Examples

Warning

If you want to run the examples, make sure you execute them in a directory where you have write permissions, or you copy the examples into such a directory. If you install nilearn manually, make sure you have followed the instructions.

Basic tutorials

Introductory examples that teach how to use nilearn.

3D and 4D niimgs: handling and visualizing

3D and 4D niimgs: handling and visualizing

A introduction tutorial to fMRI decoding

A introduction tutorial to fMRI decoding

Basic nilearn example: manipulating and looking at data

Basic nilearn example: manipulating and looking at data

Basic numerics and plotting with Python

Basic numerics and plotting with Python

Intro to GLM Analysis: a single-run, single-subject fMRI dataset

Intro to GLM Analysis: a single-run, single-subject fMRI dataset

Working with Surface images

Working with Surface images

Visualization of brain images

See Plotting brain images for more details.

Basic Atlas plotting

Basic Atlas plotting

Colormaps in Nilearn

Colormaps in Nilearn

Controlling the contrast of the background when plotting

Controlling the contrast of the background when plotting

Glass brain plotting in nilearn

Glass brain plotting in nilearn

Glass brain plotting in nilearn (all options)

Glass brain plotting in nilearn (all options)

Loading and plotting of a cortical surface atlas

Loading and plotting of a cortical surface atlas

Making a surface plot of a 3D statistical map

Making a surface plot of a 3D statistical map

More plotting tools from nilearn

More plotting tools from nilearn

NeuroImaging volumes visualization

NeuroImaging volumes visualization

Plot Haxby masks

Plot Haxby masks

Plotting images with transparent thresholding

Plotting images with transparent thresholding

Plotting tools in nilearn

Plotting tools in nilearn

Seed-based connectivity on the surface

Seed-based connectivity on the surface

Technical point: Illustration of the volume to surface sampling schemes

Technical point: Illustration of the volume to surface sampling schemes

Visualizing 4D probabilistic atlas maps

Visualizing 4D probabilistic atlas maps

Visualizing Megatrawls Network Matrices from Human Connectome Project

Visualizing Megatrawls Network Matrices from Human Connectome Project

Visualizing a probabilistic atlas: the default mode in the MSDL atlas

Visualizing a probabilistic atlas: the default mode in the MSDL atlas

Visualizing global patterns with a carpet plot

Visualizing global patterns with a carpet plot

Visualizing multiscale functional brain parcellations

Visualizing multiscale functional brain parcellations

Decoding and predicting from brain images

See Decoding and MVPA: predicting from brain images for more details.

Cortical surface-based searchlight decoding

Cortical surface-based searchlight decoding

Decoding of a dataset after GLM fit for signal extraction

Decoding of a dataset after GLM fit for signal extraction

Decoding with ANOVA + SVM: face vs house in the Haxby dataset

Decoding with ANOVA + SVM: face vs house in the Haxby dataset

Decoding with FREM: face vs house vs chair object recognition

Decoding with FREM: face vs house vs chair object recognition

Different classifiers in decoding the Haxby dataset

Different classifiers in decoding the Haxby dataset

Encoding models for visual stimuli from Miyawaki et al. 2008

Encoding models for visual stimuli from Miyawaki et al. 2008

Example of pattern recognition on simulated data

Example of pattern recognition on simulated data

FREM on Jimura et al “mixed gambles” dataset

FREM on Jimura et al "mixed gambles" dataset

ROI-based decoding analysis in Haxby et al. dataset

ROI-based decoding analysis in Haxby et al. dataset

Reconstruction of visual stimuli from Miyawaki et al. 2008

Reconstruction of visual stimuli from Miyawaki et al. 2008

Searchlight analysis of face vs house recognition

Searchlight analysis of face vs house recognition

Setting a parameter by cross-validation

Setting a parameter by cross-validation

Show stimuli of Haxby et al. dataset

Show stimuli of Haxby et al. dataset

The haxby dataset: different multi-class strategies

The haxby dataset: different multi-class strategies

Understanding Decoder

Understanding Decoder

Voxel-Based Morphometry on Oasis dataset

Voxel-Based Morphometry on Oasis dataset

Voxel-Based Morphometry on Oasis dataset with Space-Net prior

Voxel-Based Morphometry on Oasis dataset with Space-Net prior

Functional connectivity

See Clustering to parcellate the brain in regions, Extracting functional brain networks: ICA and related or Extracting times series to build a functional connectome for more details.

Classification of age groups using functional connectivity

Classification of age groups using functional connectivity

Clustering methods to learn a brain parcellation from fMRI

Clustering methods to learn a brain parcellation from fMRI

Comparing connectomes on different reference atlases

Comparing connectomes on different reference atlases

Computing a connectome with sparse inverse covariance

Computing a connectome with sparse inverse covariance

Connectivity structure estimation on simulated data

Connectivity structure estimation on simulated data

Deriving spatial maps from group fMRI data using ICA and Dictionary Learning

Deriving spatial maps from group fMRI data using ICA and Dictionary Learning

Extract signals on spheres and plot a connectome

Extract signals on spheres and plot a connectome

Extracting signals from a brain parcellation

Extracting signals from a brain parcellation

Extracting signals of a probabilistic atlas of functional regions

Extracting signals of a probabilistic atlas of functional regions

Group Sparse inverse covariance for multi-subject connectome

Group Sparse inverse covariance for multi-subject connectome

Producing single subject maps of seed-to-voxel correlation

Producing single subject maps of seed-to-voxel correlation

Regions extraction using dictionary learning and functional connectomes

Regions extraction using dictionary learning and functional connectomes

GLM: First level analysis

These are examples focused on showcasing first level models functionality and single subject analysis.

See Analyzing fMRI using GLMs for more details.

Analysis of an fMRI dataset with a Finite Impule Response (FIR) model

Analysis of an fMRI dataset with a Finite Impule Response (FIR) model

Default Mode Network extraction of ADHD dataset

Default Mode Network extraction of ADHD dataset

Example of MRI response functions

Example of MRI response functions

Example of surface-based first-level analysis

Example of surface-based first-level analysis

Examples of design matrices

Examples of design matrices

First level analysis of a complete BIDS dataset from openneuro

First level analysis of a complete BIDS dataset from openneuro

Generate an events.tsv file for the NeuroSpin localizer task

Generate an events.tsv file for the NeuroSpin localizer task

Predicted time series and residuals

Predicted time series and residuals

Simple example of two-runs fMRI model fitting

Simple example of two-runs fMRI model fitting

Single-subject data (two runs) in native space

Single-subject data (two runs) in native space

Understanding parameters of the first-level model

Understanding parameters of the first-level model

GLM: Second level analysis

These are examples focused on showcasing second level models functionality and group level analysis.

See Analyzing fMRI using GLMs for more details.

Example of generic design in second-level models

Example of generic design in second-level models

Example of second level design matrix

Example of second level design matrix

Second-level fMRI model: one sample test

Second-level fMRI model: one sample test

Second-level fMRI model: true positive proportion in clusters

Second-level fMRI model: true positive proportion in clusters

Second-level fMRI model: two-sample test, unpaired and paired

Second-level fMRI model: two-sample test, unpaired and paired

Statistical testing of a second-level analysis

Statistical testing of a second-level analysis

Voxel-Based Morphometry on OASIS dataset

Voxel-Based Morphometry on OASIS dataset

Manipulating brain image volumes

See Manipulating images: resampling, smoothing, masking, ROIs… for more details.

Breaking an atlas of labels in separated regions

Breaking an atlas of labels in separated regions

Comparing the means of 2 images

Comparing the means of 2 images

Computing a Region of Interest (ROI) mask manually

Computing a Region of Interest (ROI) mask manually

Extracting signals from brain regions using the NiftiLabelsMasker

Extracting signals from brain regions using the NiftiLabelsMasker

Image thresholding

Image thresholding

Negating an image with math_img

Negating an image with math_img

Region Extraction using a t-statistical map (3D)

Region Extraction using a t-statistical map (3D)

Regions Extraction of Default Mode Networks using Smith Atlas

Regions Extraction of Default Mode Networks using Smith Atlas

Resample an image to a template

Resample an image to a template

Simple example of NiftiMasker use

Simple example of NiftiMasker use

Smoothing an image

Smoothing an image

Understanding NiftiMasker and mask computation

Understanding NiftiMasker and mask computation

Visualization of affine resamplings

Visualization of affine resamplings

Advanced statistical analysis of brain images

A short demo of the surface images & maskers

A short demo of the surface images & maskers

Advanced decoding using scikit learn

Advanced decoding using scikit learn

BIDS dataset first and second level analysis

BIDS dataset first and second level analysis

Beta-Series Modeling for Task-Based Functional Connectivity and Decoding

Beta-Series Modeling for Task-Based Functional Connectivity and Decoding

Copying headers from input images with math_img

Copying headers from input images with math_img

Functional connectivity predicts age group

Functional connectivity predicts age group

Massively univariate analysis of a calculation task from the Localizer dataset

Massively univariate analysis of a calculation task from the Localizer dataset

Massively univariate analysis of a motor task from the Localizer dataset

Massively univariate analysis of a motor task from the Localizer dataset

Massively univariate analysis of face vs house recognition

Massively univariate analysis of face vs house recognition

Multivariate decompositions: Independent component analysis of fMRI

Multivariate decompositions: Independent component analysis of fMRI

NeuroVault cross-study ICA maps

NeuroVault cross-study ICA maps

NeuroVault meta-analysis of stop-go paradigm studies

NeuroVault meta-analysis of stop-go paradigm studies

Surface-based dataset first and second level analysis of a dataset

Surface-based dataset first and second level analysis of a dataset

Working with long time series fMRI images

Working with long time series fMRI images