Examples

Getting Started and IO

This notebook tests whether your cedalion installation is working

Xarray Data Structures - an fNIRS example

The Recording Container: Cedalion’s main data structure and a guide to indexing

Loading and Inspecting fNIRS Recordings

Data Structures and I/O

Convert a fNIRS dataset to BIDS

Storing estimated HRFs in snirf files

Signal Quality

Calculating the Scalp Coupling Index

Channel Quality Assessment and Pruning

Motion Artefact Detection and Correction

Using Channel Variance as Proxy for Measurement Noise and as a Weight for Global Physiology Removal

Data Loading and Preprocessing

Modeling

GLM Basis Functions

GLM Fingertapping Example

GLM Illustrative Example

Statsmodels Methods Overview

Fitting a GLM with Gaussian Kernels

Head Models and Image Reconstruction

Image Reconstruction

Photogrammetric Optode Coregistration

Constructing 10-10 coordinates on segmented MRI scans

Head Models in Cedalion: Getting Started

Head Models: MRI Segmentation and TwoSurfaceHeadModel

Scaling and Transforming Head Models

Examining and thresholding sensitivity of a probe to the cortex using the Schaefer parcellation scheme

Precomputed forward model results

Head model fiducials and landmarks

Machine Learning and Data Driven Methods

Basic single trial fNIRS finger tapping classification

Example for ICA Source Extraction

Constrained Independent Component Analysis (ICA)

Physiology

AMPD - Automatic Multiscale Peak Detection

Data Augmentation

Synthetic Artifacts

Adding Synthetic Hemodynamic Reponses to Data

Plots & Visualization

Visualization Examples using Cedalion Plot Functions