CANlab neuroimaging analysis tools

The CANlab imaging analysis tools consist of a set of linked Github repositories.

They enable interactive data analysis for fMRI and other types of neuroimaging data using objects with simple methods (or commands) customized for neuroimaging data analysis.

Interactive analysis: Philosophy and principles

Much of neuroimaging analysis, like other areas of science, has moved towards pipelines: Standardized processing streams that produce reliable results with optimized procedures. This is an essential part of any technology, and an important effort. At same time, however, there is a need for creativity and exploration of data and techniques in order to discover new ways of doing things. And there is a need to understand data — its characteristics, its quirks and outliers, and its behavior under different conditions — in order to avoid spurious results and understand what is true. Exploration and discovery require the ability to visualize data in a variety of ways, interact with it, and create analyses that fit the questions at hand.

There are many established pipelines for neuroimaging analysis, but relatively few tools that provide flexibility and the ability to interact with data. The CANlab toolboxes were designed with interactive analysis in mind. The tools provide a high-level language for interacting with neuroimaging data. The idea is to take preprocessed data or even the results of single-subject analyses—the output of established preprocessing pipelines—and import them into lightweight, flexible data objects specialized for neuroimaging visualization and analysis. These objects allow for interactive analysis with simple commands, like “plot”, “predict”, and “montage”.

There are several advantages to this type of framework. We’re not saying the code is perfect — it’s necessarily a work in progress — but here are some of the values we aspire to:

  • Interactivity: Complex operations can be done with simple commands. For example, single commands perform (a) stratified, cross validated multivariate prediction (b) rendering imaging results on brain slices or surfaces, and many other functions. This operations can thus be done interactively, allowing analysts to explore the distribution of data and the consequences of altering analysis choices.

  • Transparency: Scripts that use these commands become simple to read, write, and interpret, increasing transparency and reducing coding errors. A basic group fMRI analysis, including generating publication-quality figures and tables of results, can be performed in only a few (about 5) lines of code.

Organization of the toolbox around a few core objects makes it easier to discover what they can do (their methods). A series of executable walkthroughs—and HTML reports with expected output—demonstrate some of the core functionality.

  • Reproducibility: The use of simple, transparent commands makes it easy to share the code needed to reproduce an analysis in a format that others can understand and use.

  • Minimization of errors: Core object functions are re-used and vetted across analyses and users, reducing coding errors. The walkthroughs serve as a basic unit test for many core functions, providing a test that analyses are running and producing expected results whatever platform and software versions are being used. (A full unit test would be desirable, and is planned.)

  • Efficiency: A batch system built on simple object commands runs a variety of standard quality control checks and analyses, and saves date-stamped HTML reports with figures and statistics. This provides a base set of analyses that reduces coding time and reduces coding errors. This is good for archiving and reproducibility, and good for efficiently writing papers.

  • Shareability: The data objects are designed to be space efficient, and store imaging data in a fraction of the disk space it takes to store full images.

In the batch system, standardized variable names make it easy to understand the structure of the folders and files, which promotes meaningful sharing. Date-stamped HTML reports provide a record of analyses, figures and statistics that can be archived and shared.

  • Extensibility: The object-oriented framework is extensible, allowing developers and data scientists to add new methods or object types.

New analytic techniques can be easily “plugged in”. The objects store images in a flat 2-D matrix (voxels x images) that is very familiar to data scientists from all fields, and can be subjected to custom analyses. Core object code handles the rendering of these results back into brain space, including visualization and anatomical labeling. This makes neuroimaging accessible to a variety of data scientists developing sophisticated new analyses.

Walkthroughs and batch scripts

A series of step-by-step analysis walkthroughs are in the CANlab_help_examples repository, in the example_help_files folder.

These are executable Matlab files (.m files) that can be run. They can also be published to HTML files (see canlab_help_publish.m). A set of HTML files with figures and printouts of these help examples is in the published_html folder.

A system of batch scripts is in the CANlab_help_examples repository, in the Second_level_analysis_template_scripts folder.

types of objects

See the Interactive fMRI analysis page

fmri_dataStores neuroimaging datasets; operate on datasets by calling object methods
statistic_imageStores statistic images with stats and P-values
atlasStores atlas data with probability maps and integers for unique regions
regionStores data grouped by region/network, treating region as a unit of analysis
fmridisplayContainer for handles for brain slices and surfaces, allowing visualization

Issues and bugs

Please raise issues or document errors by posting issues on the CAN Lab Github page.