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fMRI Analysis Overview

This section of the wiki provides a comprehensive guide for analyzing fMRI data. Follow the steps below to ensure smooth data processing, from environment setup to advanced multi-variate pattern analysis (MVPA).

Analysis steps overview

  • General Information
    Overview of the pipeline, including key terminology and data structure. Start here to get a sense of the entire workflow.

  • Setting Up the Environment
    Install essential tools and software like Docker, fMRIPrep, and SPM to prepare your analysis environment.

  • Converting Data to BIDS
    Organize your raw data in the BIDS format for compatibility with neuroimaging tools. Includes step-by-step instructions for converting and validating your dataset.

  • Preprocessing & QA
    Perform quality control and preprocess your data using tools like fMRIPrep and MRIQC to ensure it's ready for statistical analysis.

  • First-Level Analysis
    Model brain activity using the General Linear Model (GLM) in SPM. Set up contrasts and extract statistical values.

  • Regions of Interest (ROIs)
    Create and analyze regions of interest for targeted brain analysis. ROIs are crucial for advanced analyses like MVPA.

  • Multi-Variate Pattern Analysis (MVPA)
    Decode complex neural patterns using machine learning methods like SVM. Analyze brain activity across different conditions.

  • Complete Workflow Example
    An end-to-end guide that ties everything together, providing an example of a full fMRI analysis pipeline.

Additional Resources