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CS 4487/9587

Algorithms for Image Analysis

The University of

CS 4487/9587 Algorithms for Image Analysis The University of Ontario Image Modalities most slides are shamelessly

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Algorithms for Image Analysis The University of Ontario Image Modalities most slides are shamelessly stolen from
Algorithms for Image Analysis The University of Ontario Image Modalities most slides are shamelessly stolen from

Image Modalities

most slides are shamelessly stolen from Steven Seitz, Aleosha Efros, and Terry Peters

CS 4487/9587 Algorithms for Image Analysis

Image Modalities

The University of

for Image Analysis Image Modalities The University of Ontario Photo/Video data • Pin-hole • Lenses •

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Image Analysis Image Modalities The University of Ontario Photo/Video data • Pin-hole • Lenses • Digital

Photo/Video data

Pin-hole

Lenses

Digital images and volumes

Medical Images and Volumes

X-ray, MRI, CT, and Ultrasound

Extra Reading: Forsyth & Ponce, Ch. 1. Gonzalez & Woods, Ch. 1

Slide by Steve Seitz

How do we see the world?

The University of

by Steve Seitz How do we see the world? The University of Ontario Let’s design a

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Seitz How do we see the world? The University of Ontario Let’s design a camera •
Seitz How do we see the world? The University of Ontario Let’s design a camera •

Let’s design a camera

Idea 1: put a piece of film in front of an object

Do we get a reasonable image?

Slide by Steve Seitz

Pinhole camera

The University of

Slide by Steve Seitz Pinhole camera The University of Ontario Add a barrier to block off

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Slide by Steve Seitz Pinhole camera The University of Ontario Add a barrier to block off
Slide by Steve Seitz Pinhole camera The University of Ontario Add a barrier to block off

Add a barrier to block off most of the rays

This reduces blurring

The opening known as the aperture

How does this transform the image?

Slide by Steve Seitz

Camera Obscura

The University of

Slide by Steve Seitz Camera Obscura The University of Ontario The first camera • Known to

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Slide by Steve Seitz Camera Obscura The University of Ontario The first camera • Known to
Slide by Steve Seitz Camera Obscura The University of Ontario The first camera • Known to

The first camera

Known to Aristotle

Depth of the room is the focal length

Pencil of rays – all rays through a point

Can we measure distances?

Figure by David Forsyth

Distant objects are smaller

The University of

Figure by David Forsyth Distant objects are smaller The University of Ontario

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Figure by David Forsyth Distant objects are smaller The University of Ontario
Figure by David Forsyth Distant objects are smaller The University of Ontario

Slide by Aleosha Efros

Camera Obscura

The University of

Slide by Aleosha Efros Camera Obscura The University of Ontario Drawing from “The Great Art of

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by Aleosha Efros Camera Obscura The University of Ontario Drawing from “The Great Art of Light

Drawing from “The Great Art of Light and Shadow

Jesuit Athanasius Kircher, 1646.

“The Great Art of Light and Shadow “ Jesuit Athanasius Kircher, 1646. How does the aperture

How does the aperture size affect the image?

Slide by Steve Seitz

Shrinking the aperture

The University of

Slide by Steve Seitz Shrinking the aperture The University of Ontario Why not make the aperture

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Steve Seitz Shrinking the aperture The University of Ontario Why not make the aperture as small
Steve Seitz Shrinking the aperture The University of Ontario Why not make the aperture as small

Why not make the aperture as small as possible?

Less light gets through

Diffraction effects…

Slide by Steve Seitz

Shrinking the aperture

The University of

Slide by Steve Seitz Shrinking the aperture The University of Ontario

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Slide by Steve Seitz Shrinking the aperture The University of Ontario
Slide by Steve Seitz Shrinking the aperture The University of Ontario

Slide by Aleosha Efros

Home-made pinhole camera

The University of

Slide by Aleosha Efros Home-made pinhole camera The University of Ontario http://www.debevec.org/Pinhole/

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Slide by Aleosha Efros Home-made pinhole camera The University of Ontario http://www.debevec.org/Pinhole/
Slide by Aleosha Efros Home-made pinhole camera The University of Ontario http://www.debevec.org/Pinhole/

http://www.debevec.org/Pinhole/

Slide by Steve Seitz

The reason for lenses

The University of

Slide by Steve Seitz The reason for lenses The University of Ontario

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Slide by Steve Seitz The reason for lenses The University of Ontario
Slide by Steve Seitz The reason for lenses The University of Ontario

Slide by Steve Seitz

Adding a lens

The University of

Slide by Steve Seitz Adding a lens The University of Ontario “circle of confusion” A lens

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Slide by Steve Seitz Adding a lens The University of Ontario “circle of confusion” A lens
Slide by Steve Seitz Adding a lens The University of Ontario “circle of confusion” A lens
Slide by Steve Seitz Adding a lens The University of Ontario “circle of confusion” A lens

“circle of confusion”

A lens focuses light onto the film

There is a specific distance at which objects are “in focus”

other points project to a “circle of confusion” in the image

Changing the shape of the lens changes this distance

Slide by Aleosha Efros

The eye

The University of

Slide by Aleosha Efros The eye The University of Ontario The human eye is a camera!

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Slide by Aleosha Efros The eye The University of Ontario The human eye is a camera!
Slide by Aleosha Efros The eye The University of Ontario The human eye is a camera!

The human eye is a camera!

Iris - colored annulus with radial muscles

Pupil - the hole (aperture) whose size is controlled by the iris

What’s the “film”?

photoreceptor cells (rods and cones) in the retina

Slide by Aleosha Efros

Cameras

The University of

Slide by Aleosha Efros Cameras The University of Ontario Really cool Not too expensive nowadays (<$200)

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Slide by Aleosha Efros Cameras The University of Ontario Really cool Not too expensive nowadays (<$200)

Really cool Not too expensive nowadays (<$200)

Slide by Aleosha Efros Cameras The University of Ontario Really cool Not too expensive nowadays (<$200)

Canon A70

Figure by Gonzalez & Woods

Digital Image Formation

The University of

& Woods Digital Image Formation The University of Ontario f(x,y) = reflectance(x,y) * illumination(x,y)

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Woods Digital Image Formation The University of Ontario f(x,y) = reflectance(x,y) * illumination(x,y) Reflectance in
Woods Digital Image Formation The University of Ontario f(x,y) = reflectance(x,y) * illumination(x,y) Reflectance in

f(x,y) = reflectance(x,y) * illumination(x,y)

Reflectance in [0,1], illumination in [0,inf]

Figure by Gonzalez & Woods

Sampling and Quantization

The University of

Figure by Gonzalez & Woods Sampling and Quantization The University of Ontario

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Figure by Gonzalez & Woods Sampling and Quantization The University of Ontario
Figure by Gonzalez & Woods Sampling and Quantization The University of Ontario

Figure by Gonzalez & Woods

Sampling and Quantization

The University of

Figure by Gonzalez & Woods Sampling and Quantization The University of Ontario

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Figure by Gonzalez & Woods Sampling and Quantization The University of Ontario
Figure by Gonzalez & Woods Sampling and Quantization The University of Ontario

Slide by Aleosha Efros

What is an image?

The University of

Slide by Aleosha Efros What is an image? The University of Ontario We can think of

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by Aleosha Efros What is an image? The University of Ontario We can think of an

We can think of an image as a function, f, from R 2 to R:

f( x, y ) gives the intensity at position ( x, y ) Realistically, we expect the image only to be defined over a rectangle, with a finite range:

f : [a,b]x[c,d] [0,1]

A color image is just three functions pasted

together. We can write this as a “vector-valued”

function:

(,

r x

g

b x

(, x

(,

y

y

y

)

)

)

⎥ ⎦

f

(, x

y

)

=

Slide by Aleosha Efros

Images as functions

The University of

Slide by Aleosha Efros Images as functions The University of Ontario f(x,y) y x

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Slide by Aleosha Efros Images as functions The University of Ontario f(x,y) y x
Slide by Aleosha Efros Images as functions The University of Ontario f(x,y) y x
Slide by Aleosha Efros Images as functions The University of Ontario f(x,y) y x
Slide by Aleosha Efros Images as functions The University of Ontario f(x,y) y x
f(x,y) y x
f(x,y)
y
x

Slide by Aleosha Efros

What is a digital image?

The University of

by Aleosha Efros What is a digital image? The University of Ontario We usually operate on

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Efros What is a digital image? The University of Ontario We usually operate on digital (

We usually operate on digital (discrete) images:

Sample the 2D space on a regular grid

Quantize each sample (round to nearest integer)

If our samples are Δ apart, we can write this as:

f[i ,j] = Quantize{ f(i Δ, j Δ) } The image can now be represented as a matrix of integer values

as: f [ i , j ] = Quantize{ f ( i Δ , j Δ

3D Image Volumes?

The University of

3D Image Volumes? The University of Ontario - Medical volumetric data (MRI, CT) Video 3D =

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3D Image Volumes? The University of Ontario - Medical volumetric data (MRI, CT) Video 3D =

- Medical volumetric data (MRI, CT)

Video

3D = X*Y*Time

-

3D = X*Y*Z

k
k

Combine multiple images (slices) into a volume

CS 4487/9587 Algorithms for Image Analysis

Image Modalities

The University of

for Image Analysis Image Modalities The University of Ontario PART II: Medical images and volumes •

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Image Analysis Image Modalities The University of Ontario PART II: Medical images and volumes • X-ray

PART II:

Medical images and volumes

X-ray

CT

MRI

Ultrasound

The University of

The University of Ontario Slides from Terry Peters In the beginning… X-rays Discovered in 1895 Mainstay

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Slides from Terry Peters

In the beginning… X-rays

Ontario Slides from Terry Peters In the beginning… X-rays Discovered in 1895 Mainstay of medical imaging
Discovered in 1895 Mainstay of medical imaging till 1970’s 1971 – Computed Tomography (CAT, CT)
Discovered in 1895
Mainstay of medical imaging till 1970’s
1971 – Computed Tomography (CAT, CT) scanning
1978 - Digital Radiography
………
1980 Magnetic Resonance Imaging

The University of

The University of Ontario X-rays Wilhelm Conrad Röntgen (1845-1923) Nobel Prise in Physics, 1901 • “X”

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X-rays

The University of Ontario X-rays Wilhelm Conrad Röntgen (1845-1923) Nobel Prise in Physics, 1901 • “X”

Wilhelm Conrad Röntgen (1845-1923)

Nobel Prise in Physics, 1901

Conrad Röntgen (1845-1923) Nobel Prise in Physics, 1901 • “X” stands for “unknown” • X-ray imaging
Conrad Röntgen (1845-1923) Nobel Prise in Physics, 1901 • “X” stands for “unknown” • X-ray imaging

“X” stands for “unknown” X-ray imaging is also known as - radiograph - Röntgen imaging

The University of

The University of Ontario X-rays Bertha Röntgen’s Hand 8 Nov, 1895 A m o d e

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X-rays

The University of Ontario X-rays Bertha Röntgen’s Hand 8 Nov, 1895 A m o d e
The University of Ontario X-rays Bertha Röntgen’s Hand 8 Nov, 1895 A m o d e

Bertha Röntgen’s Hand 8 Nov, 1895

of Ontario X-rays Bertha Röntgen’s Hand 8 Nov, 1895 A m o d e r n

A modern radiograph of a hand

Calcium in bones absorbs X-rays the most

Fat and other soft tissues absorb less, and look gray

Air absorbs the least, so lungs look black on a radiograph

The University of

The University of Ontario X-rays 2D “ projection ” imaging 1895 - 1970’s

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X-rays

The University of Ontario X-rays 2D “ projection ” imaging 1895 - 1970’s

2D “projection” imaging 1895 - 1970’s

The University of Ontario X-rays 2D “ projection ” imaging 1895 - 1970’s

From Projection Imaging Towards True 3D Imaging

The University of

Imaging Towards True 3D Imaging The University of Ontario X-ray imaging 1895 Mathematical results: Radon

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Imaging Towards True 3D Imaging The University of Ontario X-ray imaging 1895 Mathematical results: Radon
X-ray imaging 1895
X-ray imaging
1895
Mathematical results: Radon transformation 1917
Mathematical results:
Radon transformation
1917
Computers can perform complex mathematics to reconstruct and process images Late 1960’s:
Computers can perform
complex mathematics to
reconstruct and process images
Late 1960’s:

Development of CT

(computed tomography)

Late 1960’s: Development of CT (computed tomography) 1972 • Image reconstruction from projection • Also
Late 1960’s: Development of CT (computed tomography) 1972 • Image reconstruction from projection • Also

1972

Image reconstruction from projection Also known as CAT

(Computerized Axial Tomography)

"tomos" means "slice" (Greek)

Radon Transformation

The University of

Radon Transformation The University of Ontario • Mathematical transformation (related to Fourier) • Reconstruction of

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Radon Transformation The University of Ontario • Mathematical transformation (related to Fourier) • Reconstruction of
Radon Transformation The University of Ontario • Mathematical transformation (related to Fourier) • Reconstruction of
Radon Transformation The University of Ontario • Mathematical transformation (related to Fourier) • Reconstruction of

Mathematical transformation (related to Fourier) Reconstruction of the shape of object (distribution f(x,y)) from the multitude of 2D projections g(s,θ )

Figure from www.imaginis.com/ct-scan/how_ct.asp

CT imaging

The University of

Figure from www.imaginis.com/ct-scan/how_ct.asp CT imaging The University of Ontario

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Figure from www.imaginis.com/ct-scan/how_ct.asp CT imaging The University of Ontario
Figure from www.imaginis.com/ct-scan/how_ct.asp CT imaging The University of Ontario

CT imaging, inventing (1972)

The University of

CT imaging, inventing (1972) The University of Ontario Sir Godfrey Hounsfield Engineer for EMI PLC 1972

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CT imaging, inventing (1972) The University of Ontario Sir Godfrey Hounsfield Engineer for EMI PLC 1972

Sir Godfrey Hounsfield Engineer for EMI PLC

1972

Nobel Prize 1979 (with Alan Cormack)

(1972) The University of Ontario Sir Godfrey Hounsfield Engineer for EMI PLC 1972 Nobel Prize 1979
(1972) The University of Ontario Sir Godfrey Hounsfield Engineer for EMI PLC 1972 Nobel Prize 1979

CT imaging, availability (since 1975)

The University of

CT imaging, availability (since 1975) The University of Ontario 1974 Original axial CT image from the

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imaging, availability (since 1975) The University of Ontario 1974 Original axial CT image from the dedicated
1974
1974

Original axial CT image from the

dedicated Siretom CT scanner circa 1975.

The EMI-Scanner

This image is a coarse 128 x 128 matrix;

however, in 1975 physicians were fascinated by the ability to see the soft tissue structures of the brain, including the black ventricles for the first

time (enlarged in this patient)

25 years later

for the first time (enlarged in this patient) 25 years later Axial CT image of a

Axial CT image of a normal brain using a state-of-the-art CT system and a 512 x 512 matrix image. Note the two black "pea-shaped" ventricles in the middle of the brain and the subtle delineation of gray and white matter (Courtesy: Siemens)

Slides from Terry Peters

Clinical Acceptance of CT!?

The University of

Terry Peters Clinical Acceptance of CT!? The University of Ontario Dr James Ambrose 1972 • Radiologist,

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Peters Clinical Acceptance of CT!? The University of Ontario Dr James Ambrose 1972 • Radiologist, Atkinson

Dr James Ambrose 1972

Radiologist, Atkinson - Morley’s Hospital London

Recognised potential of EMI- scanner

“Pretty pictures, but they will never replace radiographs” – Neuroradiologist 1972

potential of EMI- scanner “Pretty pictures, but they will never replace radiographs” – Neuroradiologist 1972

Slides from Terry Peters

Then ……………and Now

The University of

Terry Peters Then ……………and Now The University of Ontario 80 x 80 image 3 mm pixels

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Peters Then ……………and Now The University of Ontario 80 x 80 image 3 mm pixels 13

80 x 80 image 3 mm pixels 13 mm thick slices Two simultaneous slices!!! 80 sec scan time per slice 80 sec recon time

512 x 512 image <1mm slice thickness <0.5mm pixels 0.5 sec rotation 0.5 sec recon per slice Isotropic resolution Spiral scanning - up to 16 slices simultaneously

Slides from Terry Peters

30 Years of CT

The University of

Slides from Terry Peters 30 Years of CT The University of Ontario

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Slides from Terry Peters 30 Years of CT The University of Ontario
Slides from Terry Peters 30 Years of CT The University of Ontario
Slides from Terry Peters 30 Years of CT The University of Ontario
Slides from Terry Peters 30 Years of CT The University of Ontario
Slides from Terry Peters 30 Years of CT The University of Ontario
Slides from Terry Peters 30 Years of CT The University of Ontario

Slides from Terry Peters

Birth of MRI

The University of

Slides from Terry Peters Birth of MRI The University of Ontario Paul Lautebur 1975 • Presented

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from Terry Peters Birth of MRI The University of Ontario Paul Lautebur 1975 • Presented at

Paul Lautebur 1975

Presented at Stanford CT meeting

“Zeugmatography”

Raymond Damadian 1977 – Sir Peter Mansfield early

1980’s

• “Zeugmatography” Raymond Damadian 1977 – Sir Peter Mansfield early 1980’s Early Thorax Image Nottingham
• “Zeugmatography” Raymond Damadian 1977 – Sir Peter Mansfield early 1980’s Early Thorax Image Nottingham

Early Thorax Image

Nottingham

Slides from Terry Peters

Birth of MRI

The University of

Slides from Terry Peters Birth of MRI The University of Ontario Early Thorax Image Nottingham •

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from Terry Peters Birth of MRI The University of Ontario Early Thorax Image Nottingham • Electro
from Terry Peters Birth of MRI The University of Ontario Early Thorax Image Nottingham • Electro
from Terry Peters Birth of MRI The University of Ontario Early Thorax Image Nottingham • Electro
from Terry Peters Birth of MRI The University of Ontario Early Thorax Image Nottingham • Electro

Early Thorax Image

Nottingham

Electro Marnetic signal emitted (in harmless radio frequensy) is acquired in the time domain image has to be reconstructed (Fourier transform)

Birth of MRI

The University of

Birth of MRI The University of Ontario Lauterbur and the first magnetic resonance images (from Nature

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Birth of MRI The University of Ontario Lauterbur and the first magnetic resonance images (from Nature
Birth of MRI The University of Ontario Lauterbur and the first magnetic resonance images (from Nature

Lauterbur

and the

first

magnetic

resonance

images

(from

Nature )

and the first magnetic resonance images (from Nature ) In 1978, Mansfield presented his first image

In 1978, Mansfield presented his first image through the abdomen.

and the first magnetic resonance images (from Nature ) In 1978, Mansfield presented his first image

Slides from Terry Peters

30 Years of MRI

The University of

Slides from Terry Peters 30 Years of MRI The University of Ontario F i r s

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from Terry Peters 30 Years of MRI The University of Ontario F i r s t
from Terry Peters 30 Years of MRI The University of Ontario F i r s t

First brain MR image

Typical T2-weighted MR image
Typical T2-weighted MR image

Slides from Terry Peters

MR Imaging

The University of

Slides from Terry Peters MR Imaging The University of Ontario “Interesting images, but will never be

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Slides from Terry Peters MR Imaging The University of Ontario “Interesting images, but will never be

“Interesting images, but will never be as useful as CT”

(A different) neuroradiologist, 1982

Slides from Terry Peters

MR Imaging

…more than T1 and T2

The University of

Peters MR Imaging …more than T1 and T2 The University of Ontario MRA - Magnetic resonance

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MR Imaging …more than T1 and T2 The University of Ontario MRA - Magnetic resonance angiography

MRA - Magnetic resonance angiography

images of vessels

MRS - Magnetic resonance spectroscopy

images of chemistry of the brain and muscle metabolism

fMRI - functional magnetic resonance imaging

image of brain function

PW MRI – Perfusion-weighted imaging DW MRI – Diffusion-weighted MRI

images of nerve pathways

Slides from Terry Peters

Magnetic Resonance Angiography

The University of

Peters Magnetic Resonance Angiography The University of Ontario MR scanner tuned to measure only moving structures

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Magnetic Resonance Angiography The University of Ontario MR scanner tuned to measure only moving structures

MR scanner tuned to measure only moving structures “Sees” only blood - no static structure Generate 3-D image of vasculature system May be enhanced with contrast agent (e.g. Gd-DTPA)

- no static structure Generate 3-D image of vasculature system May be enhanced with contrast agent

Slides from Terry Peters

MR Angiography

The University of

Slides from Terry Peters MR Angiography The University of Ontario GD-enhanced GD-enhanced In-flow Phase-contrast

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Slides from Terry Peters MR Angiography The University of Ontario GD-enhanced GD-enhanced In-flow Phase-contrast
Slides from Terry Peters MR Angiography The University of Ontario GD-enhanced GD-enhanced In-flow Phase-contrast

GD-enhanced

Slides from Terry Peters MR Angiography The University of Ontario GD-enhanced GD-enhanced In-flow Phase-contrast

GD-enhanced

Slides from Terry Peters MR Angiography The University of Ontario GD-enhanced GD-enhanced In-flow Phase-contrast

In-flow

Slides from Terry Peters MR Angiography The University of Ontario GD-enhanced GD-enhanced In-flow Phase-contrast

Phase-contrast

Slides from Terry Peters

Dynamic 3-D MRI of the thorax

The University of

Slides from Terry Peters Dynamic 3-D MRI of the thorax The University of Ontario 1 www.atamai.com

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Slides from Terry Peters Dynamic 3-D MRI of the thorax The University of Ontario 1 www.atamai.com
Slides from Terry Peters Dynamic 3-D MRI of the thorax The University of Ontario 1 www.atamai.com

1 www.atamai.com

Slides from Terry Peters

Diffusion-Weighted MRI

The University of

from Terry Peters Diffusion-Weighted MRI The University of Ontario Image diffuse fluid motion in brain Construct

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Peters Diffusion-Weighted MRI The University of Ontario Image diffuse fluid motion in brain Construct “Tensor

Image diffuse fluid motion in brain Construct “Tensor image” – extent of diffusion in each direction in each voxel in image Diffusion along nerve sheaths defines nerve tracts. Create images of nerve connections/pathways

voxel in image Diffusion along nerve sheaths defines nerve tracts. Create images of nerve connections/pathways

Slides from Terry Peters

Tractography

The University of

Slides from Terry Peters Tractography The University of Ontario Data analysed after scanning Identify

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from Terry Peters Tractography The University of Ontario Data analysed after scanning Identify “streamlines”

Data analysed after scanning Identify “streamlines” of vectors Connect to form fibre tracts 14 min scan time

- Dr. D Jones, NIH

Internal Capsule

Slides from Terry Peters

Tractography

The University of

Slides from Terry Peters Tractography The University of Ontario Wernicke’s area Short fibres Long fibres Insula

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from Terry Peters Tractography The University of Ontario Wernicke’s area Short fibres Long fibres Insula fibres
Wernicke’s area Short fibres Long fibres Insula fibres
Wernicke’s area
Short fibres
Long fibres
Insula
fibres

Broca’s area

Temporal fibres

Long fibres Insula fibres Broca’s area Temporal fibres “just like Gray’s Anatomy”! Superior Longitudinal

“just like Gray’s Anatomy”!

Superior Longitudinal Fasciculus

- Dr. D Jones, NIH USA

Slides from Terry Peters

Functional MRI (fMRI)

The University of

from Terry Peters Functional MRI (fMRI) The University of Ontario Active brain regions demand more fuel

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Terry Peters Functional MRI (fMRI) The University of Ontario Active brain regions demand more fuel (oxygen)

Active brain regions demand more fuel (oxygen) Extra oxygen in blood changes MRI signal Activate brain regions with specific tasks Oxygenated blood generates small (~1%) signal change Correlate signal intensity change with task Represent changes on anatomical images

Slides from Terry Peters

fMRI

The University of

Slides from Terry Peters fMRI The University of Ontario Subject looks at flashing disk while being

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Slides from Terry Peters fMRI The University of Ontario Subject looks at flashing disk while being

Subject looks at flashing disk while being scanned “Activated” sites detected and merged with 3-D MR image

Stimulus Activation
Stimulus
Activation

Slides from Terry Peters

fMRI in Neurosurgery Planning

The University of

Slides from Terry Peters fMRI in Neurosurgery Planning The University of Ontario Hand Activation Tumour Face

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Slides from Terry Peters fMRI in Neurosurgery Planning The University of Ontario Hand Activation Tumour Face
Hand Activation Tumour Face Activation
Hand Activation
Tumour
Face Activation

Slides from Terry Peters

Ultrasound

The University of

Slides from Terry Peters Ultrasound The University of Ontario Images courtesy GE Medical

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Slides from Terry Peters Ultrasound The University of Ontario Images courtesy GE Medical
Images courtesy GE Medical
Images courtesy GE Medical