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    Kalina Christ Off

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    Matin Ahmad Khan
    This document provides an overview of neuroimaging techniques and analysis methods. It discusses several neuroimaging modalities including fMRI, PET, EEG, and TMS. For fMRI specifically, it describes the BOLD signal and hemodynamic response. It covers the key steps in neuroimaging analysis including data acquisition, preprocessing such as motion correction and spatial normalization, statistical analysis using SPM, and displaying results while considering statistical thresholds. The tutorial aims to help readers interpret and critically evaluate neuroimaging papers.

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    Kalina Christ Off

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    Matin Ahmad Khan
    44 views13 pages
    This document provides an overview of neuroimaging techniques and analysis methods. It discusses several neuroimaging modalities including fMRI, PET, EEG, and TMS. For fMRI specifically, it describes the BOLD signal and hemodynamic response. It covers the key steps in neuroimaging analysis including data acquisition, preprocessing such as motion correction and spatial normalization, statistical analysis using SPM, and displaying results while considering statistical thresholds. The tutorial aims to help readers interpret and critically evaluate neuroimaging papers.

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    This document provides an overview of neuroimaging techniques and analysis methods. It discusses several neuroimaging modalities including fMRI, PET, EEG, and TMS. For fMRI specifically, it describes the BOLD signal and hemodynamic response. It covers the key steps in neuroimaging analysis including data acquisition, preprocessing such as motion correction and spatial normalization, statistical analysis using SPM, and displaying results while considering statistical thresholds. The tutorial aims to help readers interpret and critically evaluate neuroimaging papers.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    44 views13 pages

    Kalina Christ Off

    Uploaded by

    Matin Ahmad Khan
    This document provides an overview of neuroimaging techniques and analysis methods. It discusses several neuroimaging modalities including fMRI, PET, EEG, and TMS. For fMRI specifically, it describes the BOLD signal and hemodynamic response. It covers the key steps in neuroimaging analysis including data acquisition, preprocessing such as motion correction and spatial normalization, statistical analysis using SPM, and displaying results while considering statistical thresholds. The tutorial aims to help readers interpret and critically evaluate neuroimaging papers.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 13

    Neuroimaging Tutorial

    Neuroimaging Tutorial
    Kalina Christoff, Ph.D. University of British Columbia

    What lies behind pictures of brain activations?

    Behind the scene


    1. Data Acquisition 2. Data Preprocessing

    3. Statistical Analysis

    4. Display & Interpretation of Results

    Kalina Christoff

    Neuroimaging Tutorial

    Neuroimaging modalities

    Functional Magnetic Resonance Imaging (fMRI) Positron Emission Tomography (PET) Electroencephalography (EEG) Transcranial Magnetic Stimulation (TMS)

    fMRI

    NonNon-invasive Relatively high spatial resolution


    (higher than PET, EEG, TMS)

    Relatively high temporal resolution


    (higher than PET, TMS)

    Combines anatomy and function

    MRI vs fMRI

    MRI: very high resolution picture of brain anatomy

    fMRI: image reflecting levels of blood oxygenation

    Kalina Christoff

    Neuroimaging Tutorial

    MRI vs fMRI

    Spatial resolution
    voxel

    1 mm

    4 mm

    8 mm

    Temporal resolution
    TR: Time of Repetition HRF: Hemodynamic Response Function

    TR = 3 sec

    TR = 1.5 sec

    TR = 0.75 sec

    Kalina Christoff

    Neuroimaging Tutorial

    The BOLD Signal


    (blood oxygeneation level dependent signal)

    The vascular system supplies blood containing oxyhemoglobin to active regions of the brain The influx of oxygenated blood to regions that are active reduces the local concentration of deoxyhemoglobin which increases BOLD signals

    Hemodynamic Response Function (HRF)

    Kalina Christoff

    Neuroimaging Tutorial

    Kalina Christoff

    Neuroimaging Tutorial

    a lot of computers involved some very complex physics a big magnet

    Principles of Magnetic Resonance


    No radioactivity involved Uses magnetic field (measured in Tesla, e.g. 3T Scanner) Works at the level of protons Measures protons protons spin relaxation time Can be made sensitive to water content or oxygenation level

    Practical implications (most important)

    Cannot bring metal into the scanner

    Hair grip

    Metal dental work

    Kalina Christoff

    Neuroimaging Tutorial

    Practical implications (most important)

    Cannot bring metal into the scanner

    Practical implications (most important)

    Cannot bring metal into the scanner Environment is generally quite noisy Head motion can be severely detrimental

    Head Motion

    Kalina Christoff

    Neuroimaging Tutorial

    activations due motion

    TaskTask-correlated motion Watch out for: activations that trace the outline of the brain

    Preventing Motion

    Restraining the head Asking participants to remain still PrePre-training using a mock scanner

    Correcting for motion

    Part of data prepre-processing

    Ti m

    Kalina Christoff

    Neuroimaging Tutorial

    Motion correction

    Original timetime-series
    time

    Corrected timetime-series

    Spatial normalization

    Another step of data prepre-processing Allows us to combine data across individuals Matches each individual brain to a template

    Variability of brain shape and size


    (the brains of four different neurologically healthy adults)

    Kalina Christoff

    Neuroimaging Tutorial

    Original image

    Spatially normalised

    Spatial Normalisation

    Template image

    Deformation field

    Templates for normalization

    Created by averaging hundreds of healthy control individual brains


    e.g., the MNI template (created by researchers at the

    Montreal Neurological Institute)

    Are matched to a common stereotaxic space


    x, y, z coordinates can be provided a.k.a. Talairach

    space

    Special populations benefit from special templates


    e.g., children childrens brain template for ages 88-12

    1. Data Acquisition

    2. Data Preprocessing

    3. Statistical Analysis

    4. Display & Interpretation of Results

    Kalina Christoff

    10

    Neuroimaging Tutorial

    SPM: Statistical Parametric Mapping


    a voxelvoxel-based statistical analysis for every voxel in the brain:


    - ask how similarly to the task it behaves
    voxel1 voxel2

    voxel

    task

    SPM: Statistical Parametric Mapping


    a voxelvoxel-based statistical analysis for every voxel in the brain:


    - ask how similarly to the task it behaves - voxels that behave similarly are assigned warm warm colors in result displays - the more similar to the task, the warmer the color - voxels that bear no relation to the task are thresholded thresholded (not displayed)

    Group analysis: fixed vs. random effects

    Fixed effects analysis


    Similar to simple averaging across individuals Results are not generalizable to the population
    (outliers can strongly influence averages)

    Kalina Christoff

    11

    Neuroimaging Tutorial

    Group analysis: fixed vs. random effects

    Random effects analysis


    Results are more robust and replicable Generalize to the population Is a more conservative but statistically appropriate approach

    Displaying results

    The chosen statistical threshold determines what is displayed (and classified) as activated

    T = 2.10 P<0.05 (uncorrected)

    T = 3.60 P<0.001 (uncorrected)

    T = 7.15 P<0.05 (corrected)

    Displaying results
    too lenient acceptable preferable

    T = 2.10 P<0.05 (uncorrected)

    T = 3.60 P<0.001 (uncorrected)

    T = 7.15 P<0.05 (corrected)

    Kalina Christoff

    12

    Neuroimaging Tutorial

    The next time your read a neuroimaging paper paper

    Try to find out:

    Is there any evidence for motion artifacts (false activations)? Was an appropriate template used, if normalization was applied? applied? Was random effects analysis performed at the group level? Was the statistical threshold used acceptable?

    Kalina Christoff

    13

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