# Data sharing: towards large open datasets in brain imaging

Camille Maumet

<figure><img src="image_1.png" /></figure>

## To cite this version:

Camille Maumet. Data sharing: towards large open datasets in brain imaging. IABM 2024 - Colloque Français d'Intelligence Artificielle en Imagerie Biomédicale, Mar 2024, Grenoble, France. pp.1-42, 2024. [hal-04534429](https://hal-04534429)

HAL Id: hal-04534429

https://inria.hal.science/hal-04534429

Submitted on 5 Apr 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>
# Data sharing: towards large open datasets in brain imaging

Camille Maumet

<figure><img src="image_1.png" /></figure>

## To cite this version:

Camille Maumet. Data sharing: towards large open datasets in brain imaging. IABM 2024 - Colloque Français d'Intelligence Artificielle en Imagerie Biomédicale, Mar 2024, Grenoble, France. pp.1-42, 2024. [hal-04534429](https://hal-04534429v1)

HAL Id: hal-04534429

https://inria.hal.science/hal-04534429v1

Submitted on 5 Apr 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

Partage de données : vers de larges bases **de données ouvertes** en neuroimagerie
—
Data sharing: towards large **open datasets** in brain imaging

Camille Maumet

Inria, Univ Rennes, Inserm, CNRS, IRISA

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>
<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

Partage de données : vers de larges bases **de données ouvertes** en neuroimagerie
—
Data sharing: towards large **open datasets** in brain imaging

Camille Maumet

Inria, Univ Rennes, Inserm, CNRS, IRISA

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>
# Reproducible research

<figure><img src="image_7.png" /></figure>
# Reproducible research

<figure><img src="image_7.png" /></figure>
# Reproducible research

## Original study

<figure><img src="image_8.png" /></figure>
# Reproducible research

## Original study

<figure><img src="image_8.png" /></figure>
# Reproducible research

## Original study

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>
# Reproducible research

## Original study

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>
# Reproducible research

## Original study

<figure><img src="image_11.png" /></figure>

Data

<figure><img src="image_12.png" /></figure>

Results

<figure><img src="image_13.png" /></figure>

‡ Analysis

‡ Data

<figure><img src="image_14.png" /></figure>

Results

<figure><img src="image_15.png" /></figure>
# Reproducible research

## Original study

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>
# Reproducible research

## Original study

<figure><img src="image_16.png" /></figure>

<figure><img src="image_17.png" /></figure>
# Reproducible research

## Original study

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>
# Reproducible research

<figure><img src="image_18.png" /></figure>

Original study

Data

Analysis

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

Results

Did we understand
the method
correctly?

... or is this due to
my use of a different
dataset?

... a different
computing platform?

... something
else!?

Which release of
SPM was used?

Which registration
algorithm was
selected?

How was the brain
mask computed?

Hum... I can't
reproduce the original
results...

≠ Analysis

<figure><img src="image_20.png" /></figure>

≠ Data

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

Results

<figure><img src="image_22.png" /></figure>
# Reproducible research

## Original study

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

Data

Analysis

<figure><img src="image_16.png" /></figure>

Results

Did we understand
the method
correctly?

Which release of
SPM was used?

Which registration
algorithm was
selected?

... or is this due to
my use of a different
dataset?

How was the brain
mask computed?

... a different
computing platform?

... something
else!?

Hum... I can't
reproduce the original
results...

<figure><img src="image_17.png" /></figure>

≠ Analysis

≠ Data

<figure><img src="image_18.png" /></figure>

Results

<figure><img src="image_19.png" /></figure>
# Reproducible research

Original study

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

Data

<figure><img src="image_24.png" /></figure>

Results

same data

<figure><img src="image_25.png" /></figure>

different data

Reproductions

<figure><img src="image_26.png" /></figure>

Data

<figure><img src="image_27.png" /></figure>

Results

<figure><img src="image_28.png" /></figure>

Data

<figure><img src="image_29.png" /></figure>

Results

Computational
Reproducibility

<figure><img src="image_30.png" /></figure>

≠ Data

<figure><img src="image_31.png" /></figure>

Results

<figure><img src="image_32.png" /></figure>

≠ Data

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

Results

same analysis

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

different analysis

Replicability
# Reproducible research

## Original study

<figure><img src="image_20.png" /></figure>

Data

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

Results

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

## Reproductions

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

Data

<figure><img src="image_24.png" /></figure>

Results

<figure><img src="image_25.png" /></figure>

Data

<figure><img src="image_26.png" /></figure>

Results

**Computational Reproducibility**

<figure><img src="image_27.png" /></figure>

≠ Data

<figure><img src="image_28.png" /></figure>

Results

<figure><img src="image_29.png" /></figure>

≠ Data

<figure><img src="image_30.png" /></figure>

Results

**Replicability**

same analysis

<figure><img src="image_31.png" /></figure>

different analysis
<figure><img src="image_35.png" /></figure>

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

<figure><img src="image_37.png" /></figure>
<figure><img src="image_32.png" /></figure>

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

<figure><img src="image_34.png" /></figure>
# Reproducible research

## Original study

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

Data

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

Results

same data

different data

different analysis

## Reproductions

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

Data

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

Results

<figure><img src="image_42.png" /></figure>

Data

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

Results

**Computational Reproducibility**

<figure><img src="image_44.png" /></figure>

≠ Data

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

Results

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

≠ Data

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

Results

**Replicability**

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

same analysis

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

different analysis
# Reproducible research

## Original study

<figure><img src="image_35.png" /></figure>

Data

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

Results

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

same analysis

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

different analysis

## Reproductions

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

Data

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

Results

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

Data

<figure><img src="image_42.png" /></figure>

Results

**Computational Reproducibility**

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

≠ Data

<figure><img src="image_44.png" /></figure>

Results

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

≠ Data

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

Results

**Replicability**

<figure><img src="image_47.png" /></figure>
# Fixing reproducibility for different data

Small samples

Low statistical power

Power of neuroscience studies

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

(Button, Nat. Rev. Neurosci. 2013)

High rate of **false positives** in
the literature
# Fixing reproducibility for different data

Small samples

Low statistical power

Power of neuroscience studies

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

(Button, Nat. Rev. Neurosci. 2013)

High rate of **false positives** in
the literature
# Fixing reproducibility for different data

Small samples

Low statistical power

Power of neuroscience studies

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

(Button, Nat. Rev. Neurosci. 2013)

High rate of **false positives** in
the literature

Lack of representativity and
diversity of the samples

X-ray: Lung opacity detection

Model trained on male images, tested on female images

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

(Larrazabal, PNAS 2020)

Lack of **generalisability** and
**fairness**
# Fixing reproducibility for different data

Small samples

Low statistical power

Power of neuroscience studies

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

(Button, Nat. Rev. Neurosci. 2013)

High rate of **false positives** in
the literature

Lack of representativity and
diversity of the samples

X-ray: Lung opacity detection

Model trained on male images, tested on female images

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

(Larrazabal, PNAS 2020)

Lack of **generalisability** and
**fairness**
# Fixing reproducibility for different data

Small samples

Low statistical power

Power of neuroscience studies

<figure><img src="image_53.png" /></figure>

(Button, Nat. Rev. Neurosci. 2013)

High rate of **false positives** in
the literature

<figure><img src="image_54.png" /></figure>

**Solution: Data Sharing**

Lack of representativity and
diversity of the samples

X-ray: Lung opacity detection

Model trained on male images, tested on female images

<figure><img src="image_55.png" /></figure>

(Larrazabal, PNAS 2020)

Lack of **generalisability** and
**fairness**

<figure><img src="image_56.png" /></figure>
# Fixing reproducibility for different data

Small samples

Low statistical power

Power of neuroscience studies

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

(Button, Nat. Rev. Neurosci. 2013)

High rate of **false positives** in
the literature

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

**Solution: Data Sharing**

Lack of representativity and
diversity of the samples

X-ray: Lung opacity detection

Model trained on male images, tested on female images

<figure><img src="image_53.png" /></figure>

(Larrazabal, PNAS 2020)

Lack of **generalisability** and
**fairness**

<figure><img src="image_54.png" /></figure>
# Neuroimaging data sharing

Single study

30 sub.

<figure><img src="image_57.png" /></figure>

OpenNEURO

<figure><img src="image_58.png" /></figure>

NEUROVAULT

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

NITRC

<figure><img src="image_60.png" /></figure>

OSF
# Neuroimaging data sharing

Single study

30 sub.

<figure><img src="image_55.png" /></figure>

OpenNEURO

<figure><img src="image_56.png" /></figure>

NEUROVAULT

<figure><img src="image_57.png" /></figure>

NITRC

<figure><img src="image_58.png" /></figure>

OSF
# Neuroimaging data sharing

Single study

30 sub.

<figure><img src="image_61.png" /></figure>

OpenNEURO

<figure><img src="image_62.png" /></figure>

NEUROVAULT

<figure><img src="image_63.png" /></figure>

NITRC

<figure><img src="image_64.png" /></figure>

OSF

Consortium

1000 sub.

<figure><img src="image_65.png" /></figure>

ABIDE

Autism Brain Imaging
Data Exchange

<figure><img src="image_66.png" /></figure>

CORR

CONSORTium FOR
RELIABILITY AND
REPRODUCIBILITY

1000 Functional

Connectomes Project

<figure><img src="image_67.png" /></figure>
# Neuroimaging data sharing

Single study

30 sub.

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

OpenNEURO

<figure><img src="image_60.png" /></figure>

NEUROVAULT

<figure><img src="image_61.png" /></figure>

NITRC

<figure><img src="image_62.png" /></figure>

OSF

Consortium

1000 sub.

<figure><img src="image_63.png" /></figure>

ABIDE

Autism Brain Imaging
Data Exchange

<figure><img src="image_64.png" /></figure>

CORR

CONSORTium FOR
RELIABILITY AND
REPRODUCIBILITY

1000 Functional

Connectomes Project

<figure><img src="image_65.png" /></figure>
# Neuroimaging data sharing

Single study

30 sub.

<figure><img src="image_68.png" /></figure>

<figure><img src="image_69.png" /></figure>

NEUROVAULT

<figure><img src="image_70.png" /></figure>

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

OSF

Consortium

1000 sub.

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

ABIDE

Autism Brain Imaging
Data Exchange

1000 Functional
Connectomes Project

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

CORR

CONSORTium for
RELIABILITY AND
REPRODUCIBILITY

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

Cohort

100 000 sub.

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

HUMAN
Connectome
PROJECT

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

Adolescent Brain Cognitive Development®
Teens Brains. Today's Science. Brighter Futures.

biobank®
Improving the health of future generations

++ participants

++ homogeneous

-- instances
# Neuroimaging data sharing

Single study

30 sub.

<figure><img src="image_66.png" /></figure>

OpenNEURO

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

NEUROVAULT

<figure><img src="image_68.png" /></figure>

NITRC

<figure><img src="image_69.png" /></figure>

OSF

Consortium

1000 sub.

<figure><img src="image_70.png" /></figure>

ABIDE

Autism Brain Imaging
Data Exchange

ADHD
200

CORR

CONSORTium for
RELIABILITY AND
REPRODUCIBILITY

1000 Functional
Connectomes Project

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

Cohort

100 000 sub.

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

HUMAN
Connectome
PROJECT

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

Adolescent Brain Cognitive Development
Teens Brains. Today's Science. Brighter Futures.

biobank®

++ participants

++ homogeneous

-- instances
Neuroimaging data sharing

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

(Naselaris, Curr. Opin. Behav. Sci. 2021)
Neuroimaging data sharing

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

(Naselaris, Curr. Opin. Behav. Sci. 2021)
<figure><img src="image_78.png" /></figure>

# Opening up neuroimaging data
<figure><img src="image_75.png" /></figure>

# Opening up neuroimaging data
# Sharing FAIR datasets

<figure><img src="image_79.png" /></figure>
# Sharing FAIR datasets

<figure><img src="image_76.png" /></figure>
# Sharing FAIR datasets

<figure><img src="image_80.png" /></figure>

<figure><img src="image_81.png" /></figure>

<figure><img src="image_82.png" /></figure>

**Findable** we can search for
open datasets in common
repositories
# Sharing FAIR datasets

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

<figure><img src="image_78.png" /></figure>

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

**Findable** we can search for
open datasets in common
repositories
# Sharing FAIR datasets

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

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

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

**Findable** we can search for open datasets in common repositories

<figure><img src="image_86.png" /></figure>

**Accessible** Direct download (e.g. Openneuro) or with Data User Agreement (e.g. Donders)
# Sharing FAIR datasets

<figure><img src="image_80.png" /></figure>

<figure><img src="image_81.png" /></figure>

<figure><img src="image_82.png" /></figure>

**Findable** we can search for open datasets in common repositories

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

**Accessible** Direct download (e.g. Openneuro) or with Data User Agreement (e.g. Donders)
# Data sharing and privacy

## Are neuroimages anonymous?

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

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

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

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

<figure><img src="image_91.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

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

## Are neuroimages anonymous?

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

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

<figure><img src="image_86.png" /></figure>

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

<figure><img src="image_88.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>
# Data sharing and privacy

## Are neuroimages anonymous?

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

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

Name: Depont
First : Nathalie
Birth date : 10/11/1995
...

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

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

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

<figure><img src="image_97.png" /></figure>

Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)

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

## Are neuroimages anonymous?

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

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

Name: Depont
First : Nathalie
Birth date : 10/11/1995
...

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

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

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

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

Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)

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

## Are neuroimages anonymous?

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

DICOM
Digital Imaging and Communications in Medicine

Name:

First :

Birth date :

...

1. Removing directly identifiable information

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

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

<figure><img src="image_101.png" /></figure>

<figure><img src="image_102.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

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

## Are neuroimages anonymous?

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

DICOM
Digital Imaging and Communications in Medicine

Name:

First :

Birth date :

...

1. Removing directly identifiable information

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

<figure><img src="image_97.png" /></figure>

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

<figure><img src="image_99.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

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

## Are neuroimages anonymous?

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

DICOM
Digital Imaging and Communications in Medicine

Name:

First :

Birth date :

...

1. Removing directly identifiable information

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

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

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

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

<figure><img src="image_108.png" /><figcaption>Cyril Pernet Stephan Heunis</figcaption></figure>

Copenhagen Uni HospRsrch Ctr Jülich,

(Denmark)

(Germany)

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

## Are neuroimages anonymous?

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

DICOM
Digital Imaging and Communications in Medicine

Name:

First :

Birth date :

...

1. Removing directly identifiable information

<figure><img src="image_101.png" /></figure>

<figure><img src="image_102.png" /></figure>

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

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

<figure><img src="image_105.png" /><figcaption>Cyril Pernet Stephan Heunis</figcaption></figure>

Copenhagen Uni HospRsrch Ctr Jülich,

(Denmark)

(Germany)

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

## Are neuroimages anonymous?

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

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

Name:
First :
Birth date :
...

1. Removing directly identifiable information

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

2. Defacing

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

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

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

<figure><img src="image_115.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

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

## Are neuroimages anonymous?

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

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

Name:

First :

Birth date :

...

1. Removing directly identifiable information

<figure><img src="image_108.png" /></figure>

2. Defacing

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

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

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

<figure><img src="image_112.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

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

## Are neuroimages anonymous?

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

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

Name:

First :

Birth date :

...

1. Removing directly identifiable information

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

2. Defacing

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

<figure><img src="image_120.png" /></figure>

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

<figure><img src="image_122.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

<figure><img src="image_123.png" /></figure>

Anonymous (USA)
# Data sharing and privacy

## Are neuroimages anonymous?

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

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

Name:

First :

Birth date :

...

1. Removing directly identifiable information

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

2. Defacing

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

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

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

<figure><img src="image_119.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

<figure><img src="image_120.png" /></figure>

Anonymous (USA)
# Data sharing and privacy

## Are neuroimages anonymous?

<figure><img src="image_124.png" /></figure>

DICOM
Digital Imaging and Communications in Medicine

Name:

First :

Birth date :

...

1. Removing directly identifiable information

<figure><img src="image_125.png" /></figure>

2. Defacing

<figure><img src="image_126.png" /></figure>

Anonymous (USA)

<figure><img src="image_127.png" /></figure>

Not anonymous (EU)

General Data Protection Regulation (GDPR) → Individualisation

<figure><img src="image_128.png" /></figure>

<figure><img src="image_129.png" /></figure>

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

Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)
# Data sharing and privacy

## Are neuroimages anonymous?

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

DICOM
Digital Imaging and Communications in Medicine

Name:
First :
Birth date :

...

1. Removing directly identifiable information

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

2. Defacing

<figure><img src="image_123.png" /></figure>

Anonymous (USA)

<figure><img src="image_124.png" /></figure>

Not anonymous (EU)

General Data Protection Regulation (GDPR) → Individualisation

<figure><img src="image_125.png" /></figure>

<figure><img src="image_126.png" /></figure>

<figure><img src="image_127.png" /></figure>

Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)

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

## Are neuroimages anonymous?

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

DICOM
Digital Imaging and Communications in Medicine

Name:

First :

Birth date :

...

1. Removing directly identifiable information

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

2. Defacing

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

Anonymous (USA)

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

Not anonymous (EU)

General Data Protection Regulation (GDPR) → Individualisation

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

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

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

<figure><img src="image_138.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

## Open Brain Consent GDPR edition

### Consent form

Signed by participants

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

### Data User Agreement

Signed by researchers

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

(Open Brain Consent, HBM 2021)

French

<figure><img src="image_139.png" /><figcaption>Anne Hespel
CHU Rennes</figcaption></figure>

<figure><img src="image_140.png" /><figcaption>Elise Bannier
CHU Rennes</figcaption></figure>

13 languages: Bosnian, Czech, German, Greek, Spanish, Finnish, French, Italian, Dutch, Norwegian, Portuguese, Turkish
# Data sharing and privacy

## Are neuroimages anonymous?

<figure><img src="image_128.png" /></figure>

DICOM
Digital Imaging and Communications in Medicine

Name:
First :
Birth date :
...

1. Removing directly identifiable information

<figure><img src="image_129.png" /></figure>

2. Defacing

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

Anonymous (USA)

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

Not anonymous (EU)

General Data Protection Regulation (GDPR) → Individualisation

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

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

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

<figure><img src="image_135.png" /><figcaption>Cyril Pernet Stephan Heunis
Copenhagen Uni HospRsrch Ctr Jülich,
(Denmark) (Germany)</figcaption></figure>

## Open Brain Consent GDPR edition

### Consent form

Signed by participants

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

### Data User Agreement

Signed by researchers

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

(Open Brain Consent, HBM 2021)

French

<figure><img src="image_136.png" /><figcaption>Anne Hespel
CHU Rennes</figcaption></figure>

<figure><img src="image_137.png" /><figcaption>Elise Bannier
CHU Rennes</figcaption></figure>

**13 languages:** Bosnian, Czech, German, Greek, Spanish, Finnish, French, Italian, Dutch, Norwegian, Portuguese, Turkish
# Sharing FAIR datasets

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

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

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

**Interoperable?**

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

**Findable** we can search for
open datasets in common
repositories

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

**Accessible** Direct download
(e.g. Openneuro) or with Data
User Agreement (e.g.
Donders)
# Sharing FAIR datasets

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

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

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

Interoperable?

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

**Findable** we can search for
open datasets in common
repositories

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

**Accessible** Direct download
(e.g. Openneuro) or with Data
User Agreement (e.g. Donders)
# Standards for data sharing

* Data and **meta-data**

* A common “language”

<figure><img src="image_146.png" /></figure>
# Standards for data sharing

* Data and **meta-data**

* A common “language”

<figure><img src="image_143.png" /></figure>
# Community standardization efforts

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

<figure><img src="image_148.png" /><figcaption>Chris
Gorgolewski
Stanford Uni. (USA)</figcaption></figure>

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

BIDS
BRAIN IMAGING DATA STRUCTURE

## Brain Imaging Data Structure

File naming conventions + JSON sidecars

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

>1 million BIDS-compliant
images in 2024

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

(Gorgolewski, Sci. Data 2016)
# Community standardization efforts

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

<figure><img src="image_145.png" /><figcaption>Chris
Gorgolewski
Stanford Uni. (USA)</figcaption></figure>

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

BIDS
BRAIN IMAGING DATA STRUCTURE

## Brain Imaging Data Structure

File naming conventions + JSON sidecars

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

>1 million BIDS-compliant
images in 2024

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

(Gorgolewski, Sci. Data 2016)
<figure><img src="image_151.png" /><figcaption># BIDS history timeline</figcaption></figure>

(Poldrack, Imaging Neuroscience 2024)
<figure><img src="image_148.png" /><figcaption># BIDS history timeline</figcaption></figure>

(Poldrack, Imaging Neuroscience 2024)
# Extending BIDS

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

## BIDS maintainers

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

## BIDS steering

<figure><img src="image_154.png" /></figure>
# Extending BIDS

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

## BIDS maintainers

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

## BIDS steering

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

https://bids-extensions.readthedocs.io/en/latest/guide/
# Sharing FAIR datasets

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

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

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

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

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

OpenNEURO

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

LORIS

Donders Repository

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

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

SHANOIR

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

Interoperable?

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

**Findable** we can search for open datasets in common repositories

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

**Accessible** Direct download (e.g. Openneuro) or with Data User Agreement (e.g. Donders)
# Sharing FAIR datasets

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

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

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

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

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

OpenNEURO

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

LORIS

Donders Repository

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

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

SHANOIR

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

Interoperable?

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

**Findable** we can search for open datasets in common repositories

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

**Accessible** Direct download (e.g. Openneuro) or with Data User Agreement (e.g. Donders)
# Sharing FAIR datasets

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

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

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

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

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

OpenNEURO

Donders Repository

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

XNAT

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

LORIS

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

SHANOIR

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

**Interoperable** BIDS can act
as a common languages
across tools

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

**Findable** we can search for
open datasets in common
repositories

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

**Accessible** Direct download
(e.g. Openneuro) or with Data
User Agreement (e.g.
Donders)
# Sharing FAIR datasets

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

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

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

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

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

OpenNEURO

Donders Repository

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

XNAT

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

LORIS

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

SHANOIR

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

**Interoperable** BIDS can act
as a common languages
across tools

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

**Findable** we can search for
open datasets in common
repositories

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

**Accessible** Direct download
(e.g. Openneuro) or with Data
User Agreement (e.g.
Donders)
# Sharing FAIR datasets

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

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

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

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

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

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

Donders Repository

<figure><img src="image_183.png" /></figure>

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

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

**Interoperable** BIDS can act
as a common language
across tools

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

**Findable** we can search for
open datasets in common
repositories

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

**Reusable** Metadata in BIDS
were selected to enable
reuse. e.g. onsets of the task
for task-based fMRI.

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

**Accessible** Direct download
(e.g. Openneuro) or with Data
User Agreement (e.g.
Donders)
# Sharing FAIR datasets

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

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

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

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

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

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

Donders Repository

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

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

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

**Interoperable** BIDS can act
as a common language
across tools

<figure><img src="image_183.png" /></figure>

**Findable** we can search for
open datasets in common
repositories

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

**Reusable** Metadata in BIDS
were selected to enable
reuse. e.g. onsets of the task
for task-based fMRI.

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

**Accessible** Direct download
(e.g. Openneuro) or with Data
User Agreement (e.g.
Donders)
# Sharing FAIR datasets

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

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

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

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

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

OpenNEURO

Donders Repository

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

XNAT

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

LORIS

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

SHANOIR

**Findable** **Accessible** **Interoperable** **Reusable**

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

**Interoperable** BIDS can act
as a common languages
across tools

<figure><img src="image_198.png" /></figure>

**Findable** we can search for
open datasets in common
repositories

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

**Reusable** Metadata in BIDS
were selected to enable
reuse. e.g. onsets of the task
for task-based fMRI.

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

**Accessible** Direct download
(e.g. Openneuro) or with Data
User Agreement (e.g.
Donders)
# Sharing FAIR datasets

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

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

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

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

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

OpenNEURO

Donders Repository

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

XNAT

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

LORIS

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

SHANOIR

**Findable** **Accessible** **Interoperable** **Reusable**

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

**Interoperable** BIDS can act
as a common languages
across tools

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

**Findable** we can search for
open datasets in common
repositories

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

**Reusable** Metadata in BIDS
were selected to enable
reuse. e.g. onsets of the task
for task-based fMRI.

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

**Accessible** Direct download
(e.g. Openneuro) or with Data
User Agreement (e.g.
Donders)
<figure><img src="image_201.png" /></figure>

**More on reproducibility...**
<figure><img src="image_198.png" /></figure>

**More on reproducibility...**
# Reproducible research

## Original study

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

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

## Reproductions

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

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

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

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

same analysis

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

different analysis

Replicability
# Reproducible research

## Original study

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

Data

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

Results

same data

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

different data

## Reproductions

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

Data

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

Results

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

Data

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

Results

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

**Computational Reproducibility**

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

≠ Data

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

Results

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

≠ Data

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

Results

same analysis

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

**Replicability**

different analysis
# Dealing with analytical variability

## Multiverse analyses

b

Unique
Dataset

Multiverse
pipelines

Per pipeline
result

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

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

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

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

<figure><img src="image_213.png" /></figure>

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

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

Same-data
meta-analysis
result

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

<figure><img src="image_217.png" /><figcaption>Jérémy
Lefort-Besnard</figcaption></figure>

(Lefort-Besnard, OHBM 2024)

## Leveraging large and
open datasets

<figure><img src="image_218.png" /><figcaption>Elodie
Germani</figcaption></figure>

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

Original

Encoder

<figure><img src="image_220.png" /></figure>

Latent
space

Decoder

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

<figure><img src="image_222.png" /></figure>

Reconstructed

<figure><img src="image_223.png" /></figure>

(Germani, Gigascience 2023)
# Dealing with analytical variability

## Multiverse analyses

b

Unique
Dataset

Multiverse
pipelines

Per pipeline
result

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

<figure><img src="image_213.png" /></figure>

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

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

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

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

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

Same-data
meta-analysis
result

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

<figure><img src="image_220.png" /><figcaption>Jérémy
Lefort-Besnard</figcaption></figure>

(Lefort-Besnard, OHBM 2024)

## Leveraging large and
open datasets

<figure><img src="image_221.png" /><figcaption>Elodie
Germani</figcaption></figure>

<figure><img src="image_222.png" /></figure>

Original

Encoder

<figure><img src="image_223.png" /></figure>

Latent
space

Decoder

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

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

Reconstructed

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

(Germani, Gigascience 2023)
<figure><img src="image_224.png" /></figure>

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

**Supported by:** Inria Aex, Région Bretagne, ANR JCJC

**Credit:** Presentation template and icons by [SlidesCarnival](https:// slidescarnival.com), adapted

Data sharing towards
building large **open**
**datasets** in brain imaging

Camille Maumet

Thank you!

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

@cmaumet@fediscience.org

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

@cmaumet.bsky.social
<figure><img src="image_227.png" /></figure>

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

**Supported by:** Inria Aex, Région Bretagne, ANR JCJC

**Credit:** Presentation template and icons by [SlidesCarnival](https:// slidescarnival.com), adapted

Data sharing towards
building large **open**
**datasets** in brain imaging

Camille Maumet

Thank you!

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

@cmaumet@fediscience.org

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

@cmaumet.bsky.social