Contents

• Installation
  • Containerized execution (Docker and Singularity)
    • External Dependencies
  • Not running on a local machine? - Data transfer
• Usage Notes
  • Execution and the BIDS format
  • Command-Line Arguments
    • Positional Arguments
    • Options for anatomical postprocessing
    • Options for parcellation
    • Options for filtering BIDS queries
    • Specific options for FreeSurfer preprocessing
    • Options to handle performance
    • Options for performing only a subset of the workflow
    • Options for modulating outputs
    • Options for carbon usage tracking
    • Other options
  • Reusing precomputed derivatives
    • Reusing a previous, partial execution of sMRIPost-LINC
  • Troubleshooting
  • About the NiPreps framework licensing
  • License information
• Processing pipeline details
• Outputs of sMRIPost-LINC
  • Layout
  • Visual Reports
  • Parcellations and Atlases
  • Parcellated Structural Measures
  • Confounds
• Defining standard and nonstandard spaces where data will be resampled
  • TemplateFlow
  • Standard spaces
  • Custom standard spaces
  • Nonstandard spaces
  • Preprocessing blocks depending on standard templates
• FAQ - Frequently Asked Questions
  • What is fMRIPost?
• Developers - API
  • The NiPreps community and contributing guidelines
  • Setting up your development environment
  • Internal configuration system
    • Configuration sections
    • Usage
    • Logging
    • Other responsibilities
    • dumps()
    • from_dict()
    • get()
    • init_spaces()
    • load()
    • to_filename()
  • Workflows
    • sMRIPost-LINC workflows
• What’s new
  • 23.0.0 ()