Python fMRI Analysis Ecosystem

This repository contains a set of Python-based code for analyzing functional MRI data using FSL and Freesurfer tools and Nipype.

Documentation

Online documentation can be found here

Dependencies

External

• FSL

• Freesurfer

Python

• Core scientific Python environment (ipython, numpy, scipy, matplotlib)

• pandas

• scikit-learn

• nipype

• nibabel

• nipy

• nibabel

• statsmodels

• My utility packages: moss and seaborn

Some of the core dependencies require developmet code in Github master

Basic Workflow

• All stages of processing assume that your anatomical data have been processed in Freesurfer (recon-all)

• run_warp.py: perform anatomical normalization

• run_fmri.py: perform subject-level functional analyses

• run_group.py: perform basic group level mixed effects analyses

License

Simplified BSD

Notes

Although all are welcome to use this code in their own work, it is not officially "released" in any capacity and many elements of it are under active development and subject to change at any time.

Please submit bug reports/feature ideas through the Github issues framework.