Functional MRI

Jerry Allison, Ph. D.

Medical College of Georgia
 BOLD Imaging Technique
 Blood Oxygen Level Dependent contrast
can be used to map brain function
Right Hand Motor Task
 Outline
 fMRI BOLD Contrast
 An fMRI Exam
 Pulse Sequences for fMRI
 fMRI Acquisition Parameters
 fMRI Artifacts
 fMRI BOLD Contrast
 Neuronal events (cerebral activation)
 O2 consumption increases (+5%)
 Cerebral blood flow increases (+50%)
 Oxygen extraction fraction decreases
 Oxygenation increases in venous blood
 fMRI BOLD Contrast
 Concentration of paramagnetic
deoxyhemoglobin decreases
 Intravoxel dephasing decreases
 T2* increases
 T2* weighted image intensity increases
(+ few %)
Latency: 5 - 8 seconds may
elapse between neuronal
activation and T2* changes
 Idealized fMRI Study

Activate

Control

Activate

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Activate

Control

T2* Images Voxel Time Course (one voxel)

 Voxel Time Course
Voxel Time Course

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fMRI Signal from each voxel is
characterized by
  :Phase
 A : Amplitude
  : Frequency
 T2*
 T2* has two components
 1/T2* = B + 1/T2
 T2 = nmr spin-spin dephasing
 B = magnetic field inhomogeneity
 The BOLD phenomenon changes B
Magnetic Field Inhomogeneity
results from

 Inhomogeneity of the magnet’s B0 field

 Variation in magnetic susceptibility of
patient’s tissues
Magnetic Field Inhomogeneity
occurs
 Near the boundaries of tissues having
disparate susceptibility
– tissue/ air
– tissue/ bone
– The sphenoid sinus causes magnetic
susceptibility artifacts in EPI images
– Inferior frontal cortex
– Inferior lateral temporal cortex
Magnetic Field Inhomogeneity
also results from
 The BOLD effect
 Differences in magnetic susceptibility around a
paramagnetic deoxyhemoglobin molecule
 Changes in magnetic susceptibility around a small
blood vessel (capillary, venule, small vein) that
has an increased concentration/fraction of
oxygenated hemoglobin
T2* weighted images are used
in fMRI to demonstrate
changes in magnetic
susceptibility associated with
the BOLD effect
 Signal in a T2* weighted
BOLD image is affected by
 Blood volume (CBV)
 Blood flow (CBF)
 Arterial hemoglobin concentration
 Venous hemoglobin concentration
 Oxygen extraction rate
 Hematocrit
 Signal in a T2* weighted
BOLD image is thought to be
inversely proportional to the
number of deoxyhemoglobin
molecules in the voxel
 T2* Contrast is available via:
 Conventional gradient echo techniques with
one RF transmission per phase encoded line
of k-space
– FLASH
– GRASS
– FISP
 T2* Contrast is available via:
 Single shot EPI techniques with a complete
survey of k-space (and subsequent image
reconstruction) for each RF transmission
– EPI - SE techniques
– EPI - GE techniques
 Multi-shot techniques (more than one RF
transmission per image; more than one echo
per RF transmission)
 EPI Images
EPI - GE Technique
(T2* weighted)
 To Map Brain Function
 Acquire T2* weighted images during a
brain task
– Images will have slightly higher intensity in
active brain regions
 Acquire T2* weighted images during a
control state with the brain task suspended
 Statistically subtract control images from
task images to map areas of brain activation
associated with the task
 An fMRI Exam involves:
 Brain Activation Paradigm
 Task presentation systems
 Patient response monitoring
 Image acquisition
 Synchronization
 Data processing
 A brain activation paradigm
 Control task
 Activation task: a task designed to produce
brain activation (e.g. motor, sensory,
language, memory)
– Try to avoid
 Habituation
 Learning
 Inattention
 Event Related fMRI
 fMRI need not be constrained by task on/
task off block designs
 By measuring BOLD response to brief
stimuli (typically presented at irregular
intervals), it is possible to characterize the
hemodynamic response function
Noun Verb Task
Right Hand Motor Task
Left Hand Motor Task
Auditory Task
 Task presentation systems
 Audio system
– w/ Input for external sound sources such as
computer audio, VCR, stereo, microphone
– Attenuate gradient noise while enabling
communication
– Non-pneumatic audio offers improved quality
 Electrical stimulation
 A dark room and dark magnet bore
 Task presentation systems
 Visual presentation
– Slide projector
– LCD panel & overhead projector & rear screen
projection
– Large screen LCD MRI projection systems
– Electronic goggles
– MRI compatible corrective lenses
fMRI Projection System
fMRI I/O Devices
 Response monitoring
 In order to document whether the patient is
doing the task
 Key pad
 Joystick
 Track ball
MRI Control Room
 Synchronization
 Task presentation and patient response
monitoring should be in synchrony with the
acquisition of T2* weighted MRI images
 Ideally, all of this apparatus should be
controlled by one host.
 Signal conditioning

 Wires and tubes that pass in/out of the exam

room must pass through RF filters or RF
waveguides
Penetration Panel
 Image acquisition
 T2* weighted images are acquired while the
patient alternates between periods having an
activating task and periods of a control
state.
 Motor task
 Begin imaging
 Control state
– Rest for 30 seconds
 Activating task
– Finger tapping w/ Rt. hand for 30 seconds
 Alternate these activities for 6 minutes
 Motor task

 Acquire 120 T2* weighted MRI image sets

 Each set:
– Transverse oblique
– 32 Slices
– Primary motor cortex to cerebellum
 Motor task

 Thus for each brain voxel, we have

temporal data (the voxel time course)
having 120 data points (a sample every
three seconds)
 There can be hundreds of thousands of brain
voxels
 Motor task
 3840 total EPI images
– Some scanners limit the number of images in
one “study” (512, 2048, etc.)
Sagittal Localizer
 We use one of two pulse
sequences

 ep2d_fid_66b1190_62.ekc
 ep2d_fid_60b2080_62_64.ekc
 ep2d_fid_66b1190_62.ekc
 Gradient refocused single shot EPI
technique
 Uses optional hybrid gradient overdrive
amplifiers
 Matrix: 128x128
 ep2d_fid_66b1190_62.ekc
 TE: 66 msec
 TR: 3 sec
– We acquire 22 slices every 5 seconds
 ep2d_fid_66b1190_62.ekc
 22 slices
– 2.0 mm
– skip 1.0
– ascending

 Orientation: Transverse oblique:

– T --> C, - 15 o
 ep2d_fid_66b1190_62.ekc
 Phase encode: A  P (for symmetry)
 FOV: 230x230 mm:
 Voxels: 1.8 x 1.8 x 3.0 mm
ep2d_fid_66b1190_62.ekc
ep2d_fid_60b2080_62_64.ekc
 Enables up to 64 slices in one file
 We do 32 slices every 3 seconds
 64 x 64 matrix
 All slices are written into 1 512 x 512
image (mosaic mode)
 Reduces I/O time necessary to write data to
disk
ep2d_fid_60b2080_62_64.ekc
 GRASS fMRI Technique
 TR: 70 msec
 TE: 40 msec
 Flip angle: 40 o
 Matrix: 128 x 256
 Slice thickness: 6 mm
 Acquisition: 9.4 sec per image
 Computing options
 MRI scanner software
 AFNI
 STIMULATE
 SPM
 Other approaches
– Brain Voyager
– MEDx
 Data processing may include
the following
 Correction for differences in time of acquisition
across slices
 Examine the data
 Motion detection
– Plot center-of-mass time course for each slice
 Stimulate
– View Cine loop of T2* weighted images
 As native signal intensity
 As a difference image (a. la. DSA)
– fMRI activation in periphery of brain is an indication of
motion
Data processing may include
the following

 Motion correction
– Discard images showing “obvious” motion
– Image re-registration to correct for rigid body
motion
– 2D (3 parameters)
– 3D (6 parameters)
 Data processing may include
the following
 Baseline flattening
 0th order
 1st order
 2nd order
 fMRI image calculation
 Clustering of activated voxels
 Data processing may include
the following
 Image fusion
– With T2* weighted images
– With T1 weighted images
 Multi Planar Reconstruction of “fused”
images
 Volume rendering of “fused” images
Motion: Peripheral Brain
Activation
3D Image Registration
 Reference Va lue

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Cross Correlation
fMRI on T2* weighted EPI
images
fMRI on T1 weighted images
fMRI on Orthogonal T1
weighted images
 EPI (single shot) Sequence
Problems
 Nyquist ghosts: N/2 ghosts caused by odd
and even echo asymmetries
– Can “apply a correction”by measuring the
asymmetry with a phase reference FID with the
phase encode gradient switched off just prior to
each single shot image
GHOSTS!
 Artifacts in fMRI images
 Subject motion
– Bulk
– Physiologic
 Cardiac
 Respiratory
 Acquisition time (long is bad: like
mammography)
 Artifacts in fMRI images
 ROI (Are there magnetic susceptibility
artifacts in the ROI)
 Geometric distortion
 Poor shimming results in additional
geometric distortion (particularly in gradient
recalled EPI images)
Susceptibility Artifact in
Orthogonal T2* images
Phantom Susceptibility
in a T2* Weighted Sequence
 Physiologic Motion
 Bulk motion
– Settling
 Physiologic Motion
 Respiration
– Susceptibility changes caused by movement of
chest during respiration (phase changes of 2o -
6o at 40 msec)
– Slow varying
– Affects inferior images
– Proportional to B0
– Proportional to TE
 Physiologic Motion
 Cardiac pulsations
– Non-rigid body movement of brain parenchyma
caused by cardiac pulsations (Brain changes
shape)
– Image dependent brain deformation in EPI
– Image dependent motion artifact in FLASH
– Can produce artifacts as large as a few % of
BOLD contrast
– Occurs near CSF (Brainstem, Cerebellum)
Motion of as little as 0.1 pixels
can seriously degrade fMRI
images because the MRI
signal variation from pixel to
pixel is larger than the BOLD
effect that is being measured.
 Motion prevention
 An Ounce of Prevention is Worth A Pound
of Cure
– Padding
– Expandable foam (Alpha Cradle)
– Vacuum bags
– Hammock
– Bite bar
– Contour masks
 Motion prevention
 Real time
– Pressure sensors
– Infrared systems
fMRI Head Fixation