COSgen

Overview

Contrast optimized stimulus generator (COSgen) is a highly parameterized genetic algorithm implementation to produce optimized stimulus sequences for clinical and preclinical fMRI. Our package is fully compatible with a pure Micro/Python stimulus delivery solution (COSplay), and provides a convenient and well documented API. Because of its modular structure, the implementation is highly adaptable for specific use cases.

Features

• High adaptability for specific use cases
• Full compatability with COSgen
• Custom model specification (design matrix construction, covariance matrix computation)
• Custom fitness measure specification

Dependencies

• Python 2.7 or Python 3.5 and newer
• Numpy
• Scipy
• argh
• nibabel (only for Make test data and Estimation of auto-correlation)
• matplotlib (only for cosgen.models.plot_design_matrix and the example Optimal block design for contrast detection)

Installation

The module can be installed using setuptools. Run python setup.py install inside the COSgen folder you downloaded. After installation you can use COSgen, make_test_data and estimate_autocorr directly as commands.

References

• COSplay: https://readthedocs.org/projects/cosplay/
• argh: https://pypi.python.org/pypi/argh
• Python: http://www.python.org/
• Setuptools: https://setuptools.readthedocs.io/en/latest/