cnlab_pipeline

Python code for nipype pipelines used for standard lab analysis protocols

Each directory consists of a README.md, core scripts and parameter descriptions, and templates model specification files.

• BIDS - Scripts to convert raw DICOMS to BIDS-compatible niftis
• FC - Functional connectivity code
• FMRIPREP - Scripts to run fMRIPrep
• L1 - Python modules containing nipype workflow functions for first-level analysis
• L2 - Python modules containing nipype workflow functions for second-level analysis
• MVPA - Scripts to run MVPA analyses
• PE - Scripts to compute pattern expression values
• PPI - Python wrapper code to run PPI using SPM
• ROI - Scripts to extract parameter estimates from ROIs
• archive - archived scripts

Below is the file structure for the repository:

├── BIDS
│   ├── README.md
│   └── templates
├── FC
│   ├── README.md
│   ├── extract_signal.ipynb
│   ├── make_adjacency_matrix-FOR_PROJECT1.ipynb
│   ├── make_adjacency_matrix.ipynb
│   ├── make_adjacency_matrix_WITH_UPDATED_SIMILARITY_METRICS.ipynb
│   ├── make_adjacency_matrix_for_synchrony.ipynb
│   └── templates
├── FMRIPREP
│   ├── README.md
│   └── templates
├── L1
│   ├── README.md
│   ├── first_level.pyc
│   ├── l1analysis_SPM.py
│   ├── l1analysis_description.json
│   ├── l1analysis_notebook.ipynb
│   └── templates
├── L2
│   ├── README.md
│   ├── l2analysis_SPM.py
│   ├── l2analysis_description.json
│   ├── l2analysis_notebook.ipynb
│   └── templates
├── MVPA
│   ├── README.md
│   └── templates
├── PE
│   ├── README.md
│   └── templates
├── PPI
│   ├── BIDStest_ONR_gPPIv13_wrapper.ipynb
│   ├── BIDStest_ONR_gPPIv13_wrapper.m
│   ├── README.md
│   ├── batch8example_gPPIv13_wrapper.ipynb
│   └── templates
├── ROI
│   ├── README.md
│   └── templates
└── archive