Neuroscience 222: Brain Imaging and Brain Stimulation

Spring 2022

Tuesdays and Thursdays, noon - 1:50pm

Bunche Hall 2150


Shantanu Joshi

Course description and learning outcomes

You are probably aware that brain imaging and brain stimulation, especially in its noninvasive form, form large fields of the human systems and clinical neuroscience literature. There are many brain imaging and brain stimulation approaches currently available that have been also combined in many different ways. These are exciting and rapidly evolving topics. Together we will explore the variety of experimental approaches in the fields of brain imaging and brain stimulation, discussing their strengths and weaknesses. We will study the use of brain imaging in isolation or in combination with brain stimulation to better investigate and understand neural circuitry, systems and networks in health and disease. We will use critical thinking about the opportunities and limitations of the two fields, and how to overcome them by combining the two approaches for the investigation of brain systems and functions. The best way to take advantage of the opportunities this course offers is to be an active and thoughtful participant in all aspects of the course and try your best in all its components.



Course assignments

We will have weekly assigned readings relevant to each lecture to complete before the lecture so that we are all on the same page and can engage in lively interactions and discussions in class. You will be required to complete a hands-on research project for the class that will make use of computational methods for analyzing data from brain imaging and brain stimulation experiments, so that you will become more familiar with the scientific practices of the two fields and their underlying assumptions.

Student evaluation:

The course is divided into two main modules in which we will explore first the brain imaging literature and its methods, and then the brain stimulation literature, with its many forms and its many combinations with brain imaging. There will be two exams: one at the end of the Brain Imaging module and one at the end of the Brain Stimulation module. Each exam will be weighted 40% of the final grade. The exams are meant to show yourself and us what you have learned and what you still may want to learn to expand your understanding of the fields of brain imaging and brain stimulation. The research project will be weighted 20% of the final grade.

Inclusive classroom interaction and environment

We envision engaging, exciting discussions in the classroom about the possibilities, promises and limitations of current brain imaging and brain stimulation approaches. We are committed to promoting an inclusive and supporting environment for class interaction and participation.

CCLE Website:

Assigned Reading:

We will assign papers each week focused on the lecture topics. These will be added to this website once assigned.


Week Date Topic Instructor
129-Mar-2022Course Introduction
Iacoboni / Joshi / Shattuck
Allan MacKenzie-Graham, PhD
131-Mar-2022NeuroanatomyAllan MacKenzie-Graham, PhD
205-Apr-2022MR PhysicsRobert Welsh, PhD
207-Apr-2022MR PhysicsRobert Welsh, PhD
312-Apr-2022Structural and Diffusion MRI Processing and AnalysisDavid Shattuck, PhD
314-Apr-2022Diffusion MRI: Applications and In Vivo Virtual Dissection TutorialStephanie Forkel, PhD
4a19-Apr-2022Positron Emission Tomography (PET)Roger Woods, MD
4b21-Apr-2022Functional MRI (fMRI)Martin Monti, PhD
526-Apr-2022Shape Modeling/Statistical AnalysisShantanu Joshi, PhD
528-Apr-2022Review Brain Imaging
603-May-2022Project and Software Discussion / Exam I
605-May-2022Transcranial Direct Current Stimulation (tDCS) & Head Modeling/SimulationMayank Jog, PhD
7a10-May-2022Transcranial Magnetic Stimulation (TMS) Foundations, Physiology, and Circuitry Marco Iacoboni, MD PhD
7b12-May-2022TMS Perturbation and MappingMarco Iacoboni, MD PhD
8a17-May-2022TMS Treatment and SafetyMarco Iacoboni, MD PhD
8b19-May-2022Transcranial Ultrasound (tUS)Taylor Kuhn, PhD
924-May-2022Intracranial Electrophysiology and Deep Brain StimulationMatthias Stangl, PhD
926-May-2022Project & Exam I Discussion
1031-May-2022Review Brain Stimulation
102-Jun-2022Student Project Presentations


Reading assignments will be added here.
  1. Neuroanatomy
  2. MR Physics
  3. Structural and Diffusion MRI
  4. Positron Emission Tomography & Functional Magnetic Resonance Imaging
    4a. PET
  5. 4b. fMRI
  6. Shape Analysis
  7. Transcranial Direct Current Stimulation (tDCS) & Head Modeling/Simulation
  8. Transcranial Magnetic Stimulation (TMS)
    7a. TMS Foundations, Physiology, and Circuitry 7b. TMS Perturbation and Mapping 8a. TMS Treatment and Safety
  9. 8b. Transcranial Ultrasound (tUS)
  10. Intracranial Electrophysiology and Deep Brain Stimulation