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:
For additional information you may contact tutorial4@prni.org