Introduction to Brain Science and fMRI

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Akama Hiroyuki 
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Lecture notes updated
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Fall Semester
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Outline of lecture

As a new functional magnetic resonance imaging(fMRIシ影nvironment will be established in Tokyo Tech, this subject provides skills of a basic neuro-imaging technology using the fMRI scanner. Students will get the basic knowledge about the cognitive brain science which have been brought from the fMRI techniques as well as control techniques against electro-magnetic artifacts produced in the brain laboratory.

Purpose of lecture

As a new functional magnetic resonance imaging (fMRI) environment has been established in Tokyo Tech, this subject provides practical skills in neuroimaging data acquisition and analysis using the fMRI scanner (Signa HDxt 3.0T, GE Healthcare) in the O-okayama campus. The aim of this course is to bring to the potential users of the fMRI scanner at Tokyo Tech the most practical information about the software applications indispensable through the workflow of the fMRI experiments. (This lecture will be provided in English as well as in Japanese.)

Plan of lecture

No.1:November 4th, No.2:November 11th, No.3:November 18th, No.4:November 25th, No.5:December 2nd, No.6: December 9th, No.7:December 16th. Time slots: 5-6 (13:20~14:50) at the 2nd Practice room of Global Scientific Information and Computing Center (GSIC).

No.1~No.3: E-Prime2.0
First, students will learn the programming skill of E-Prime 2.0 for providing stimuli to be given to fMRI participants and recording their behavioral responses during the task. The information given here will be directly useful for running fMRI experiments at Tokyo Tech.
1)Making a program for trigger synchronization
2)Recording responses made by the fMRI-safe response pad
3)Visual stimuli through the projector
4)Auditory stimuli through the fMRI-safe headset
5)Multimodal stimuli using a slide object
6)Jittering (how to randomize duration times)
7)Running the E-run programs for fMRI experiments
(how to collaborate with the operator)

No.4~No.6: SPM8 (enhanced with Python2.5)
Second, there will be a practice of SPM8 using the educational computer system at GSIC from the preprocessing of the brain images through the statistical analyses applied to the treated data.
1)File formats of brain images (DICOM, Analyze, NIFTI)
2)Concept of dependency in SPM8
3)Preprocessing from realignment through smoothing
4)ROI analysis using masks by wfu_pickatlas
5)First-level analysis using GLM
6)Second-level analysis (Fixed effect and random effect)
7)2-sample t-test and factorial design

No.7: MRICron, FSL-View or Matlab
Third, various techniques using MRICron (run on the platform of the Educational Computer System), FSL-View or Matlab will be introduced for manipulating the voxel-based information for the extended approaches in brain science.
1)Voxel coordinate system
2)MNI, Talairach and coordinate conversion
3)How to extract the voxel values from image files
4)Advanced topics: ICA, MVPA, fcMRI, etc.

Textbook and reference

Lecture note will be downloadable from
Students wishing to attend the course are requested to watch the program of this course held last year by Prof. Jorge Jovicich (University of Trento, Italy) to gain knowledge about the fMRI basics.
and to read beforehand to get the flavor of this research field. If you want to study fMRI seriously, it is highly recommended to read Scott A. Huettel, Allen W. Song, and Gregory McCarthy, Functional Magnetic Resonance Imaging, Second Edition, Sinauer, 2009

Related and/or prerequisite courses

Computational Brain Science and Complex Networks with Matlab (SPM) (2010, Spring semester)
Applied Programming(Social Engineering)


Full attendance is required.

Comments from lecturer

Attention: This course is subject to further revisions. Credit from this course can be counted towards completing the International Human Economic Science Special Course. For the more detailed information about the course, please refer to
(Sorry! only in Japanese)
Also, feel free to contact Prof. Akama (

Contact Information

The lecturer is available after each session in the same Practice room.

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