Complete MIT course "The Human Brain"
Goal Accomplishment Criteria
All papers are read, all assignments are completed, all lectures are watched
Lecture 1: Introduction
Kanwisher, N. "Functional specificity in the human brain: A window into the functional architecture of the mind." PNAS 107, no. 25 (2010): 11163–70.
Marr, D. "General Introduction" and "Chapter 1: The Philosophy and Approach" in Vision: A Computational Investigation in the Human Representation and Processing of Visual Information.
Notes: that was a rather challenging reading.
What I got from the chapter:
1. Historical views and methods to describe vision.
2. How to approach perceive: how, what, why. Levels of perceptions, what we need to be able to perceive, what is primary and without what we can not understand and describe.
3. Fly vision. Purposes of vision of animals. How human vision is different and more advanced. Difficlties in understanding that.
Visual pathways from retina to cortex
retina, photoreceptor, rods and cones, fovea, retinal ganglion cells, receptive field, LGN(lateral geniculate nucleus), retinotopy(we’ll go over this in class), orientation selectivity, and ocular dominance columns.
Introduction to Neuroscience
Bear, Mark F., Barry W. Connors, and Michael A. Paradiso. Neuroscience: Exploring the Brain, 3rd ed. Baltimore, MD: Lippincott Williams & Wilkins, 2006. ISBN: 9780781760034
Part 1: Neurons
Cellular neuroanatomy: neurons and glia
Neurophysiology 1: resting potential
Neurophysiology 2: action potential
Synaptic transmission 1: physiology
Synaptic transmission 2: chemistry
Part 2: Neural systems
Organization of the vertebrate brain
Vision 1: the eye Vision 2: thalamus and V1 cortex
Vision 3: beyond V1
Motor system 1
Motor system 2
Part 3: Brain and behavior
Chemical control of brain 1
Chemical control of brain 2 motivation
Learning and memory 1
Learning and memory
Lecture 2: Neuroanatomy
Note: Lecture 2 should help but hopefully not be required for this assignment.
Article: Tootell, R.B.H., J.B. Reppas, et al. "Visual Motion Aftereffect in Human Cortical Area MT Revealed by Functional Magnetic Resonance Imaging." Nature 375 (1995): 139–41. DOI: 10.1038/375139a0
Assignment: Read the assigned article carefully (expect to spend at least one hour on this, possibly more) and think about it, then provide short answers to the questions below.
- What is the characteristic functional (response) property of cortical area MT (V5)? Answer in a phrase or sentence.
- Which aspect of Figure 2 shows the central new finding of the paper?
- Does activity in cortical area MT reflect what the subject is perceiving, or what visual information is arriving on the retina? Answer and explain in at most 3 clear sentences.
Thorpe, S., D. Fize, and C. Marlot. "Speed of Processing in the Human Visual System." Nature 381, no. 6582 (1996): 520–22. DOI: 10.1038/381520a0
Lecture 3: Master Class: Human Brain Dissection with Guest Lecturer Ann Graybiel (video not recorded)
Find another similar lecture
Lecture 4: Cognitive Neuroscience Methods I
Article: Downing, P.E., Y. Jiang, et al. "A Cortical Area Selective for Visual Processing of the Human Body." Science 293 (2001): 2470–73. DOI: 0.1126/science.1063414
Assignment: Read the assigned article carefully and think about it, then provide short answers to the questions below. Be clear and concise, points will be taken off for unnecessary words.
- Give three pieces of evidence that the selectivity for the EBA does not simply reflect the presence of particular low-level visual features.
- The authors state that they identified the EBA in each subject with a localizer scan. What is a localizer scan and why is it important?
- Do the findings in this paper show that the EBA meets all the criteria for a distinct cortical area? Explain.
- What do you want to know next about the EBA and how might you test it with fMRI?
a) State a specific hypothesis that you could test with fMRI (one sentence).
b) What conditions would you need to include to test your hypothesis? Describe each briefly.
c) What, specifically, would you expect to find empirically in your conditions if your hypothesis is true?
Lecture 5: Cognitive Neuroscience Methods II
Haxby, J.V., M.I. Gobbini, et al. "Distributed and Overlapping Representations of Faces and Objects in Ventral Temporal Cortex." Science 293 (2001): 2425–30. DOI: 10.1126/science.1063736
Pitcher, D., L. Charles, et al. "Triple Dissociation of Faces, Bodies, and Objects in Extrastriate Cortex." Current Bio. 19 (2009): 319–24. DOI: 10.1016/j.cub.2009.01.007
Assignment: Design two fMRI experiments to test whether the brain contains regions that are selectively involved in perceiving snakes. In each case, state i) the specific hypothesis you are testing, ii) the experimental conditions you will test (including what study participants will see and do in your experiment), iii) what exactly you will measure, and iv) what your hypothesis predicts you will see. You can describe stimuli with words, sketch them, or find them and paste them in (with appropriate explanations). Next, list the alternative accounts that might remain even if the data from this experiment are consistent with the predictions of your hypothesis. Then, describe a second experiment to test one or more of those alternative hypotheses. Finally, list two important questions about snake-specific regions in the brain that can never be tested with fMRI, and give a different method that could be used to test each.
Article: Knops, A., B. Thirion, et al. "Recruitment of an Area Involved in Eye Movements During Mental Arithmetic." Science 324, no. 5934 (2009): 1583–85. DOI: 10.1126/science.1171599
Assignment: Read the assigned article carefully and think about it, then provide short answers to the questions below. You can do this by responding straight on this document or by submitting a separate document with numbered answers. Be clear and concise—points will be taken off for unnecessary words.
- What is the central empirical claim of the paper in a single sentence?
- Is the data in this paper consistent with the idea that a brain region exists that is specifically engaged in processing number and arithmetic only? Why or why not.
- What is the contrast that Knops et al. used to identify the standard brain regions engaged in saccades (eye movements)? Is this contrast a minimal pair? Is that important for this study?
- Can you think of a more general version of Knops et al.’s hypothesis, that applies not just to eye movements but to any rightward versus leftward movement? How might you test this hypothesis using motor cortex? What would the key prediciton be?
Lecture 6: Experimental Design
Lecture 7: Category Selectivity, Controversies, and Multiple Voxel Pattern Analysis (MVPA)
Bryan, P.B., J.B. Julian, and R.A. Epstein. "Rectilinear Edge Selectivity Is Insufficient to Explain the Category Selectivity of the Parahippocampal Place Area." Front. Hum. Neurosci. 10, no. 137 (2016): 1–12. DOI: 10.3389/fnhum.2016.00137in Assignment 4
Robin, J., M.X. Lowe, et al. "Selective Scene Perception Deficits in a Case of Topographical Disorientation." Cortex 92 (2017): 70–80. DOI: 10.1016/j.cortex.2017.03.014
This optional background reading covers much of the material for this week:
Epstein, R.A., E.Z. Patai, et al. "The Cognitive Map in Humans: Spatial Navigation and Beyond." Nature Neuroscience 20 (2017): 1504–13. DOI: 10.1038/nn.4656
Article: Bryan, P.B., J.B. Julian, and R.A. Epstein. "Rectilinear Edge Selectivity Is Insufficient to Explain the Category Selectivity of the Parahippocampal Place Area." Front. Hum. Neurosci. 10, no. 137 (2016): 1–12. DOI: 10.3389/fnhum.2016.00137
Assignment: Read the paper and answer the questions below.
- Describe the main conclusion of the paper in one sentence.
- Explain the main point of Figure 4 in one sentence.
- Describe the stimulus conditions you would need and the key prediction you would make to test the hypothesis that the FFA contains information about the curviness of faces.
Lecture 8: Navigation I
Lecture 9: Navigation II
Development, Nature & Nurture
Sugita, Y. "Face Perception in Monkeys Reared with No Exposure to Faces." PNAS 105, no. 1 (2008): 394–98. DOI: 10.1073/pnas.0706079105
Ullman, S., D. Harari, and N. Dorfman. "From Simple Innate Biases to Complex Visual Concepts." PNAS 109, no. 44 (2012): 18215–20. DOI: 10.1073/pnas.1207690109
Article: Sugita, Y. "Face Perception in Monkeys Reared with No Exposure to Faces." PNAS 105, no. 1 (2008): 394–98. DOI: 10.1073/pnas.0706079105
Assignment: Read the assigned article carefully and think about it, then provide short answers to the questions below. Be clear and concise—points will be taken off for unnecessary words.
Notes: This is a hard assignment. Two videos that might also be helpful are:
- Nancy's Brain Talks: How do you ask a preverbal infant what she can see?
- Nancy's Brain Talks: What is the role of experience in the development of face recognition?
Read whole assignment -> https://ocw.mit.edu/courses/brain-and-cognitive-sc...
Lecture 10: Development, Nature & Nurture I
Lecture 11: Development, Nature & Nurture II (class canceled; students watched lecture from 2018)
Lecture 13: Number Even infants, spiders, and frogs can count. What is the nature of the human representation of number, and how is it imple
Lecture 12: Brain-Machine Interface with Guest Lecturer Michael Cohen
Lecture 14: New Methods Applied to Number (video not recorded)
Number, Hearing, and Speech
Knops, A., B. Thirion, et al. "Recruitment of an Area Involved in Eye Movements During Mental Arithmetic." Science 324, no. 5934 (2009): 1583–85. DOI: 10.1126/science.1171599
Tang, C., S. Hamilton, and E.F. Chang. "Intonational Speech Prosody Encoding in the Human Auditory Cortex." Science 357, no. 6353 (2017): 797–801. DOI: 10.1126/science.aam8577
Fisher, J., J.G. Mikhael, et al. "Functional Neuroanatomy of Intuitive Physical Inference." PNAS 113, no. 34 (2016): E5072–E5081. DOI: 10.1073/pnas.1610344113
Music and Language
Lagrois, M., and I. Peretz. "The Co-occurrence of Pitch and Rhythm Disorders in Congenital Amusia." Cortex 113 (2019): 229–38. DOI: 10.1016/j.cortex.2018.11.036
Wurm, M.F., and A. Caramazza. "Distinct Roles of Temporal and Frontoparietal Cortex in Representing Actions across Vision and Language." Nature Communications 10, no. 289 (2019): 1-10. DOI: 10.1038/s41467-018-08084-y
Article: Tang, C., S. Hamilton, and E.F. Chang. "Intonational Speech Prosody Encoding in the Human Auditory Cortex." Science 357, no. 6353 (2017): 797–801. DOI: 10.1126/science.aam8577
Assignment: Read the assigned article carefully (expect this to take at least two hours, possibly more) and think about it, then provide short answers to the questions below. You can do this by responding straight on this document or by submitting a separate document with numbered answers. Be clear and concise, points will be taken off for unnecessary words.
A few things that are not well explained in the paper:
- I didn’t see a definition of H gamma (indicated as the Greek letter which I cannot get my text editor to make) in the figures – this is just “high gamma power”, which is the main measure of neural response used in this paper and in other intracranial recording studies.
- When the paper refers to “spectral information” (which I highlighted in orange), that just refers to different amounts of power at different frequencies. See the “spectrogram” in Figure 1A, which shows auditory power (darkness) as a function of time (x axis) and auditory frequency (y axis).
- You can ignore the stuff about the “missing fundamental” (highlighted in orange).
TA tip: when reading, try to focus on the figures and make sure you understand them. Refer back to the text for supporting information when needed.
- What method does this paper use?
- What is the main (most important) empirical finding in the paper? What figure illustrates this finding?
- What is the design of this experiment? That is, what factors were manipulated (list each), and how many different conditions were used?
- What does Figure 1E show?
- The middle graph in figure 2N shows 147 electrodes that had information about which sentence was spoken. Could you decode from these electrodes whether the speaker saying those sentences was male or female?
- Would you expect the electrodes that can discriminate intonation to be able to discriminate musical melodies (in which each note has a different pitch)? If so, how would you characterize the function of those sites?
- If the same experiment were repeated using fMRI, what results would you expect?
Article: Fischer, J., J.G. Mikhael, et al. "Functional Neuroanatomy of Intuitive Physical Inference." PNAS 113, no. 34 (2016): E5072–E5081. DOI: /10.1073/pnas.1610344113
Assignment: Read the assigned article and think big about the problem it addresses. Think of this article as essentially a first baby step in a broader line of work. What questions does this article answer, and what do you want to know next?
For the next assignment you will have a significant written experimental design assignment (15% of your course grade) designing your own experiment (or two) to ask one of the next questions about intuitive physics in the brain, using any of the methods you have learned about in the course.
For now you are asked only to read this article and answer questions about it. But as you read it, start thinking about the broader space of questions this article opens up, and what you might propose for the larger experimental design assignment.
Provide short answers to the questions below. Be clear and concise—points will be taken off for unnecessary words.
- What is the main question addressed in this article?
- What is the main answer the article provides about that question?
- Briefly contrast the logic of Experiment 1 and Experiment 2. In what way are the two designs complementary?
- Scrutinize the data shown for regions P3R and P1R in Figure 3B. What do these data suggest to you?
- Are the frontal and parietal regions identified in this study highly specialized for intuitive physical reasoning per se?
- List three big questions you might want to answer next in this line of work, and for each one list a method that might be able to answer (or start to answer) that question.
Lecture 15: Hearing and Speech Humans use hearing in species-specific ways, for speech and music. Ongoing research is just now working out t
Lecture 16: Music
Lecture 17: MEG Decoding and RSA (video not recorded)
Find something similar
Lecture 18: Language I Language is our signature human cognitive skill. Cognitive neuroscience has only recently started to understand its b
Lecture 19: Language II (class canceled, video not recorded))
Theory of Mind and Brain Networks
Ullman, T.D., E. Spelke, et al. "Mind Games: Game Engines as an Architecture for Intuitive Physics." Trends in Cognitive Sciences 21, no. 9 (2017): 649–65. DOI: 10.1016/j.tics.2017.05.012
Kubrich, J.R., K.J. Holyoak, et al. "Intuitive Physics: Current Research and Controversies." Trends in Cognitive Sciences 21, no. 10 (2017): 749–59. 10.1016/j.tics.2017.06.002
Lecture 20: Mentalizing and Theory of Mind From an early age, humans spend much of their time thinking about what other people are thinking.
Experimental Design Assignment
Assignment: Design an experiment using any of the methods of human cognitive neuroscience that we have discussed in the class to address the brain basis of intuitive physics. The biggest part of this task is to come up with a good idea for an experiment that asks an important, interesting, and theoretically motivated question about intuitive physical inference in the human brain. Because a single experiment rarely definitively answers a question, you should include two linked experiments, the second one addressing questions left unanswered by the first. Think hard about and provide important details about your task and stimuli. The difference between a beautiful experiment and a "meh" experiment is often in the specifics of the stimuli. (Work to come up with good ones and show examples!) Extra points for creativity, but note that usually the best experiments are simple and elegant. (Crazy-complicated experiments almost never work.)
Beyond coming up with two successive nicely designed experiments that ask important questions, it is also important to write up your ideas clearly. So, edit your prose multiple times to remove extra words and promote clarity. This assignment counts for 15% of your course grade. Expect to spend many hours on it. You may not propose an experiment that has already been published.
You have already read the very relevant Fischer et al. (2016) paper. I recommend you brainstorm for a while on your own, taking notes, and only after that read Ullman et al. (2017) and/or Kubrich et al. (2017), then revisit and perhaps revise your ideas.
Your writeup may be only a few pages (short is good), but must do the following (for each of your two experiments):
- Clearly state your hypothesis and motivate on theoretical and empirical grounds why it is important. This should require 1–3 clearly written paragraphs referring to what we already know from common sense / everyday experience and/or prior studies (including citations, with full references at the end).
- Describe your experimental design, listing all factors manipulated, all conditions within each factor, and measures collected.
- Describe what subjects will actually do (the task) and what happens in each trial including the precise sequence of events and their timing.
- How will the data be analyzed? I don’t need the level of detail of a methods section in a published paper, but I do need enough to understand the logic of the experiment (at the level used in lectures in class).
- State or draw the precise predictions of your hypothesis and note which (if any) are main effects and which are interactions.
- Discuss what you can infer from each of the main possible data outcomes. Consider alternative accounts of each of these possible outcomes. Especially if the prediction of your hypothesis is borne out by the data, what would you still need to worry about, and what other experiments might address those remaining concerns? This is how you will motivate your second experiment, and even after the second experiment you may still be left with alternative accounts and unanswered questions, which you should describe.
Lecture 21: Brain Networks
Lecture 22: Experimental Design (video not recorded) Lecture 23: Deep Networks (updated 2021 video)
Lecture 24: Attention and Awareness
- 06 November 2021, 17:46
Don't miss new posts!
Subscribe for the Goal and follow through to its completion