MRI notes and advice,

To accompany Poldrack, et al., Handbook of Functional MRI Data

Analysis

FOLLOW THE HANDOUT AND COMPREHEND THE BOOK, AND YOU WILL
UNDERSTAND MRI! (As is required of a professional in the field as well
as a Trinity research student...)

Overall, the meanings of italicized terms and the main ideas under
each bold heading should be understood and remembered. These are
not listed here, so your notetaking task should be focused on them
(italics, section heads). This handout points to background and
exceptions to what you need to know.

BEFORE YOU BEGIN:

--"sfn" in these notes means "skip for now (also "Society for
Neuroscience"). These are terms that will become more
important later and will figure in your methods sections (so
indeed you will have to know them eventually). So, read the sfn
but don't worry if you don't fully understand. However, assume
that if a term/section is not on the sfn list below, then you should
know it.

--the boxes scattered throughout the text are sfn.

--all equations are sfn.

THE BOOK:
The links below are chosen to illuminate parts of the book that are
obscure (or presupposed). You should read the webpages with good
understanding.

Book website: http://www.fmri-data-analysis.org/resources

, however I did not find as much helpful material as I had hoped.

Preface:
fMRI uses magnetic resonance imaging to measure brain activity
o It is measured by monitoring changes in oxygenated blood
o Measuring oxygen levels in blood reflects amount of brain
activity
Creates a statistical map of brain regions responding to mental
or perception functions
1.1:
fMRI provides a great noninvasive and safe way to measure brain
activity with great resolutions

1
1.1.1 Blood flow and neuronal activity:
when neurons in the brain become active
o blood flow through the area is increased
o oxygen needed to replenish due to the amount of activity
o neuronal activity could last for milliseconds
leads to a surplus of local blood oxygen
signal measured depends on change in oxygenation
o BOLD signal= blood oxygenation level dependent
Hemodynamic response= increase in blood flow following a brief
period of neuronal activity
o The response is slow
o Increase in blood flow after this response takes 5 seconds
to reach max.
o Peaks and does not return to baseline for at least 10-20
seconds
Linear time-invariant
o Adding shifted versions of hemodynamic response to a
short train of activity to make it linear providing a time
course of neuronal activity
1.2-5 Magnetic resonance imaging & History of Cognitive
Neuroscience
Before the development of neuroimaging methods to understand
function would be to observe those with brain damage
fMRI achieved greater dominance than PET due to:
o not a lot of PET machines
o safer and noninvasive
o could be used with children
o no radiation exposure concerns
o more accessible
o has spatial resolution (ability to resolve small structures)
o PET scans require at least a minute fMRI can examine more
quickly
b/c BOLD is linear it simplifies analysis by using a linear model
New approach to fMRI that is becoming common:
o Analyze info in patterns of activity instead of response at
an individual voxel
This is known as multi-voxel pattern analysis
(MVPA)
Analyzes the degree in which different stimuli
can be distinguished or classified on fMRI
activation patterns
Attempting to understand what kind of
information is present in those patterns

2
 Focuses on making predictions about new data
rather than describe the patterns that exist
Data is liable to issues (artifacts)
o Ex: issues that are caused by head movements
o There is a lot of variability between individuals and across
time
o Dimensionality of the data is large instead of small
datasets
o to deal with these issues:
Quality control: makes sure that the data is not corrupted by
these issues
Distortion correction: correcting spatial distortions that can
happen in fMRI images
Motion correction: realigns scans across time it corrects for
head motion
Slice timing correction: correcting differences in timing across
different slices in the images.
Spatial normalization: aligning data from different individuals
into a common spatial framework allows data to be combined
for group analysis
Temporal filtering: filters data in time to remove low frequency
noise
Statistical modeling: fitting statistical model to data to
estimate response to a task/stimulus
Statistical inference: estimating statistical significance to the
results correcting large number of statistical tests performed
across the brain
Visualizing: visualizes results and estimates of effect sizes.
1.7-1.8 processing streams and pre-req for fMRI analysis
Processing stream= sequence of operations performed
Differs depending on which software package is being used

One non-italicized concept that you should know:

Dimensionality (p. 7) = the number of variables being observed.
For example, in a study of student performance, if you are comparing
GPA and number of hours of sleep, your data would have two
dimensions (two variables) (and could easily be plotted on a 2-d
graph). An MR image will have variable numeric values at each pixel
(voxel). Therefore, if an image has 100,000 voxels, you have that
many variables, and a dimensionality of 100,000. Obviously high
dimensions are tough to compute and make sense of; so much of MRI
science includes dimensionality reduction.

2.1 What is an image?

Digital image= matrix of numbers that are related to spatial
locations
Voxel= three dimensional element similar to a pixel
Processing an image there is a mathematical operation involved
o Make an image brighter=increase value in the matrix
Images are binary so they are represented in terms of ones and
zeros
Larger numbers represented by combining the ones and zeros
o Numeric formats:
o Information can be lost if the representation isnt
appropriate
o Dont use floating numbers so no 0s
o 3,280 becomes 32.8

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 o Metadata:
o Beyond voxel values store other information from the
image which is known as metadata
o Data is stored in a header which can be a separate file or
part of the image file
o File formats to store the info could be NIfTI, DICOM, or
Analyze etc.
o Storing time series data:
o In an structural MRI images are usually a single three
dimensional image
o fMRI is a time series of three dimensional images
ex: collecting an image every two seconds for a total
of 6 minutes which creates a time series of 180 three
dimensional images
some file formats allow representation of four
dimensional datasets
so the whole time series could be saved in a
single data file and time would be the fourth
dimension
Other formats the time series is stored as a series of
separate three-dimensional data files.
2.2 Coordinate systems
MRI images are related to physical objects
A coordinate system is used to relate data points in the image to
spatial locations in a physical object
Data matrix for a single brain image usually three dimensional
o Each dimension corresponds to a dimension in space
These dimensions (axes) are called X, Y, and Z.
In a standard space for neuroimaging data:
o X represents: left-right dimension
o Y represents: anterior-posterior dimension
o Z represents: inferior-superior dimension

5
2.3.2, 2.3.3, 2.3.4, read and comprehend the main section discussion
but sfn the subsections, 2.3.2.1, etc.

2.4 -- overview of Fourier analysis:

http://hyperphysics.phy-astr.gsu.edu/hbase/audio/fourier.html
You should be comfortable with thinking of signals (like voxel intensity
time series) both in the "time domain" and the "frequency domain."

3.1 The physics of MRI is assumed by the book. Terms needed include
T1 and T2 images. Learn about these via
http://www.brainrules.net/pdf/JohnMedina_PsychTimes_Apr09.pdf
...with a big grain of salt. Functional MRI is a subtype of MRI in general
(Anatomical MR images are not "functional.") The author of this piece
describes MR in general, not just fMR. What makes it functional is its
capacity to detect compounds created by differential physiological
function. In most fMRI, the image detects oxygenated hemoglobin
(oxyhemoglobin), which concentration varies according to how hard
the neural tissue is working. The author is also wrong when he claims
that MRI involves injecting radioactive tracers. As you probably know,
nothing is injected in subjects. MRI detects the substances (e.g.
oxyhemoglobin) that are already there, naturally.

T1 and T2 images distinguished, briefly:

http://fmri.ucsd.edu/Howto/3T/structure.html
and more thoroughly:
https://www.quora.com/What-is-the-difference-between-T1-and-T2-
imaging-in-MRI

6
3.3.3 ICA. Learn background at:
https://en.wikipedia.org/wiki/Independent_component_analysis
...which gets technical pretty fast -- the math is sfn.

3.6.2 - 3.6.8 sfn

3.7 spatial smoothing. A little background (I find the book obscure on

this): http://support.brainvoyager.com/functional-analysis-
preparation/27-pre-processing/279-spatial-smoothing-in-
preparation.html

4.5.1 sfn

4.6, 4.9, 4.12 sfn (But Tommy see 4.12.2)

5. General Linear Model -- The intro in Appendix A presupposes matrix

math. (Brain images are matrices.) If you don't know much of that,
then read through https://en.wikipedia.org/wiki/Matrix_(mathematics)
(Keep this bookmarked as the terms will often appear in theoretical
discussions of MRI.)
And some stats review: t-tests:
http://www.investopedia.com/terms/t/t-test.asp
ANOVA: https://en.wikipedia.org/wiki/Analysis_of_variance

5.1.2, 5.1.3 sfn

5.2.2 - 5.2.4 sfn

5.3 - 5.3.3 sfn

6.2 -end sfn

7 All of this is relevant to MRI research. However, it gets technical. For

a first pass, I suggest identifying the main ideas and defining them
where possible, but tolerating blanks and ????? as you go.

8 Connectivity is the theme of much recent work. However, it may not

be the focus of your particular research. Nonetheless, pay attention to
8.1 and 8.2, while subsections of 8.2 through 8.2.4.2 are sfn.

Note, however, box 8.2.2 -- the last paragraph is a typical methods

paragraph. Your research will probably include these details. Though
they will be already determined in any data you use, you should
understand their meaning.

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8.2.5 introduces methods that are relevant to many aspects of fMRI
research, so pay attention to PCA and ICA. Also note box 8.2.5. We are
likely to work with rest-state data.

8.2.6 sfn.

8.3 (all) sfn

8.4 sfn but do read it. This is an attractive way to think about brain
function, and possibly you may want to run with it. We have the data
to do so.

9. This short chapter is a pretty good introduction to another hot topic.

While you don't have to learn its concepts yet, please do read it. We
may end up using these approaches.

10. Visualizing -- very important but 10.4.3 ff sfn

Appendix A: General Linear Model - math! sfn

Appendix B: important background info

Appendix C: fyi (a quick read)