PETFit

Getting Started

  • Installation
    • Docker
      • Pull the pre-built image
    • Apptainer
      • Build from the Docker image
      • Prerequisites
    • R package (for development)
      • Prerequisites
  • Quick start
    • Step 1: Define regions
    • Step 2: Run kinetic modelling
      • Plasma input models
      • Reference tissue models
    • Step 3: Review reports
    • Key arguments

User Guide

  • Usage guide
    • The two-step workflow
    • The three apps
    • Interactive vs automatic mode
    • Configuration files
    • Analysis folders
      • PETFit folder structures
      • Region definition
      • Modelling with plasma input
      • Modelling with reference tissue
      • Parameterised reports
  • Container usage
    • Docker
      • Getting the image
      • Docker wrapper
      • Interactive mode
      • Automatic mode
      • Command-line options
      • Mount points
      • Port configuration
      • File permissions on Linux
    • Apptainer
      • Building the container
      • Simplified workflow: the petfit alias
      • Interactive mode
      • Automatic mode
      • HPC integration
      • Volume mounting
      • Troubleshooting
  • Outputs
    • Directory structure
    • Region definition outputs
      • petfit_regions.tsv
      • desc-combinedregions_tacs.tsv
    • Modelling outputs
      • Individual TAC files
      • Weight files
      • Kinetic parameter files
      • Configuration file
      • HTML reports
    • BIDS metadata integration
  • Supported models
    • Plasma input models
    • Reference tissue models

Reference

  • Troubleshooting
    • Data and file issues
      • No TAC files found
      • TACs and morph file mismatch
    • Reference tissue issues
      • Reference region not found in analysis data
      • Poor R1 estimates from MRTM1 / MRTM2
    • Blood data issues
      • Noisy or unreliable blood data
      • PETFit cannot find the blood / input function files
    • Model fitting issues
      • Model fails to converge
      • Unexpected parameter estimates
      • Extremely high VT values
      • Logan / refLogan give lower estimates than the nonlinear models
      • Unstable or noisy binding estimates
      • Nonlinear models unstable but linearised models stable
      • Unreliable delay or k2prime estimates
    • Ancillary analysis issues
      • Ancillary folder not found
      • Missing delay or k2prime files in ancillary folder
    • Performance
      • Processing is too slow
    • Docker issues
      • Output files owned by root
      • Port already in use
    • Apptainer / HPC issues
      • Port already in use
      • No internet access on compute nodes
      • Home directory size limits
      • Finding the Apptainer module
  • API reference
    • Interactive apps
      • petfit_interactive()
    • Automatic pipelines
      • petfit_auto()
      • petfit_regiondef_auto()
      • petfit_modelling_auto()
    • Container command-line options
  • Citation
    • kinfitr references
  • Changelog
    • 0.1.5 (current)
    • 0.1.4
    • 0.1.3
    • 0.1.2
  • License

Development

  • Contributing
    • Development setup
    • Repository structure
    • Coding standards
      • Tidyverse conventions
      • File I/O
      • Spelling
      • Documentation
    • Testing
      • Running tests
      • Unit tests
      • Integration tests
      • Test infrastructure
      • CI/CD
    • Configuration management
    • Building documentation
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