Welcome to mriqc’s documentation!

MRIQC is developed by the Poldrack Lab at Stanford University for use at the Center for Reproducible Neuroscience (CRN), as well as for open-source software distribution.

Tip

Try MRIQC online on OpenNeuro - without installation!

Contents

• Introduction
  • Citation
  • Support and communication
  • Authors
  • License information
• Installation
  • Containerized versions
  • “Bare-metal” installation (only Python 3)
    • Execution system dependencies
• Running mriqc
  • Command line interface
    • Positional Arguments
    • Named Arguments
    • Options for filtering the input BIDS dataset
    • Instrumental options
    • Options to handle performance
    • Workflow configuration
    • Specific settings for ANTs
    • Specific settings for AFNI
  • Running MRIQC on HPC clusters
    • Singularity containers
    • Requesting resources
• Run mriqc with docker
  • Preliminaries
  • Running mriqc
  • Explaining the mriqc-docker command line
• Image Quality Metrics (IQMs)
  • IQMs for structural images
    • Measures based on noise measurements
    • Measures based on information theory
    • Measures targeting specific artifacts
    • Other measures
    • mriqc.qc.anatomical module
  • IQMs for functional images
    • Measures for the spatial information
    • Measures for the temporal information
    • Measures for artifacts and other
    • mriqc.qc.functional module
• Visual reports
  • Demo: anatomical reports
  • Demo: functional reports
  • How reports work
    • Group reports
    • T1 and T2 -weighed images
    • BOLD images
    • mriqc.reports package
• The MRIQC workflows
  • The anatomical workflow
  • The functional workflow
• The MRIQC classifier for T1w images
  • Using the classifier
    • The Random Forests Classifier in MRIQC
    • Building your custom classifier
    • Usage of mriqc_clf
    • Data handler module
    • Cross-validation helper
  • Cross-validation in MRIQC
    • Experiment 0: What makes a good cross-validation split in this application?
• Data Sharing Agreement
  • Foundations
  • MRIQC DSA (Data Sharing Agreement)
    • Withdrawing records and period of agreement
    • Intended use of the data
    • Constraints on use of the data
    • Data confidentiality
    • Financial costs of data-sharing

Indices and tables

• Index
• Module Index
• Search Page