Lecture 02:

Basic Neuroanatomy and MR Imaging

BME 234: Neuroimaging Data Analysis, Spring 2016, Course Code 14310

Frithjof Kruggel, M.D.

Department of Biomedical Engineering, University of California, Irvine
Office: REC 204, Phone: 4-3729, Email: fkruggel@uci.edu

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Methods
Neuroimaging comprises all methods for obtaining structural and functional
images of the nervous system, in particular the modern, non-invasive techniques:
aMRI: anatomical Magnetic Resonance Imaging - structural imaging of
the nervous system,
fMRI: functional Magnetic Resonance Imaging - measurement of
oxygen-level dependent signal changes due to neural activity via diamagnetic properties of hemoglobin (BOLD effect),
EEG/MEG: Electro- (Magneto-) Encephalography - measurement of the
electromagnetic activity of the brain.
PET: Positron Emission Tomography - measurement of water exchange, metabolism (e.g., glucose), and transmitter binding sites (e.g.,
dopamine).

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Why is anatomical neuroimaging difficult?

Subjects have an individual neuroanatomy. Consider brain surface structures
in a pair of monozygotic twins: Already major structures vary considerably,
making automatical identification a hard problem. More recent parts of the
brain (in terms of evolution) show an even higher variability.

Individual structural differences must be considered when studying the functional organization of the brain.
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Why is functional neuroimaging difficult?

The signal-to-noise ratio is low.
Methods have either a high temporal res-

olution (EEG, MEG) or a high spatial

resolution (fMRI), both not both.
The observed signal is an indirect correlate of the neuronal activity.
The brain is a parallel processor. The induced task is just one of many currently
active.
Functional networks may be implemented differently in subjects.
Subjects have different skills and pursue different strategies. Mood and actual
performance play a role.
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Macroscopic Anatomy I
Lateral and dorsal (top) view of a human brain.

Neuroanatomy Interactive Atlas (http://www9.biostr.washington.edu)

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Macroscopic Anatomy II
Medial and ventral (bottom) view of a human brain.

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Macroscopic Anatomy III

Axial slices at three different levels through the human brain.

Try to distinguish: the cerebrum, the cerebellum, the grey matter, the white
matter, the ventricles, the basal ganglia. Understand their relationship in 3D.

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Functional Areas
There is a close correspondence between the functional organization of the
neocortex and its parcellation into cytoarchitectonic fields that have been
characterized by histological staining techniques during the last 100 years.

This information is tedious to obtain, and available post-mortem only.

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Macrovasculature I
Three major arteries supply each hemisphere of the brain: (1) anterior (in
grey), (2) middle (in white), (3) posterior cerebral artery (in light grey). Each
artery splits up into several major branches, that supply specific territories
of the cortex and the underlying white matter of the brain:

Nieuwenhuys et al., The human central nervous system. Springer, Berlin.

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Macrovasculature II
The core structures of the brain are supplied by small, short branches of the
middle and posterior artery.

Nieuwenhuys et al., The human central nervous system. Springer, Berlin.

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Lesion
Knowledge about the extent of vascular territories is important to pinpoint
the vessels occluded by a cerebral infarction.

Until the invention of the modern functional neuroimaging methods, lesion

studies provided the only approach to relate brain structures to function.
Damasio et al., Lesion analysis in neuropsychology. Oxford Univ. Press.
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Microvasculature
The deep portions of the white matter are supplied by small, long penetrating arteries. They enter perpendicular to the cortex. Hypertension and
diabetes are the most common diseases affecting these vessels, leading to
small lesions deep in the white matter

Nonaka et al. (2003), Neuropathology 23, 111-118.

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Anatomical MR imaging
Magnetic resonance imaging (MRI) is the imaging modality to obtain 2D
and 3D imaging information of the human brain today.
For more information about the physical basis, the technique, and image
acquisition issues, refer to the tutorial at
http://www.cis.rit.edu/htbooks/mri/inside.htm.
Advantages are:
Non-invasiveness.
No relevant negative effects of scanning are known. Even pregnant
women may be scanned.
A range of different imaging technique allow studying different tissue
properties.
MRI scanners are widely available.
Data are provided in digital format.
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Magnetic Resonance (MR) - Basics I

Protons (the nucleus of hydrogen) have a spin.
When placed in a (static) magnetic field, spins take a preferred (parallel)

direction.
Protons in a magnetic field can absorbe a photon to reach a state with
higher energy and anti-parallel spin direction (excitation).
Excited protons fall back to the lower energy state by emitting a photon.
This decay process is governed by the spin lattice relaxation time T1 .
Excited protons also dephase with time due to their different molecular
environment, governed by the spin-spin relaxation time T2 .
The most simple MR experiment consists of an object (say, a glass of
water) into a magnetic field, an excitation by pumping RF energy via a
transmission coil into this field, an receiving the emitted RF signal using
a receiver coil.
This signal is called the free induction decay (FID).
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Magnetic Resonance (MR) - Basics II

The previous experiment was not selective in space, i.e., the source of the
FID signal is undetermined.
The trick to determine the origin of the signal is to restrict the resonance
condition to a small known portion in space, and execute the experiment
above.
The static magnetic field is varied in space by adding a magnetic gradient
field in the spatial directions x, y, and z, so that the resonance condition
is only valid in a single small volume (voxel) in space.
If a linear gradient field is applied in one direction, the resonance frequency is proportional to the position of the spin.
Gradients are switched to scan the volume of interest, and at each line in
space, the excitation experiment is repeated.
Switching gradients in the coils cause mechanic stress resulting in
acoustic noise with levels between 50-130db.
Switching of the three gradients, the RF excitation, and the listening
period are coordinated in a timing diagram.
Different timing diagrams result in different MR imaging protocols.
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MR protocols
The set of device settings of the MR apparatus define the MR (imaging)
protocol. The most important information is:
Manufacturer, model, field strength.
Type of head coil.
Acquistion modality and pulse sequence.
Echo time TE and repetition time TR .
Field-of-view (FOV).
Matrix size.
Number of slices.
Slice thickness and gap.
MRI acquisition was performed on a Bruker 3T Medspec 100 system
equipped with a bird cage quadrature coil using a T1 -weighted 3D MDEFT
protocol: FOV 240240192 mm, matrix 256256, TR = 1.3 s, TE = 10
ms, 128 sagittal slices, voxel size 0.90.9 mm, 1.5 mm slice thickness.
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MRI weightings
The most common weightings in terms of tissue contrast are:
T1: shows anatomy, high spatial resolution possible.
T2: sensitive to changes of water content in tissue (e.g., edema).
P D: (proton density): sensitive to changes of proton content in tissue
(e.g., bone vs. brain).

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Artifacts in MRI data

Intensity inhomogeneities: The B1-field (gradient field) is not homogeneous throughout the whole volume under study. This leads to an
intensity loss from the center to boundary portions of the image volume
which often make up to 20 % of the image intensity.
Subject motion: Head motion is hard to avoid, especially when examining patients. Post-hoc correction of motion-artifacts in MR volume data
sets is considered useless.
Folding artifacts: If a part of this image is folded over onto itself, this is
generally considered as a consequence of misccspecification of parameters during image reconstruction.
Gibbs ringing: Ring artifacts are consequences of sub-optimal scanner
adjustments.

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Tips and pitfalls

Acquisition of high-resolution T1-weighted images is sufficient if

anatomical images of (healthy) subjects are needed.

Additional weighting (T2 , P D, DW I ) are necessary for patient studies.
Discuss the protocol with the radiologists and the technical personell.
Take care that all data of a study are acquired by the same protocol.
Take care that the whole brain is imaged.
Check all recorded data for artifacts (garbage in - garbage out).

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