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Functional Brain Imaging Experimental Design and Analysis

Course Syllabus

Description

This course will provide theoretical and practical training on functional magnetic resonance imaging (fMRI) experimental design, data preprocessing, and analysis. The fMRI data analysis programs and tools used in this course will be Statistical Parametric Mapping 12 (SPM12) running on Matlab, Mricron, AAL Atlas, MarsBar toolbox, REST toolbox. Other tools will also be introduced as needed.

Objective

  • Understand basic concepts underlying fMRI experimental design for investigating human mental processes.
  • Understand basic concepts underlying fMRI human brain data preprocessing and statistical analysis.(3) Use SPM and Matlab software tools to analyze sample human fMRI data.
  • Write up a manuscript reporting the background, methods, results, and conclusions regarding the in-class analysis practicum.|

Requirements

Admission priority is given to graduate students of the Graduate Institute of Brain and Mind Sciences. Students external to this institute are encouraged to seek approval from their advisors and the course instructors regarding suitability.

Students must bring their own computers with their own copy of Matlab installed. Basic familiarity with the Matlab environment is not required but strongly recommended prior to this course.

There are three general course assignment types.

  • Students will be given a sample fMRI dataset to analyze. There will be some exercises based on the dataset provided in some weeks to help students apply lecture content. Exercises will be graded as complete/incomplete. Completion of all exercises will count towards 30% of the total grade. Students are free to work individually for these exercises or engage in team work (see below).
  • There will be a team in-class presentation based on the fMRI dataset on the last day of class. Teams will be decided in-class pending class size. It is recommended each team have at least 3 persons. A team grade will be applied that is peer assigned based on presentation quality. The presentation will count towards 10% of the total grade.
  • Finally, students will then submit a research report as individuals based on their team analysis. The report must be in a standard research manuscript format consisting of a title, abstract, introduction with background and hypothesis, methods, results, discussion, and references. The report must be in English, APA format, Times New Roman font, 12 pt font size, double-spaced, and no more than 30 pages. The report will include appropriate Tables and Figures. The report is due 1 week after the last class by 2359hrs. This final report will count towards 60% of the total grade.

Workload

Weekly word load will vary widely. Students should expect to spend approximately 1 hr everyday (total 7 hrs/week) on average to try out data analysis programs and to completely process the data set for the class assignments and engage in team work.

References

  • Functional Magnetic Resonance Imaging, Second Edition (2004) by Scott A. Huettel, Allen W. Song, Gregory McCarthy, Sinauer Associates, Sunderland, MA, USA.
  • https://andysbrainbook.readthedocs.io/en/latest/
  • https://textbook.nipraxis.org/intro.html
  • Applied Linear Regression Models- 4th Edition with Student CD. (2004) (4 edition). Boston; New York: McGraw-Hill Education.
  • Introduction to the Practice of Statistics: w/Student CD. (2007) (6th edition). Basingstoke: W. H. Freeman.
  • Ballesteros et al. (2013). Neural correlates of conceptual object priming in young and older adults: an event-related functional magnetic resonance imaging study, 34, 1254-1264.