Brain network study during resting states

Second project of the Bioinformatics & Network Medicine 20/21 course, Sapienza University of Rome.

We conducted the study of the a brain network during resting phase with eyes open and eyes closed. We used the EEG data of subject S003 from the dataset of PhysioNet (reachable here) to perform functional connectivity analysis. The study is divided into four steps; connectivity estimation and network creation, network analysis through local and global indices, motif analysis and community detection. We developed these tests in a python environment. Full report is avilable here.

Notes

Run

To install all dependencies run

$ pip3 -r requirements.txt

Fixing broken EDF headers

Before using EDF files fix the header using EDFBrowser

$ sudo apt install edfbrowser

See differences in the screenshot.

Installing bctpy

To install bctpy for python

$ git clone https://github.com/aestrivex/bctpy
$ cd bctpy
$ python3 setup.py build
$ python3 setup.py install
$ sudo mv motif34lib.mat /usr/local/lib/python3.6/dist-packages/bctpy-0.5.2-py3.6.egg/bct
$ cd \usr\local\lib\python3.6\dist-packages\bctpy-0.5.2-py3.6.egg\bct\algorithms

Then open file motifs.py and change array sizes to 200 at lines 701-702 (refer to the second screenshot).

Authors

• Giammarco D'Alessandro
• Luca Gioffrè (username changed from balthier)
• Narges Sharghi