RABIES Documentation

Content

  • Installation
    • Container (Apptainer/Docker) **RECOMMENDED**
    • PyPi
    • Neurodesk
  • Running The Software
    • Input data in BIDS standard
    • Command Line Interface
    • Example execution syntax
    • Execution syntax with containerized installation (Apptainer and Docker)
    • Additional Resources
  • Preprocessing stage
    • Structural inhomogeneity correction
    • Common space alignment (i.e. Unbiased template generation + Atlas registration)
    • 3D EPI generation
    • Head motion estimation
    • Functional inhomogeneity correction
    • Susceptibility distortion estimation
    • Frame-wise resampling
    • Resampling of masks and labels
    • Adapted workflow without structural scans (i.e. –bold_only)
  • Preprocessing quality control (QC)
    • Recommendations for registration troubleshooting
  • Confound Correction stage
    • rabies.confound_correction_pkg.confound_correction.init_confound_correction_wf [source code]
  • Connectivity Analysis
    • Correlation-based connectivity
    • ICA-based connectivity
  • Data quality assessment
    • Scan diagnosis report
    • Distribution plot
    • Group stats
    • Optimization of confound correction strategy
    • Generating the reports
    • Guidelines for analysis quality control
  • Understanding the Outputs
    • Preprocessing Outputs
    • Confound Correction Outputs
    • Analysis Outputs
  • Metric definitions
    • Nuisance regressors for confound regression
    • Temporal scan diagnosis
    • Spatial scan diagnosis
    • Distribution plot
    • Group statistical QC report
  • Troubleshooting
    • Checking Image Orientation with ITK-SNAP
    • See Also
  • Contributing to RABIES
    • Dev environment
    • Instructions to create a pull request
    • Interactive debugging with Spyder and debug_workflow.py
    • Creation of a new module and integration within a Nipype workflow
  • Bibliography
RABIES Documentation
  • Search

© Copyright 2019, CoBrALab and Gabriel Desrosiers-Gregoire and Gabriel A. Devenyi and Mallar Chakravarty.

Built with Sphinx using a theme provided by Read the Docs.