# An introduction to neuroinformatics

Camille Maumet

► To cite this version:

Camille Maumet. An introduction to neuroinformatics. Joint meeting of R-Ladies Gaborone and PyData Botswana, May 2022, R Ladies Gaborone and PyData Botswana, Botswana. 2022. hal-03670072

HAL Id: hal-03670072

https://inria.hal.science/hal-03670072v1

Submitted on 17 May 2022

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# An introduction to neuroinformatics

Camille Maumet

Univ Rennes, Inria, Inserm, CNRS, IRISA
# Who am I?

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Neuroinformatician

Data science + brain imaging

* PhD in computer science applied to neuroimaging data analysis

* Rennes (France)

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Inserm

Institut national
de la santé et de la recherche médicale

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UNIVERSITÉ DE

RENNES 1

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ueb

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UMR

IRISA
Brain imaging
# Imaging the brain

<figure><img src="image_12.png" /><figcaption>Magnetic resonance imaging (MRI)</figcaption></figure>

<figure><img src="image_13.png" /><figcaption>Near infrared spectroscopy (NIRS)</figcaption></figure>

<figure><img src="image_14.png" /><figcaption>Electroencephalography (EEG)</figcaption></figure>
Images of the brain

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Credits: Brain, [Life Science Databases (LSDB)](http://www.lifesciencesdatabases.com/) (CC-BY-SA) - Globe by, Kevin Gill, [Wikipedia](http:// Wikipedia (CC-BY-SA) - Earth layers, Domaine public / [ck12](https://ck12.org/) - Grey and white matter, [Flickr](https://www.flickr.com/) (Public Domain)
Brain images

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Credits: Brain, [Life Science Databases (LSDB)](http://www.lifesciencesdatabases.com/) (CC-BY-SA) - Globe by, Kevin Gill, [Wikipedia](http:// Wikipedia (CC-BY-SA) - Earth layers, Domaine public / [ck12](https://ck12.org) - Grey and white matter, [Flickr](https://www.flickr.com/) (Public Domain)
Brain images

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Credits: Brain, [Life Science Databases (LSDB)](http://www.bioprojects.org/livedatabases/index.html) (CC-BY-SA) - Globe by, Kevin Gill, [Wikipedia](https://www.wikipedia.org) (CC-BY-SA) - Earth layers, Domaine public / [ck12](https://ck12.org) - Grey and white matter, [Flickr](https://www.flickr.com) (Public Domain)
Brain images

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Credits: Brain, [Life Science Databases (LSDB)](http://www.lifesciencesdatabases.com/) (CC-BY-SA) - Globe by, Kevin Gill, [Wikipedia](http:// Wikipedia (CC-BY-SA) - Earth layers, Domaine public / [ck12](https://ck12.org/) - Grey and white matter, [Flickr](https://www.flickr.com/) (Public Domain)
Anatomy: cortical surfaces

Plis de passage
(Song et al., 2021)

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Song et. al (2021)

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Connectivity

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Credits: Tractography, group work [Wikipedia](https:// Wikipedia (CC-BY-SA) - Gaborone road map by OpenStreetMap contributors, [Wikipedia](https:// Wikipedia (CC-BY-SA)).
Brain function

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Leaflet | © OpenStreetMap contributors © CARTO

<figure><img src="image_32.png" /><figcaption>Auditory
network</figcaption></figure>

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(x=3, y=-17, z=1)

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(x=11, y=-82, z=0)

Credits: Large scale brain networks, group work [Wikimedia](https://open街机map.org) (CC-BY) - R-ladies meetup locations, [R-Ladies](https://www.r-ladies.org) 1:1
# Many types of brain maps

<figure><img src="image_35.png" /><figcaption>Human brain</figcaption></figure>

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

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

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

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# Many types of brain maps

<figure><img src="image_43.png" /><figcaption>Human brain</figcaption></figure>

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

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

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

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# Example functional MRI study

Studying developmental Language disorder

Study started in 2005 in Rennes.

Team of clinicians and research scientists.

40 children participated.

De Guibert et. al (2010), De Guibert et. al (2011)
# fMRI protocol

<table><tr><td>Action</td><td>Rest</td><td>Action</td><td>Rest</td><td>Action</td><td>Rest</td></tr></table>

* Language paradigm using a block design

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"gant"

Action

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Rest
# Results

## DLD Group activity during the Phon-diff task

Phon-diff

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## Comparison of DLD group activity versus controls during the Phon-diff task

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# Demo : exploring fMRI data

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NiBabel

Access a cacophony of neuro-imaging file formats

https://nipy.org/nibabel/

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ni
learn

Nilearn:

Statistics for Neurolmaging in Python

https://nilearn.github.io/

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repronim/neurodocker

By repronim • Updated a year ago

Container

https://github.com/ReproNim/neurodocker
## Demo : exploring fMRI data

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From **brain data** to
**findings** about the
brain
# Functional MRI: raw data

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* 64 brain volumes / subject / paradigm

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# Data analysis

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Motion correction

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Motion correction

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Motion correction

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Motion correction

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Motion correction

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Motion correction

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Motion correction

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# Motion correction

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# Demo : motion correction

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https://www.fil.ion.ucl.ac.uk/spm/

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Nipype:

Neuroimaging in Python
Pipelines and Interfaces

https://nipype.readthedocs.io

## Interfaces

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Idiosyncratic, Heterogeneous APIs

## Workflow Engine

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# Demo : motion correction

<figure><img src="image_106.png" /><figcaption>Elodie Germani</figcaption></figure>

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Motion correction

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<figure><img src="image_109.png" /><figcaption>Quentin
Duché</figcaption></figure>
More preparation steps...

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# Demo : Preprocessing

<figure><img src="image_111.png" /><figcaption>Elodie Germani</figcaption></figure>

Reproduction of [SPM tutorial](https://gitlab.inria.fr/egermani/reproduced_tutorial) using Nipype: [https://gitlab.inria.fr/egermani/reproduced_tutorial](https://gitlab.inria.fr/egermani/reproduced_tutorial)

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https://www.fil.ion.ucl.ac.uk/spm/

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Nipype:
Neuroimaging in Python
Pipelines and Interfaces

https://nipype.readthedocs.io
# And even more preparation...

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More preparation steps...

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More preparation steps...

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Motion
correction

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Realignement

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Statistics

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Segmentation

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Statistical analysis

Goal: Get areas of activations and deactivations for a given participant or for a group of participants.

<figure><img src="image_126.png" /><figcaption>Design matrix</figcaption></figure>

<figure><img src="image_127.png" /><figcaption>STATISTIQUES INDIVIDUELLES-Catég: Active > Rest (red) / Rest > Active (blue) (none: 0.001)
control (control01)</figcaption></figure>
Collaborative and
community-driven
research
# Brainhack: project-based community science

<figure><img src="image_128.png" /><figcaption>A. Anatomy of a Brainhack</figcaption></figure>

<figure><img src="image_129.png" /><figcaption>C. Brainhack Cartography</figcaption></figure>

<figure><img src="image_130.png" /><figcaption>B. Timeline of a Single Event</figcaption></figure>

<figure><img src="image_131.png" /><figcaption>D. Brainhack Timeline</figcaption></figure>

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# OHBM Brainhack - hybrid!

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<figure><img src="image_134.png" /><figcaption>Locations of the 2020 OHBM Brainhack attendees</figcaption></figure>
**Coming soon!**

OHBM Brainhack June 16-18, 2022

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OHBM Brainhack Hybrid|

June 16-18th 2022

REGISTER

https://ohbm.github.io/hackathon2022/

Registration: [here]() (fee waiver available)
Advances in FAIR data management and sharing practices
for neuroscience research, infrastructures, and tools

Abstract submission open until MAY 23

neuroinformatics.incf.org
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An introduction to neuroinformatics

Camille Maumet

Thank you!

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