FC_AoNBrainhackWarsaw
Theoretical Motivation:
Functional connectivity (FC) research has become one of the leading concepts used for characterizing network dynamics across multiple disciplines, from neuroimaging, through gene expression networks, to social networks. It is also a basis for graph theoretical biomarkers of psychiatric disorders and as such, it become an important subfield of cognitive neuroimaging. FC is usually operationalized by means of Pearson’s and partial correlation, however the implementation of FC can vary between different fields, and different applications. Then, there is a question: does an optimal method to quantify functional connectivity exist? Or is the choice dependent on the data properties? How to choose the right method? In this project, we will use open-access data from functional Magnetic Resonance Imaging, EEG, gene expression data, stock exchange data and a few other open-access datasets, and we will compare the leading methods for computing FC when applied to these datasets. We will attempt to answer the questions: what are the pros and cons of different methods for quantifying FC? What are the differences and the similarities between different datasets, and how to choose the right method for the given dataset?
Research Design:
In this project, we are building a pipeline for the incoming AoN Brainhack Warsaw, 17-19th Nov 2017. The pipeline consists of three components:
[1] a selection of open datasets appropriate for the network research. We brainstormed about this in a group, and we selected seven topics we would like to further investigate. We divided the topics so that each one of us, finds and prepares a dataset a open dataset as follows: 1.1 resting state MRI datasets ---> Natalia + Małgosia 1.2 EEG / EMG datasets ---> Evangeline + Florencia + Małgosia 1.3 gene expression datasets ---> Małgosia + Evangeline 1.4 social network datasets ---> Evangeline +Florencia 1.5 stock exchange datasets ---> Natalia 1.6 weather / climate datasets ---> Natalia 1.7 neuromarketing → Florencia The datasets will all be formatted in CSV, with variables in columns, and the variable names in the first row. Each subject in a separate file, each dataset in a separate folder. Name Slack name Google Skype Affiliation Time zone Natalia Bielczyk nataliabielczyk natalia.bielczyk @gmail.com natalia-bielczyk Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands +2 UTC Małgorzata Wierzba mwierzba gosia.wierzba@ gmail.com malgorzata.wierzba Laboratory of Brain Imaging (LOBI), Neurobiology Center, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland +2 UTC Florencia Garro florgarro florgarro314@gm ail.com flor-garro Buenos Aires, Argentina -3 UTC Evangeline See evangeliney yee.evangeline@ gmail.com evangeliney Simon Fraser University, Burnaby, Canada -7UTC
[2] a Python notebook which [a] loads the data from a CSV file [b] applies a set of codes for functional connectivity research [c] applies a set of visualisation tools for connectomes We have creates a germ of such a Python notebook (screen in the Supplementary Material), and placed it in the GitHub project. This code will further be developed once the datasets are completed.
[3] an Overleaf project for this purpose: https://www.overleaf.com/read/dxdxkvvrdgqv where we have put the frame of the project so that the Brainhack participants can place their results and discussion straight into this frame. In this LaTeX document, the documentation for all the data will also be stored.
Statistical Analysis:
Statistical analysis in this case will include two main steps: [1] the preprocessing of selected datasets [2] finding and testing the routines for functional connectivity At the moment, we are at a premature stage in which we are collecting the datasets and the routines for functional connectivity.
Code Development:
We have created a Python notebooks and placed it in the GitHub repository. The notebooks will be fully developed before the deadline for project submission (1st November 2017). We made an agreement that we will be meeting online on a weekly basis in order to further develop.
Contact: Natalia Bielczyk natalia.bielczyk@gmail.com
Team:
nataliabielczyk (Natalia Bielczyk, Nijmegen, the Netherlands)
mwierzba (Małgorzata Wierzba, Warsaw, Poland)
florgarro (Florencia Garro, Buenos Aires, Argentina)
evangeliney (Evangeline, Simon Fraser University, Burnaby, Canada)
