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Semi-blind deconvolution for fMRI (BOLD signal)
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README.rst

Travis Codecov Python27 Python35

pyBOLD

pyBOLD is a Python module for semi-blind deconvolution of the fMRI signal (BOLD). This package reproduces the results of the Cherkaoui et al., ICASSP 2019, paper :

[1] Hamza Cherkaoui, Thomas Moreau, Abderrahim Halimi, Philippe Ciuciu, "Sparsity-based blind deconvolution of neural activation signal in fMRI", 2019 IEEE International Conference on Acoustic Speech and Signal Processing, May 2019, Brighton, United Kingdom.

Important links

Dependencies

The required dependencies to use the software are:

  • Numba
  • Joblib
  • Numpy
  • Scipy
  • PyWavelets
  • Matplotlib (for examples)

License

All material is Free Software: BSD license (3 clause).

Installation

In order to perform the installation, run the following command from the pybold directory:

python setup.py install --user

To run all the tests, run the following command from the pybold directory:

python -m unittest discover pybold/tests

To run the synthetic examples, go to the directories examples/synth_data and run a script, e.g.:

python deconv.py

To reproduce the ICASSP 2019 plots, go to the directories examples/icassp_2019 and run the scripts, e.g.:

python validation.py
python simulation.py

Development

Code

GIT

You can check the latest sources with the command:

git clone git://github.com/CherkaouiHamza/pybold

or if you have write privileges:

git clone git@github.com:CherkaouiHamza/pybold
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