RABIES Documentation
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Content
Installation
PyPi
Container (Singularity/Docker)
Neurodesk
Running The Software
Input data in BIDS standard
Command Line Interface
Example execution syntax
Execution syntax with containerized installation (Singularity and Docker)
Additional Resources
Preprocessing Pipeline
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
Adapted workflow without structural scans (i.e. –bold_only)
Preprocessing quality control (QC)
Recommendations for registration troubleshooting
Confound Correction pipeline
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
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
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