Contact Session #1
Human brain networks: What and why. Nodes, edges, and brain graphs.
Intended learning outcomes:
- Understand why we want to study brain connectivity and model the brain as a network
- List brain networks and recognize different methods to define nodes and edges
- Critically consider the multiple aspects of brain connectivity
You have three tasks before the first contact session
- Go to https://version.aalto.fi/ (or https://github.com/ if you don't have an Aalto accountn) and create an empty GIT project with a name that is relevant to this course. Write a README.md file about what you would like to learn and do in this course hands on sessions. Use the markdown language so that you have headers, bold, italic, links, a list, an image and a table. Be creative.
Here a cheat sheet for you to use markdown https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet
Here a quick intro to GIT https://eglerean.wordpress.com/2016/04/19/git-in-10-minutes/
You do not NEED to use GIT with the terminal, it is fine if you do the edits using the web interface.
Make sure the project is visible by everyone.
- Introduce yourself in the forum and, for those who need, familiarize yourself with mycourses interface, make sure you add the link to your GIT project from point 1.
Check these 10 papers about brain connectivity https://users.aalto.fi/~eglerean/NBEHBC/ . Do not read them carefully. Only read the title, skim the abstract and look at the figures (read the captions if you are intrigued). Now sort the papers in order from the one you liked most to the one you liked least. Submit your answer as ordered list in one single row (e.g.: 10 5 3 4 6 8 2 1 9 7) as a csv file saved in your git repository from point 1. Call it pretask1.csv
- Chai, L. R., Mattar, M. G., Blank, I. A., Fedorenko, E., & Bassett, D. S. (2016). Functional network dynamics of the language system. Cerebral Cortex.
- Cole, M. W., Bassett, D. S., Power, J. D., Braver, T. S., & Petersen, S. E. (2014). Intrinsic and task-evoked network architectures of the human brain.Neuron, 83(1), 238-251.
- Smith, S. M., Nichols, T. E., Vidaurre, D., Winkler, A. M., Behrens, T. E., Glasser, M. F., ... & Miller, K. L. (2015). A positive-negative mode of population covariation links brain connectivity, demographics and behavior.Nature neuroscience, 18(11), 1565-1567.
- Finn, E. S., Shen, X., Scheinost, D., Rosenberg, M. D., Huang, J., Chun, M. M., ... & Constable, R. T. (2015). Functional connectome fingerprinting: identifying individuals using patterns of brain connectivity. Nature neuroscience.
- Drysdale, A. T., Grosenick, L., Downar, J., Dunlop, K., Mansouri, F., Meng, Y., ... & Schatzberg, A. F. (2016). Resting-state connectivity biomarkers define neurophysiological subtypes of depression. Nature Medicine.
- Mueller, S., Wang, D., Fox, M. D., Yeo, B. T., Sepulcre, J., Sabuncu, M. R., ... & Liu, H. (2013). Individual variability in functional connectivity architecture of the human brain. Neuron, 77(3), 586-595.
- Margulies, D. S., Ghosh, S. S., Goulas, A., Falkiewicz, M., Huntenburg, J. M., Langs, G., ... & Jefferies, E. (2016). Situating the default-mode network along a principal gradient of macroscale cortical organization. Proceedings of the National Academy of Sciences, 113(44), 12574-12579.
- Power, J. D., Cohen, A. L., Nelson, S. M., Wig, G. S., Barnes, K. A., Church, J. A., ... & Petersen, S. E. (2011). Functional network organization of the human brain. Neuron, 72(4), 665-678.
- Poldrack, R. A., Laumann, T. O., Koyejo, O., Gregory, B., Hover, A., Chen, M. Y., ... & Hunicke-Smith, S. (2015). Long-term neural and physiological phenotyping of a single human. Nature communications, 6.
- Smith, S. M., Miller, K. L., Salimi-Khorshidi, G., Webster, M., Beckmann, C. F., Nichols, T. E., ... & Woolrich, M. W. (2011). Network modelling methods for FMRI. Neuroimage, 54(2), 875-891.
Lecture slides and material
Slides and materials are at the bottom of this page.
If you couldn't make it to the first contact session, please catch up with the others with the assignment here below.