Documentation

This page indexes the documentation for the CANlab tools: reference docs in the CanlabCore repository, the runnable walkthroughs and tutorials on this site, and the Interactive fMRI overview. Reference docs are Markdown files rendered on GitHub; walkthroughs and tutorials are on this site.

Start here: Interactive fMRI analysis for the philosophy and object model, the Object methods index for the class-by-class reference, or the Quick-start walkthrough to install and run.

Object references

Per-class references — properties, methods grouped by category, and worked examples. See the Object methods index for the class hierarchy and overview.

Class	What it holds
`fmri_data`	The workhorse image object; most analysis methods live here
`image_vector`	Abstract base; source of shared methods
`statistic_image`	Statistic maps (t / p / effect size) with thresholding
`atlas`	Atlases / parcellations with labels and probability maps
`fmri_surface_data`	New. CIFTI-style surface / grayordinate data
`region`	Contiguous clusters / ROIs as a unit of analysis
`fmridisplay`	Figure-handle container for layered brain montages
`glm_map`	New. First- and second-level GLM / regression estimator
`fmri_glm_design_matrix`	First-level GLM design matrix (onsets, basis set, X)
`predictive_model`	New. Fitted multivariate prediction model and artifacts
`canlab_dataset`	Subject × variable behavioral / clinical data
`brainpathway`	Connectivity / pathway model (single- & multi-subject)
`fmri_timeseries`	Raw timeseries container
`fmri_mask_image`	Binary mask (legacy)

Workflows

End-to-end recipes that chain several methods together. Each comes as a roadmap (choose the right approach) and a how-to (runnable code). See the Workflows overview.

Workflow	Roadmap	How-to
ROI / atlas data extraction	roadmap	how-to
First-level fMRI GLM (`glm_map`)	roadmap	how-to
Second-level group GLM (`glm_map`)	roadmap	how-to
Surface & grayordinate data	`fmri_surface_data`	how-to
Loading & using image sets	—	how-to

Visualization

A multi-page guide to rendering images and results — montages, 3-D surfaces, colormaps, the interactive controller, and atlases/regions.

Concepts & reference

Atlases, regions, and patterns — how atlases, region objects, and signature patterns relate.
Recasting objects — converting between object types.
Sample datasets — built-in datasets and how to load them (load_image_set).
Toolbox folders — how CanlabCore is organized.

Long-form tutorials

Multi-part didactic tutorials with runnable code.

Multivariate classification & decoding with SVM

Walkthroughs & tutorials on this site

Walkthroughs — step-by-step, runnable analyses (installing tools, group stats, ROI analysis, prediction, mediation, meta-analysis, visualization).
fMRI tutorials — longer-form didactic tutorials using MATLAB live scripts.
Batch system — the second-level analysis batch-script system.
Interactive fMRI analysis — philosophy, object model, and a simple analysis flow.

Help and issues

In MATLAB, doc <class_name> (e.g. doc fmri_data) or methods <class_name> lists a class’s properties and methods.
Report bugs or documentation errors on the CanlabCore issues page.