hcherkaoui / pybold

Semi-blind deconvolution for fMRI (BOLD signal)

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

• Official source code repo: https://github.com/CherkaouiHamza/pybold
• Cherkaoui et al., ICASSP 2019, paper

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 [email protected]:CherkaouiHamza/pybold