More on methods

2025-09-02

Rick Gilmore

Department of Psychology

Prelude

Eames Office (2010)

Today’s topics

  • Announcement
  • Warm up
  • Wrap up on structural methods
  • Functional methods

Announcement

Warm up

Why should we care?

  • “We just have to see the wires.” (J. Lichtman)
  • What are the parts?
  • How do they connect?
  • How do they interact?
  • Different methods reveal different aspects of structure & function

What method does the image reflect?

  • A. Retrograde tract tracing
  • B. Magnetic Resonance Imaging (MRI)
  • C. Computed Tomography (CT)
  • D. Nissl (whole cell) stain

What method does the image reflect?

  • A. Retrograde tract tracing
  • B. Magnetic Resonance Imaging (MRI)
  • C. Computed Tomography (CT)
  • D. Nissl (whole cell) stain

Descartes thought that the pineal gland…

  • A. Was where the soul controlled the body
  • B. “Inflates” the muscles
  • C. Both A and B.
  • D. Releases melatonin into the blood stream

Descartes thought that the pineal gland…

  • A. Was where the soul controlled the body
  • B. “Inflates” the muscles
  • C. Both A and B.
  • D. Releases melatonin into the blood stream

Study suggestions

  • Identify key vocabulary and ideas
  • Look away from the slides or book
  • Quiz yourself (or work with others)
    • Who’s Descartes? What did he do/think?
    • Spatial resolution means…
  • Look at a figure, explain what it is/means
  • Spend ~2-3 hours outside of class for every hour in class

Wrap-up on structural methods

Cellular methods

Functional methods

Types of functional methods

  • Recording from the brain
  • Interfering with the brain
  • Stimulating the brain
  • Simulating the brain

Recording from the brain

  • Single/multi unit recording
    • Microelectrodes
    • Units -> Small numbers of nerve cells

Single/multi-unit Recording

  • What does neuron X respond to?
  • High temporal (ms) & spatial resolution (um)
  • Invasive
  • Used in non-human animals for purely research purposes

Figure 1 from Nishimura, Ikegaya, & Sasaki (2021)

Electrocorticography (ECoG)

  • Used in human neurosurgery

ECoG

AANSNeurosurgery (2019)

Positron Emission Tomography (PET)

  • Radioactive tracers (glucose, oxygen) delivered intravenously
  • Positron decay
  • Experimental condition - control
  • Average across individuals

National Institute of Biomedical Imaging and Bioengineering (2013)

PET

  • Temporal (~ s) and spatial (mm-cm) resolution worse than fMRI
  • Radioactive exposures + mildly invasive
  • Dose < airline crew exposure in 1 yr

Petersen, Fox, Posner, Mintun, & Raichle (1988)

Functional Magnetic Resonance Imaging (fMRI)

  • Neural activity -> local \(O_2\) consumption increase

fMRI data on emotion processing: https://www.cmu.edu/news/stories/archives/2013/june/images/happysadbrainactivity_400x200.jpg”

fMRI

  • Blood Oxygen Level Dependent (BOLD) response
    • Oxygenated vs. deoxygenated hemoglobin creates magnetic contrast
    • Do regional blood \(O_2\) volumes (and flow) vary with behavior X?

https://mriquestions.com/does-boldbrain-activity.html

Mapping visual cortex

  • “Mapping” = what areas respond to what input


Charting (2020a)

Charting (2020b)

fMRI

  • Non-invasive, but expensive ($500/hr)
  • Moderate but improving spatial (mm), temporal (~sec) resolution
  • Indirect measure of brain activity

fMRI

“Magnetism” (n.d.)

Electroencephalography (EEG)

  • How does it work?
    • Electrodes on scalp or brain surface
  • What do we measure?
    • Combined activity of huge # of neurons
  • High/fine temporal resolution (detect fast changes) but poor spatial resolution

Wikimedia

EEG

  • Activity in different frequency bands
    • LOW (slow changes): deep sleep
    • MIDDLE: Quiet, alert state
    • HIGH (fast changes): “Binding” information across senses

Vallat (n.d.)

Brain Computer Interface (BCI)

  • Often based on EEG.

Magneto-encephalography (MEG)

  • Like EEG, but measures magnetic fields
  • High temporal resolution, low spatial resolution
  • Magnetic field propagates with minimal distortion from brain/skull, unlike electric field

Manipulating the brain

  • Nature’s “experiments”
    • Stroke, head injury, tumor
    • Neuropsychology
  • If damage to X impairs performance on Y -> X critical for/controls Y
  • Poor spatial/temporal resolution, limited experimental control

The case of Phineas Gage

Stimulating the brain

Trans-cranial Direct Current Stimulation (tDCS)

Dayan, Censor, Buch, Sandrini, & Cohen (2013)

Trans-cranial Magnetic Stimulation (TMS)

Dayan et al. (2013)

Optogenetic stimulation

Video (2010)

Evaluating stimulation methods

  • Spatial/temporal resolution?
    • Does stimulation mimic natural activity?
    • Optogenetic stimulation highly similar, others less so
  • Deep brain stimulation as therapy
    • Parkinson’s Disease
    • Depression
    • Epilepsy

Deep brain stimulation (DBS)

Understanding Animal Research (2009)

Simulating the brain

  • Computer/mathematical models of brain function
  • Example: neural networks
  • Cheap, noninvasive, can be stimulated or “lesioned”

Application: AI

Redmon (2018)

Spatial and Temporal Resolution revisited

Sejnowski, Churchland, & Movshon (2014)

Take homes

  • Functional methods differ in
    • Spatial resolution
    • Temporal resolution
    • What’s measured
    • Invasiveness
    • Cost
  • Which one is best? Depends on your question.

Next time

  • Cells of the nervous system
  • Neuroanatomy

Resources

About

This talk was produced using Quarto, using the RStudio Integrated Development Environment (IDE), version 2025.5.1.513.

The source files are in R and R Markdown, then rendered to HTML using the revealJS framework. The HTML slides are hosted in a GitHub repo and served by GitHub pages: https://psu-psychology.github.io/psych-260-2025-fall/

References

AANSNeurosurgery. (2019). Intraop awake brain mapping & multimodal image-guided resection of dominant side glioma. Youtube. Retrieved from https://www.youtube.com/watch?v=gFky09ekmzw
Charting, I. B. (2020a). Retinotopy task – ring-expanding run. Youtube. Retrieved from https://www.youtube.com/watch?v=DcgHJIlwQCo
Charting, I. B. (2020b). Retinotopy task – wedge-clockwise run. Youtube. Retrieved from https://www.youtube.com/watch?v=rsykP-9-moA
Dayan, E., Censor, N., Buch, E. R., Sandrini, M., & Cohen, L. G. (2013). Noninvasive brain stimulation: From physiology to network dynamics and back. Nature Neuroscience, 16, 838–844. https://doi.org/10.1038/nn.3422
Eames Office. (2010). Powers of Ten™ (1977). YouTube. Retrieved from https://www.youtube.com/watch?v=0fKBhvDjuy0
Magnetism. (n.d.). Retrieved August 19, 2025, from http://mriquestions.com/does-boldbrain-activity.html
National Institute of Biomedical Imaging and Bioengineering. (2013). How does a PET scan work? YouTube. Retrieved from https://www.youtube.com/watch?v=GHLBcCv4rqk
Nishimura, Y., Ikegaya, Y., & Sasaki, T. (2021). Prefrontal synaptic activation during hippocampal memory reactivation. Cell Reports, 34(12), 108885. https://doi.org/10.1016/j.celrep.2021.108885
Petersen, S. E., Fox, P. T., Posner, M. I., Mintun, M., & Raichle, M. E. (1988). Positron emission tomographic studies of the cortical anatomy of single-word processing. Nature, 331, 585–589. https://doi.org/10.1038/331585a0
Redmon, J. (2018). YOLOv3. YouTube. Retrieved from https://www.youtube.com/watch?v=MPU2HistivI
Sejnowski, T. J., Churchland, P. S., & Movshon, J. A. (2014). Putting big data to good use in neuroscience. Nat. Neurosci., 17(11), 1440–1441. https://doi.org/10.1038/nn.3839
Understanding Animal Research. (2009). Parkinson’s disease. YouTube. Retrieved from https://www.youtube.com/watch?v=KDjWdtDyz5I
Vallat, R. (n.d.). Bandpower of an EEG signal. Retrieved August 19, 2025, from https://raphaelvallat.com/bandpower.html
Video, N. (2010). Method of the year 2010: Optogenetics - by nature video. Youtube. Retrieved from https://www.youtube.com/watch?v=I64X7vHSHOE&list=PLRstm0n591-rBbOeC0SJEy20-NwXpLo4G