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HAL Id: inserm-02986992

https://www.hal.inserm.fr/inserm-02986992

Submitted on 3 Nov 2020

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.

Sharing more than research papers for transparent &

reusable research

Camille Maumet

To cite this version:

Camille Maumet. Sharing more than research papers for transparent & reusable research. 2020 -Workshop “Open and reproducible neuroimaging”, Nov 2020, Oldenburg (online), Germany. pp.1-39. �inserm-02986992�

(2)

Camille Maumet

Univ Rennes, Inria, CNRS, Inserm

@cmaumet

more than

research papers

Workshop “Open and reproducible neuroimaging”

(3)

Statistical analysis

Preprocessing

(4)

Statistical analysis

Preprocessing

(5)

Incomplete reporting

(6)

Hard to summarize the

literature

Incomplete reporting

Difficult to build on

existing work

(7)

Hard to summarize the

literature

Low sample sizes

Incomplete reporting

Difficult to build on

existing work

(8)

Hard to summarize the

literature

Low sample sizes

Incomplete reporting

Difficult to build on

existing work

Unreliability

Lack of diversity

(9)

Hard to summarize the

literature

Low sample sizes

Incomplete reporting

Difficult to build on

prior work

Unreliability

Lack of diversity

We need bigger, more

representative and

diverse samples

enough details to

enable reuse

(10)

Sharing

(11)

Statistical analysis

Preprocessing

(12)

Paper

Peak locations

Figure

(selected slices)

Thresholded

statistics

(13)

Paper

Peak locations

Figure

(selected slices)

Thresholded

statistics

❌ Incomplete statistical results

❌ Ambiguous/incomplete methods

❌ Metadata is not searchable

(14)

(15)
(16)

NIDM-Results

.nidm.zip

[Maumet et al.,

Sci. Data 2016]

(17)
(18)

Data reuse

(19)

Statistical analysis

Preprocessing

(20)

Statistical analysis

Preprocessing

Derived data

(21)

Sharing

(22)

Statistical analysis

Preprocessing

Derived data

(23)

Statistical analysis

Preprocessing

Derived data

(24)

Statistical analysis

Preprocessing

Derived data

NIDM

+ NIDM-Terms

NIDM-Terms: A Community-Driven

Controlled Vocabulary of Brain

Initiative Imaging Experiments

(25)

Statistical analysis

Preprocessing

Derived data

NIDM

+ NIDM-Terms

NIDM-Terms: A Community-Driven

Controlled Vocabulary of Brain

Initiative Imaging Experiments

Nazek Queder

(26)

Statistical analysis

Feature extraction

Derived data

“Different acceptable analysis methods”

Carp et al. (2012)

(27)
(28)

Spatial registration

Segmentation

Cross-modality registration

etc.

(29)
(30)

algorithm

(31)

software

software

(32)

software

version

software

software version

(33)

parameters

software

parameters

software version

(34)

environment

software

parameters

software version

environment

algorithm

(35)

software

parameters

software version

environment

(36)

software

parameters

software version

environment

algorithm

BIDS Prov: Representation of neuroimaging

provenance (analysis workflows)

(37)

BIDS Prov

BIDS

NIDM

File naming convention + JSON files

60 labs worldwide

Semantic web (RDF)

(38)

BIDS

NIDM

File naming convention + JSON files

60 labs worldwide

Semantic web (RDF)

10 labs US / Europe / Canada

Enabler

JSON-LD

(39)

Statistical analysis

Preprocessing

Derived data

(40)

Credit: Presentation template by SlidesCarnival, adapted

@cmaumet

more than research

papers

Join BIDS Prov - BEP028

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