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Parietal INRIA

Gaël Varoquaux

Danilo Bzdok

Uniklinik RWTH Aachen

PRNI 2016 - TUTORIAL 4

NILEARN: Machine learning for Neuro-Imaging in Python

There is growing interest in data-driven analysis, multivariate statistics and predictive modeling for neuroimaging. Datasets are also constantly growing in sample size, resolution, and complexity. Nilearn is a Python package designed to address these new challenges in contemporary data analysis for imaging neuroscience. It provides state-of-the-art machine-learning methods for convenient pre-processing, analysis, and visualization of various types of neuroimaging results (i.e., experimental fMRI, VBM, and resting-state correlations). The tutorial will cover: (i) plotting and image manipulation with nilearn; (ii) decoding and predictive models; (iii) functional connectivity and resting-state data analysis.

MONDAY, JUNE 20th

08:30 :: Registration

09:00 :: Overview

Different applications: brain maps and decoding versus mapping connectivity

11:00 :: Plotting and simple image manipulation

10:30 :: Coffee Break

12:30 :: Lunch Break

13:30 :: Brain Decoding

- SVM on a mask or ROI (reproduce Haxby 2001)
- Evaluating prediction accuracy
- Without a mask: feature selection followed by SVM
- Plotting and saving decoder map
- Advanced decoding

15:00 :: Coffee Break

15:30 :: General philosophy & design principles

- niiimg
- NiftiMasker
- fit, transform, predict

TUESDAY, JUNE 21st

09:00 :: Functional connectivity: building a connectome

11:00 :: Functional connectivity: building a connectome

10:30 :: Coffee Break

12:30 :: Lunch Break

13:30 :: Extracting brain spatial networks

15:00 :: Coffee Break

15:30 :: Wrapping up

- Signal extraction on a maxprob atlas
- Signal cleaning
- Signal extraction on a probabilistic atlas

- A connectome and its visualization
- Graph extraction: inverse covariance
- Comparison of subjects

- Independent Component Analysis (ICA)
- Dictionary learning
- Separating networks in regions
- A data-driven connectome from these regions

- Summary on NiftiMaskers
- Summary on image manipulation

Setting up your system

Download and install Nilearn following the instructions at:

     http://nilearn.github.io/user_guide.html

For additional information you may contact tutorial4@prni.org

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