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Introduction to Neuroimaging



Image (neuroimaging)

What is Neuroimaging?




Image (fMRI)

functional Magnetic Resonance Imaging (fMRI)

  • Explanation of principles, equipments, methods and analysis and Information of websites related to functional Magnetic Resonance Imaging: fMRI.

      About principles and equipments of fMRI
    • About fMRI movie icon
      • This video is an excerpt a portion of fMRI in the tutorial video how to operate the equipment and measurement principles of brain activity measurements.(You can watch a full-length video from the preceding paragraph "What is Neuroimaging?")

    • explanation of the principle of MRI
      • under construction


      About an analysis program in a fMRI study
    • SPM (Statistical Parametric Mapping)
      • Comprehensive free software used for PET/fMRI analysis. However, numerical computation software MATLAB (commercial) is necessary for operation. The software is quite refined and has been referenced often in studies. Moreover, it is frequently updated, and an extensive mailing list is offered.

    • BrainVoyager
      • Comprehensive commercial software used for PET/fMRI analysis. It has abilities such as 2-dimensional cortical flatmaps which cannot be performed in the above-mentioned SPM software. It is also able to link with applied analysis such as independent component analysis, as well as with signal source analysis software BESA.

      Useful software of fMRI imaging
    • MRIcro
      • Free software that can display various medical images such as MRI.



Image (MEG)

Magnetoencephalography (MEG)

  • Explanation of principles, equipments, methods and analysis and Information of websites related to Magnetoencephalography: MEG.

      About principles and equipments of MEG
    • About MEG movie icon
      • This video is an excerpt a portion of MEG in the tutorial video how to operate the equipment and measurement principles of brain activity measurements.(You can watch a full-length video from the preceding paragraph "What is Neuroimaging?" )

    • Examination of brain function: measurement and analysis of MEG (written in Japanese) (PDF)
      • Basic principles, methods, analyses of MEG are explained.

    • Training text: "Measurement and Analysis of MEG", Research and Education Center for Brain Science, Hokkaido Univ. (written in Japanese) (HTML slides)
      • Principle of SQUID, measurement and analysis methodology, and signal source localization are simply explained.

      About an analysis program in an MEG study
    • BESA
      • Commercial software used to analyze EEG and MEG. Signal source analysis (a.k.a. dipole estimation) is possible with this software.

    • BrainStorm
      • Free software used for EEG and MEG analysis. Various signal source analyses are possible.

    • EEGLAB
      • Free software used for EEG and MEG analysis. Many analyses can be done, including preprocessing (various filters, artifact removal, etc.), additive averaging, frequency analysis, and independent component analysis.

    • FieldTrip
      • Free software used for EEG and MEG analysis. Analyses such as preprocessing, additive averaging, and frequency analysis can be performed. Multiple signal source analyses are also possible.

    • SPM
      • SPM, which is widely used for PET/fMRI analysis, supports EEG and MEG. The SPM8 software is dependant on FieldTrip. It can do preprocessing, additive averaging, signal source estimation, and more. As of March 2009, some parts are still in development; please use accordingly.



Image (NIRS)

Near Infrared Spectroscopy (NIRS)

  • Explanation of principles, equipments, methods and analysis and Information of websites related to Near Infrared Spectroscopy: NIRS.

      About principles and equipments of NIRS
    • about NIRS movie icon
      • This video is an excerpt a portion of NIRS in the tutorial video how to operate the equipment and measurement principles of brain activity measurements.(You can watch a full-length video from the preceding paragraph "What is Neuroimaging?" )

      About an analysis program in a NIRS study
    • NIRS-SPM
      • A NIRS analysis program based on SPM, used for PET/fMRI analysis.



Image (EEG)

Electroencephalography (EEG)

  • Explanation of principles, equipments, methods and analysis and Information of websites related to Electroencephalography: EEG.

      About principles and equipments of EEG
    • about EEG
      • Under construction

      About an analysis program in a EEG study
    • BESA
      • Commercial software used to analyze EEG and MEG. Signal source analysis (a.k.a. dipole estimation) is possible with this software.

    • BrainStorm
      • Free software used for EEG and MEG analysis. Various signal source analyses are possible.

    • EEGLAB
      • Free software used for EEG and MEG analysis. Many analyses can be done, including preprocessing (various filters, artifact removal, etc.), additive averaging, frequency analysis, and independent component analysis.

    • FieldTrip
      • Free software used for EEG and MEG analysis. Analyses such as preprocessing, additive averaging, and frequency analysis can be performed. Multiple signal source analyses are also possible.

    • SPM
      • SPM, which is widely used for PET/fMRI analysis, supports EEG and MEG. The SPM8 software is dependant on FieldTrip. It can do preprocessing, additive averaging, signal source estimation, and more. As of March 2009, some parts are still in development; please use accordingly.



Image (control)

Experimental Control

  • In neuroimaging, it is necessary to present visual and auditory stimuli and collect subject reactions. Here, the software for the experimental control is introduced.

      General stimulus presentation software
    • Presentation
      • Multimedia stimulus presentation and control software which supports fMRI, MEG, NIRS, EEG, and more. It is also possible to collect subject reactions.

    • Cogent
      • This software can interact with fMRI, MEG, etc. Especially used for accurate, real time control of visual stimulus presentation.

    • Psychophysics Toolbox
      • Stimulus presentation control software that works with MATLAB.



Image (software)

Softwares

  • Neuroimaging studies require various techniques of image processing and signal processing. Here, the software that generally used for the basic processing is introduced.

      Numerical Analysis software
    • MATLAB
      • Necessary to use SPM, EEGLAB, BrainStorm, Cogent, Psychophysics Toolbox, etc.



Image (textbook)

Text Books

  • Neuroimaging is an integrated science. For this research, therefore, basic knowledge in various areas is necessary, including neuroscience, anatomy, physiology, psychology, statistics, and others. Here, introductory books, reference books, and related URLs are introduced to help obtain this basic knowledge.

      Introduction to neuroscience

    • Principles of Neural Science
      • Eric R. Kandel, James H. Schwartz, Thomas M. Jessell (ed.)
      • Appleton & Lange
           A standard neuroscience textbook written in English. This book offers comprehensive coverage of neuroscience topics. More suitable for group study than for individual reading. The 5th edition is scheduled to be published in 2010.

    • Essentials of Neural Science and Behavior
      • Eric R. Kandel
      • Mcgraw-Hill
           An English textbook written by the author of "Principles of Neural Science", however the entries are comparatively limited and are written more simply. The latest edition is scheduled to be published in 2009.

    • Cognitive Neuroscience: The Biology of the Mind
      • Michael S. Gazzaniga, Richard B. Ivry, G. R. Mangun
      • W W Norton & Co Inc
           An English language cognitive neuroscience textbook. Compared to the "Principles of Neural Science", there are fewer neuroscience entries in physiology and biology. Instead, more space is devoted to neuroimaging topics on psychological and cognitive science. Many newer studies are introduced, and this is the best textbook for learning the cognitive neuroscience field where the power of neuroimaging is utilized extensively.


      Introduction to neuroimaging

    • Functional Magnetic Resonance Imaging
      • Scott A. Huettel, Allen W. Song, Gregory McCarthy
      • Sinauer Associates Inc
           An English-language introductory text of neuroimaging via functional magnetic resonance image. From the principles of MRI to experimental methodology to analysis, this book covers the whole subject. Once acquiring the basic knowledge of neuroscience, this is the best textbook to use once neuroimaging is finally put into practice.

    • Functional MRI: An Introduction to Methods
      • Peter Jezzard, Paul M. Matthews, Stephen M. Smith (ed.)
      • Oxford University Press
           An English language neuroimaging textbook of functional magnetic resonance image methods, slightly more advanced and specialized than the previous book.



Training Courses

Training Courses

  • Following URLs offer information on training courses on neuroimaging.