#1 - 10.04.2018

  • #1 - 10.04.2018

    Contact Session #1

    Human brain networks: What and why. Nodes, edges, and brain graphs.

    Intended learning outcomes:

    1. Understand why we want to study brain connectivity and model the brain as a network
    2. List brain networks and recognize different methods to define nodes and edges
    3. Critically consider the multiple aspects of brain connectivity

    Pre-assignment

    You have three tasks before the first contact session

    1. Go to https://github.com/ (register if you don't have an account) 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.
    2. 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.

    3. 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

    Pre-assignment references

    1. Chai, L. R., Mattar, M. G., Blank, I. A., Fedorenko, E., & Bassett, D. S. (2016). Functional network dynamics of the language system. Cerebral Cortex.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.

    Make-up assignment

    If you couldn't make it to the first contact session, please catch up with the others with the assignment that will appear here below.


    • Restricted Not available unless: You are a(n) Student
      icon for activity Inbox: Return your make up assignment here

      The purpose of the substitute assignment is only for you to be at the same level of other students who attended the first session. If you missed the first contact session, please return your make-up assignment as a single PDF file.

      First, your reading tasks are

      1. Go through the slides of session 1 (link at the bottom of this page)
      2. Go through the interactive work done by other course participants in the forum (threads: what is a node in a brain network? what is a link in a brain network?)
      3. Read the paper  Alex Fornito et al (2013) Graph analysis of the human connectome: Promise, progress, and pitfalls. NeuroImage http://www.sciencedirect.com/science/article/pii/S1053811913004345 (PDF at http://ai2-s2-pdfs.s3.amazonaws.com/0f38/481a31af65a0d43daeebc8fafc0a8d7c3943.pdf)

      Finally, given what you have read, reflect on what is a node and what is a link in a brain network. 
      Write a 800 words essay where you:

      i)  try to summarise the forum discussions combined with what you have read on the paper
      ii) propose your own interpretations of what (could be) a node and a link in a brain network (feel free to include other methods that were not mentioned especially if you are a doctoral student with specific research interests)
      iii) Conclude by highlighting some of the pitfalls as described in the paper and clearly express what you consider to be the major pitfall in your opinion

      Submit the 800 words assignment (Arial 11pt, 1.5 line spacing) as a single PDF file by end of Monday 16/April. If necessary, please include references to other articles (references do not add on word count).


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