>

OPEN
SCIENCE

2022

Ouvrir
la science !

how to
open up
software?

If you would like to share your software and/or others with us, you must organize them in a way that is accessible both legally and technically. You also need to think about the kind of information you want to share and the kind of implementation you want to promote.

### Choosing the license or more licenses

Choosing the license is an important step in the open access process, and one that can have significant consequences for the software's evolution.

The first step is to identify who holds the economic rights on the software. If the software is not the rights holder, it is NOT up to them to choose the licence.

The person, group or entity responsible for this choice can adopt a proprietary open approach and analyse a free software license. The * licence is an example of *open source initiative* or *free software foundation*.

The * licence* provides a list of licenses that can be used for production of *free public software*. In other cases, you may wish to refer to this list compiled by the *Open Source Initiative* or *Free Software Foundation*. In some situations, it is possible to use more restrictive licences that allow you to be controlled or limited by third parties. For instance, *open source* licences can be used to create academic content for scientific productivity only.

If the software uses a *non-free* component, you may need to add an academic content for scientific productivity only.

* That the *license* chosen legally compatible with those of the different pre-existing components.

* That the *license* of the different components are compatible with one another.

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GitHub

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GitLab
# Open codes

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Archived

Sustainability

* Archived for long-term preservation
  (e.g. using Software Heritage, Zenodo)

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Software Heritage

zenodo

https://zenodo.org/

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Software Heritage

Mission

Archive

Community

Grants

Support us

About

News

Q

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Software is the key

to access information and
a fundamental part of
human heritage

We are building the universal software archive

https://www.softwareheritage.org/
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Documented
Reusability

```yaml
...
|--- CITATION
|--- README
|--- LICENSE
|--- requirements.txt
|--- data
|   -- birds_count_table.csv
|--- doc
|   -- notebook.md
|   -- manuscript.md
|   -- changelog.txt
|--- results
|   -- summarized_results.csv
|--- src
|   -- sightings_analysis.py
|   -- runall.py
```

[Wilson et. al, PlosCompBio 2017]

* Credit authors with varied contributions

* Software development best practices

* Document: naming, commenting, examples

* List dependencies

### Project/Paper Title

### Table of contents

* How to cite?

* Contents overview

* Reproducing figures and tables

* Table 1

* Fig. 1

* Fig. 2

* Reproducing full analysis

### How to cite?

See CITATION.

### Contents overview

<Summarise what's in this repository>

### Reproducing figures and tables

<Instructions on how to use summary/derived data in the results directory to create figures and tables>

<Specify precise steps, including any datasets that need to be downloaded and path variables that need to be set>

### Table 1

Fig. 1

Fig. 2

### Reproducing full analysis

<Instructions on how to (1) obtain raw data; (2) process it to create summary/derived data in the results>

<Specify precise steps, including any datasets that need to be downloaded and path variables that need to be set>
Are my results
(computationally) reproducible now?
Are my results
(computationally) reproducible now?

Not really...
But that's okay!
# Are my results (computationally) reproducible now?

Beyond source code, **environments** (OS, libraries, etc.) are required for re-execution...

→ *docker, Guix, Nix*
# Are my results (computationally) reproducible now?

Beyond source code, **environments** (OS, libraries, etc.) are required for re-execution...

→ **docker**, **Guix**, **Nix**

**Computational reproducibility in 10 years** is still an open question...

Perkel, Jeffrey M. "Challenge to scientists: does your ten-year-old code still run?." *Nature* 584.7822 (2020): 656-659.

## TEN YEARS REPRODUCIBILITY CHALLENGE

RESCIENCE SPECIAL ISSUE
FREE TO READ - FREE TO PUBLISH

Workshop
June 22, 2020
BORDEAUX

<figure><img src="image_130.png" /></figure>

Would you dare to run the
code from your past self ?

(the one that does not answer mail)

SUBMISSION DEADLINE 01/04/2020

http://rescience.github.io/ten-years
In association with Iona, OMS, Software Heritage, Néos科恩, Comité pour la Science Cuveau,
UNIST Bordeaux & Muscat de la Pêche et duNUMÉRIQUE pour l'enseignement supérieur,
Contact: nicolas.rougengenva.fr
# Are my results (computationally) reproducible now?

<figure><img src="image_131.png" /></figure>

Beyond source code, **environments** (OS, libraries, etc.) are required for re-execution...

→ **docker**, **Guix**, **Nix**

**Computational reproducibility in 10 years** is still an open question...

Perkel, Jeffrey M. "Challenge to scientists: does your ten-year-old code still run?." *Nature* 584.7822 (2020): 656-659.

**Computational environment**
*Executable*

## TEN YEARS REPRODUCIBILITY CHALLENGE

RESCIENCE SPECIAL ISSUE
FREE TO READ - FREE TO PUBLISH

Workshop
June 22, 2020

BORDEAUX

<figure><img src="image_132.png" /></figure>

Would you dare to run the
code from your past self ?

(the one that does not answer mail)

SUBMISSION DEADLINE 01/04/2020

http://rescience.github.io/ten-years
In association with Iona, OAS, Software Heritage, Science, Conti pour la Science Cuvert.
UNIST Bordeaux & Muscat de la Pêche et duNUMERIQUE pour l'enseignement supérieur.
Contact: nicolas.rougengenva.fr
# How-to open your code

<figure><img src="image_133.png" /></figure>

**MANDATORY**

Open source +
archived
Transparency

* With an **open source licence** and accessible in a **public forge**.

* Archived for **long-term preservation** (e.g. using Software Heritage, Zenodo)

**RECOMMENDED**

Documented
Reusability

* Crediting authors with varied contributions

* **Documented** (names, ex., dependencies)

**OPTIONAL**

Computational
environment
Executable

* With a **computational environment**.
# Towards reproducible research

**Computational reproducibility**

Ability to reproduce **exactly the same results** using the **same data** and **same code**.

**Replicability**

Ability to reach the **same scientific findings** using
**similar data** and a **similar method**.
# Towards reproducible research

**Computational reproducibility**

Ability to reproduce **exactly the same results** using the **same data** and **same code**.

**Replicability**

Ability to reach the **same scientific findings** using
**similar data** and a **similar method**.

**Reusability**

Ability to reuse some research **artefacts for purposes**
**(secondary use)**
# Towards reproducible research

**Computational reproducibility**

Ability to reproduce **exactly the same results** using the **same data** and **same code**.

**Replicability**

Ability to reach the **same scientific findings** using
**similar data** and a **similar method**.

**Reusability**

Ability to reuse some research **artefacts for purposes**
**(secondary use)**
Going further: collaborate

<figure><img src="image_134.png" /></figure>

Who can access
and use the
software?

<figure><img src="image_135.png" /></figure>

Open source
# Going further: collaborate

<figure><img src="image_136.png" /></figure>

Who can **access** and **use** the software?

<figure><img src="image_137.png" /></figure>

Open source

* Code of conduct

* Set expectations in terms of contributions
# Going further: collaborate

<figure><img src="image_138.png" /></figure>

Who can access and use the software?

<figure><img src="image_139.png" /></figure>

## Open source

* Code of conduct

* Set expectations in terms of contributions

Who can contribute?

<figure><img src="image_140.png" /></figure>

## Open development

* Accept external contributions (e.g. Github PR)

* Be transparent in terms of **development choices** (e.g. issues, project board)
# Going further: collaborate

<figure><img src="image_141.png" /></figure>

Who can access and use the software?

<figure><img src="image_142.png" /></figure>

## Open source

* Code of conduct

* Set expectations in terms of contributions

Who can contribute?

<figure><img src="image_143.png" /></figure>

## Open development

* Accept external contributions (e.g. Github PR)

* Be transparent in terms of **development choices** (e.g. issues, project board)

Who can decide for future directions?

<figure><img src="image_144.png" /></figure>

## Open governance

* Transparency in how decision are made

* Possibility to join the leadership of the project
# The CODE roadmap

Collaborative

Open

Documented

Executable

<figure><img src="image_145.png" /></figure>

## OPEN

* Publish your source code on a public forge

* Save your repository on dedicated archive

* License your code with an open license

* Declare authorship & rightholders

mandatory
mandatory
strongly recommended
recommended

## DOCUMENT

* Choose meaningful names

* Comment code

* Provide examples, notebooks & tutorials

* Describe API

recommended
recommended
recommended
optional

## EXECUTE

* List software & hardware dependencies

* Provide a computational environment

* Implement a test suite

* Show real-life usage example with expected results

recommended
optional
optional
optional

## COLLABORATE

* Respond to issues & feature requests

* Describe maintenance, features & support limits

* Explain how to contribute

* Build and animate a community

optional
optional
optional
optional

<figure><img src="image_146.png" /></figure>

MINISTÈRE
DE L'ENSEIGNEMENT
SUPÉRIEUR
ET DE LA RECHERCHE

Liberté
Égalité
Fraternité

Ouvrir
la science !

(Di Cosmo et al, Nature 2025 & Preprint 2025)
# Towards reproducible research

<figure><img src="image_147.png" /></figure>

Acquisition

<figure><img src="image_148.png" /></figure>

<figure><img src="image_149.png" /></figure>

Pré-traitements

<figure><img src="image_150.png" /></figure>

Données dérivées

<figure><img src="image_151.png" /></figure>

Statistiques

<figure><img src="image_152.png" /></figure>

CODE

<figure><img src="image_153.png" /></figure>

<figure><img src="image_154.png" /></figure>

Open data

(FAIR principles)

<figure><img src="image_155.png" /></figure>

OpenNEURO

Radboud Data
Repository

Public-nEUro

<figure><img src="image_156.png" /></figure>

LORIS

shancir

<figure><img src="image_157.png" /></figure>

Open codes

<figure><img src="image_158.png" /></figure>

Software Heritage

zenodo

<figure><img src="image_159.png" /></figure>

Open access

(pre-prints, diamond open access, etc.)
# Towards reproducible research

<figure><img src="image_160.png" /></figure>

Acquisition

<figure><img src="image_161.png" /></figure>

<figure><img src="image_162.png" /></figure>

Pré-traitements

<figure><img src="image_163.png" /></figure>

Données dérivées

<figure><img src="image_164.png" /></figure>

Statistiques

<figure><img src="image_165.png" /></figure>

CODE

<figure><img src="image_166.png" /></figure>

<figure><img src="image_167.png" /></figure>

Open data

(FAIR principles)

<figure><img src="image_168.png" /></figure>

OpenNEURO

Radboud Data
Repository

Public-nEUro

<figure><img src="image_169.png" /></figure>

LORIS

shancir

<figure><img src="image_170.png" /></figure>

Open codes

<figure><img src="image_171.png" /></figure>

Software Heritage

zenodo

Open access

(pre-prints, diamond open access, etc.)

<figure><img src="image_172.png" /></figure>
<figure><img src="image_173.png" /></figure>

Improving computational
reproducibility or **how-to
share *your* research code**

Camille Maumet

Thank you!

My research is supported by
# Towards reproducible research

<figure><img src="image_174.png" /></figure>

Acquisition

<figure><img src="image_175.png" /></figure>

<figure><img src="image_176.png" /></figure>

Preprocessing

<figure><img src="image_177.png" /></figure>

Données dérivées

<figure><img src="image_178.png" /></figure>

Stats

<figure><img src="image_179.png" /></figure>

<figure><img src="image_180.png" /></figure>

Open access

(pre-prints, diamond open access, etc.)

<figure><img src="image_181.png" /></figure>

<figure><img src="image_182.png" /></figure>

Credits: MRI by Flowicon [Noun Project](CC BY), process by Konkapp [Noun Project](CC-BY), analysis by Siti Solekah [Noun Project](CC-BY), Parcel [PublicDomainPictures](CC0), Git [Wikimedia](CC0)
The ‘FAIR’ principles

<figure><img src="image_183.png" /></figure>
# The ‘FAIR’ principles

<figure><img src="image_184.png" /></figure>

<figure><img src="image_185.png" /></figure>

<figure><img src="image_186.png" /></figure>

OpenNEURO

<figure><img src="image_187.png" /></figure>

LORIS

Donders Repository

<figure><img src="image_188.png" /></figure>

<figure><img src="image_189.png" /></figure>

SHANOIR

<figure><img src="image_190.png" /></figure>

Findable

... deposited in a data repository.
# The ‘FAIR’ principles

<figure><img src="image_191.png" /></figure>

<figure><img src="image_192.png" /></figure>

<figure><img src="image_193.png" /></figure>

OpenNEURO

<figure><img src="image_194.png" /></figure>

LORIS

Donders Repository

<figure><img src="image_195.png" /></figure>

<figure><img src="image_196.png" /></figure>

SHANOIR

<figure><img src="image_197.png" /></figure>

Findable

... deposited in a **data repository**.

<figure><img src="image_198.png" /></figure>
# Data sharing and privacy

Is a brain image anonymous?

<figure><img src="image_199.png" /></figure>

(Open Brain Consent, HBM 2021)
# Data sharing and privacy

## Is a brain image anonymous?

<figure><img src="image_200.png" /></figure>

DICOM
Digital Imaging and Communications in Medicine

Name: White

First Name : Alicia

Date of birth :
10/11/1995

...

(Open Brain Consent, HBM 2021)
# Data sharing and privacy

## Is a brain image anonymous?

<figure><img src="image_201.png" /></figure>

DICOM
Digital Imaging and Communications in Medicine

Name: __________
First Name : __________
Date of birth : __________
...

1. Deleting directly
identifiable infos

(Open Brain Consent, HBM 2021)
# Data sharing and privacy

## Is a brain image anonymous?

<figure><img src="image_202.png" /></figure>

WDICOM

Digital Imaging and Communications in Medicine

Name: [redacted]
First Name: [redacted]

Date of birth: [redacted]

...

1. Deleting directly identifiable infos

<figure><img src="image_203.png" /></figure>

2. Defacing

(Open Brain Consent, HBM 2021)
# Data sharing and privacy

## Is a brain image anonymous?

<figure><img src="image_204.png" /></figure>

DICOM

Digital Imaging and Communications in Medicine

Name: __________
First Name : __________
Date of birth : __________
...

1. Deleting directly identifiable infos

<figure><img src="image_205.png" /></figure>

2. Defacing

(Open Brain Consent, HBM 2021)
# Data sharing and privacy

## Is a brain image anonymous?

<figure><img src="image_206.png" /></figure>

WDICOM
Digital Imaging and Communications in Medicine

Name: __________
First Name : __________

Date of birth : __________

...

1. Deleting directly identifiable infos

<figure><img src="image_207.png" /></figure>

2. Defacing

<figure><img src="image_208.png" /></figure>

Anonymous (USA)

(Open Brain Consent, HBM 2021)
# Data sharing and privacy

## Is a brain image anonymous?

<figure><img src="image_209.png" /></figure>

WTDICOM
Digital Imaging and Communications in Medicine

Name: __________
First Name : __________
Date of birth : __________
...

1. Deleting directly identifiable infos

<figure><img src="image_210.png" /></figure>

2. Defacing

<figure><img src="image_211.png" /></figure>

Anonymous (USA)

<figure><img src="image_212.png" /></figure>

X Personal / non anonymous (EU) →
Individualization

(Open Brain Consent, HBM 2021)

Raw brain images must comply with the
**European General Data Protection Regulation (GDPR)**

<figure><img src="image_213.png" /></figure>
# Data sharing and privacy

## Is a brain image anonymous?

<figure><img src="image_214.png" /></figure>

WDICOM
Digital Imaging and Communications in Medicine

Name: __________
First Name : __________
Date of birth : __________
...

1. Deleting directly identifiable infos

<figure><img src="image_215.png" /></figure>

2. Defacing

<figure><img src="image_216.png" /></figure>

Anonymous (USA)

<figure><img src="image_217.png" /></figure>

X Personal / non anonymous (EU) →
Individualization

(Open Brain Consent, HBM 2021)

Raw brain images must comply with the
**European General Data Protection Regulation (GDPR)**

<figure><img src="image_218.png" /></figure>

OpenNEURO

**FAQ - Are there any restrictions on the uploaded data?**

Yes. By uploading this dataset to OpenNeuro you have to agree to the following conditions: [...]

* This dataset is **not subject to GDPR protections.**

<figure><img src="image_219.png" /></figure>

General
Data
Protection
Regulation
<figure><img src="image_220.png" /></figure>

Which data repository can I use to share?
# Finding a data repository

Which data repository can I use to share?

From the French Open Science committee (“CoSO”)

Unique
id

EU-
based
server
s

Long-
term

...

Ouvrir
la science !

* Thematic data repositories

* Methodology
# Finding a data repository

Which data repository can I use to share?

Ouvrir la science !

From the French Open Science committee (“CoSO”)

Unique
id

EU-
based
server
s

Long-
term

...

* Thematic data repositories

* Methodology

## Repositories for human brain data

- Open download

- Open or restricted deposit

→ 9 data repositories

<figure><img src="image_221.png" /></figure>

Glimr

<figure><img src="image_222.png" /><figcaption>Jérémy Lefort-
Besnard</figcaption></figure>

<figure><img src="image_223.png" /><figcaption>Alexandre
Pron</figcaption></figure>

https://glimr.eu/

(Lefort-Besnard*, Pron*, Aperture Neuro 2025)
# The ‘FAIR’ principles

<figure><img src="image_224.png" /></figure>

<figure><img src="image_225.png" /></figure>

<figure><img src="image_226.png" /></figure>

OpenNEURO

<figure><img src="image_227.png" /></figure>

LORIS

Donders Repository

<figure><img src="image_228.png" /></figure>

XNAT

<figure><img src="image_229.png" /></figure>

SHANOIR

<figure><img src="image_230.png" /></figure>

Findable

... deposited in a data repository
# The ‘FAIR’ principles

<figure><img src="image_231.png" /></figure>

<figure><img src="image_232.png" /></figure>

<figure><img src="image_233.png" /></figure>

OpenNEURO

Donders Repository

<figure><img src="image_234.png" /></figure>

<figure><img src="image_235.png" /></figure>

LORIS

<figure><img src="image_236.png" /></figure>

SHANOIR

<figure><img src="image_237.png" /></figure>

**Findable**

... deposited in a data repository

<figure><img src="image_238.png" /></figure>

**Accessible**

... via **direct download** (e.g. Openneuro) or with **Data Use Agreement** (e.g. for GDPR)
# Data sharing and privacy

<figure><img src="image_239.png" /></figure>

<figure><img src="image_240.png" /></figure>

<figure><img src="image_241.png" /></figure>

<figure><img src="image_242.png" /><figcaption>Cyril Pernet</figcaption></figure>

Copenhagen Uni Hosp
(Denmark)

<caption>Stephan Heunis</caption>

Rsrch Ctr Jülich
(Germany)

## Open Brain Consent RGPD edition

### Consent form

Signed by participants of the
research protocol

"[...] data might also be used for other future research projects in the field of medical and cognitive neuroscience."

### Data Use Agreement

Signed by the scientists who want
to reuse the data

"[...] I will not attempt to [...] retrieve the identity of the study participants."

(Open Brain Consent, HBM 2021)
# Data sharing and privacy

<figure><img src="image_243.png" /></figure>

<figure><img src="image_244.png" /></figure>

<figure><img src="image_245.png" /></figure>

<figure><img src="image_246.png" /><figcaption>Cyril Pernet
Copenhagen Uni Hosp
(Denmark)</figcaption></figure>

<caption>Stephan Heunis
Rsrch Ctr Jülich
(Germany)</caption>

## Open Brain Consent RGPD edition

### Consent form

Signed by participants of the
research protocol

"[...] data might also be used for other future research projects in the field of medical and cognitive neuroscience."

### Data Use Agreement

Signed by the scientists who want
to reuse the data

"[...] I will not attempt to [...] retrieve the identity of the study participants."

<figure><img src="image_247.png" /><figcaption>Anne Hespel
CHU Rennes</figcaption></figure>

<figure><img src="image_248.png" /><figcaption>Elise Bannier
CHU Rennes</figcaption></figure>

French

Translated in 13 languages

Bosnian, Czech, German, Greek, Spanish,
Finnish, French, Italian, Dutch, Norwegian,
Portuguese and Turkish

(Open Brain Consent, HBM 2021)
# The ‘FAIR’ principles

<figure><img src="image_249.png" /></figure>

<figure><img src="image_250.png" /></figure>

<figure><img src="image_251.png" /></figure>

OpenNEURO

Donders Repository

<figure><img src="image_252.png" /></figure>

<figure><img src="image_253.png" /></figure>

LORIS

<figure><img src="image_254.png" /></figure>

SHANOIR

<figure><img src="image_255.png" /></figure>

**Findable**

... deposited in a data repository

<figure><img src="image_256.png" /></figure>

**Accessible**

... via **direct download** (e.g. Openneuro) or with **Data Use Agreement** (e.g. for GDPR)
# The ‘FAIR’ principles

<figure><img src="image_257.png" /></figure>

<figure><img src="image_258.png" /></figure>

OpenNEURO

Donders Repository

<figure><img src="image_259.png" /></figure>

XNAT

<figure><img src="image_260.png" /></figure>

LORIS

<figure><img src="image_261.png" /></figure>

SHANOIR

<figure><img src="image_262.png" /></figure>

**Findable**

... deposited in a data repository

<figure><img src="image_263.png" /></figure>

**Interoperable**

... using existing **formats and standards**

<figure><img src="image_264.png" /></figure>

**Accessible**

... via direct download (e.g. Openneuro) or with **Data Use Agreement** (e.g. for GDPR)
<figure><img src="image_265.png" /></figure>

<figure><img src="image_266.png" /><figcaption>Chris
Gorgolewski
Stanford Uni. (USA)</figcaption></figure>

<figure><img src="image_267.png" /></figure>

**BIDS**
BRAIN IMAGING DATA STRUCTURE

**Brain Imaging Data Structure**

Naming convention + JSON files

<figure><img src="image_268.png" /></figure>

my_dataset/

<figure><img src="image_269.png" /></figure>

participants.csv

<figure><img src="image_270.png" /></figure>

sub-01/

<figure><img src="image_271.png" /></figure>

anat/

<figure><img src="image_272.png" /></figure>

sub-01_T1w.nii.gz

<figure><img src="image_273.png" /></figure>

func/

<figure><img src="image_274.png" /></figure>

sub-01_task-rest bold.nii.gz

<figure><img src="image_275.png" /></figure>

sub-01_task-rest bold.json

<figure><img src="image_276.png" /></figure>

dwi/

<figure><img src="image_277.png" /></figure>

sub-01_dwi.nii.gz

<figure><img src="image_278.png" /></figure>

sub-01_dwi.json

<figure><img src="image_279.png" /></figure>

sub-01_dwi.bval

<figure><img src="image_280.png" /></figure>

sub-01_dwi.bvec

<figure><img src="image_281.png" /></figure>

sub-02/

<figure><img src="image_282.png" /></figure>

sub-03/

>1 million data in BIDS
in 2024

Source: [MRIQC Api](https://api.mriqc.org)

(Gorgolewski, Sci. Data 2016)
<figure><img src="image_283.png" /></figure>

<figure><img src="image_284.png" /><figcaption>Chris
Gorgolewski
Stanford Uni. (USA)</figcaption></figure>

<figure><img src="image_285.png" /></figure>

BIDS
BRAIN IMAGING DATA STRUCTURE

Brain Imaging Data Structure

Naming convention + JSON files

<figure><img src="image_286.png" /></figure>

my_dataset/

<figure><img src="image_287.png" /></figure>

participants.tsv

<figure><img src="image_288.png" /></figure>

sub-01/

<figure><img src="image_289.png" /></figure>

anat/

<figure><img src="image_290.png" /></figure>

sub-01_T1w.nii.gz

<figure><img src="image_291.png" /></figure>

func/

<figure><img src="image_292.png" /></figure>

sub-01_task-rest bold.nii.gz

<figure><img src="image_293.png" /></figure>

sub-01_task-rest bold.json

<figure><img src="image_294.png" /></figure>

dwi/

<figure><img src="image_295.png" /></figure>

sub-01_dwi.nii.gz

<figure><img src="image_296.png" /></figure>

sub-01_dwi.json

<figure><img src="image_297.png" /></figure>

sub-01_dwi.bval

<figure><img src="image_298.png" /></figure>

sub-01_dwi.bvec

<figure><img src="image_299.png" /></figure>

sub-02/

<figure><img src="image_300.png" /></figure>

sub-03/

>1 million data in BIDS
in 2024

Source: [MRIQC Api](https://api.mriqc.org)

(Gorgolewski, Sci. Data 2016)

• For other domains?

FAIR sharing.org
standards, databases, policies
# The ‘FAIR’ principles

<figure><img src="image_301.png" /></figure>

<figure><img src="image_302.png" /></figure>

<figure><img src="image_303.png" /></figure>

<figure><img src="image_304.png" /></figure>

<figure><img src="image_305.png" /></figure>

OpenNEURO

<figure><img src="image_306.png" /></figure>

LORIS

Donders Repository

<figure><img src="image_307.png" /></figure>

<figure><img src="image_308.png" /></figure>

SHANOIR

<figure><img src="image_309.png" /></figure>

Findable

... deposited in a data repository

<figure><img src="image_310.png" /></figure>

Interoperable

... using existing formats and standards

<figure><img src="image_311.png" /></figure>

Accessible

... via direct download (e.g. Openneuro) or with Data Use Agreement (e.g. for GDPR)
# The ‘FAIR’ principles

<figure><img src="image_312.png" /></figure>

<figure><img src="image_313.png" /></figure>

<figure><img src="image_314.png" /></figure>

<figure><img src="image_315.png" /></figure>

<figure><img src="image_316.png" /></figure>

OpenNEURO

<figure><img src="image_317.png" /></figure>

LORIS

Donders Repository

<figure><img src="image_318.png" /></figure>

<figure><img src="image_319.png" /></figure>

SHANOIR

<figure><img src="image_320.png" /></figure>

**Findable**

... deposited in a data repository

<figure><img src="image_321.png" /></figure>

**Interoperable**

... using existing formats and standards

<figure><img src="image_322.png" /></figure>

**Accessible**

... via direct download (e.g. Openneuro) or with Data Use Agreement (e.g. for GDPR)

<figure><img src="image_323.png" /></figure>

**Reusable**

... with **sufficient metadata** to enable reuse
# The ‘FAIR’ principles

<figure><img src="image_324.png" /></figure>

<figure><img src="image_325.png" /></figure>

<figure><img src="image_326.png" /></figure>

<figure><img src="image_327.png" /></figure>

<figure><img src="image_328.png" /></figure>

OpenNEURO

<figure><img src="image_329.png" /></figure>

LORIS

Donders Repository

<figure><img src="image_330.png" /></figure>

<figure><img src="image_331.png" /></figure>

SHANOIR

Findable, Accessible, Interoperable and Reusable

<figure><img src="image_332.png" /></figure>

**Findable**

... deposited in a **data repository**

<figure><img src="image_333.png" /></figure>

**Interoperable**

... using existing **formats and standards**

<figure><img src="image_334.png" /></figure>

**Accessible**

... via **direct download** (e.g. Openneuro) or with **Data Use Agreement** (e.g. for GDPR)

<figure><img src="image_335.png" /></figure>

**Reusable**

... with **sufficient metadata** to enable reuse