Brain imaging for
fun and profit
Daniel Marcus, PhD
Director, Neuroinformatics
Research Group @ Washington
University School of Medicine
Outline
‣ Brain imaging 101
‣ Brain imaging & emerging technologies
‣ Brain imaging for hackers
100 billion
neurons in the
human brain
100 trillion
synapses in
the human
brain
Neuron is the basic computational unit in the brain
Neurons are organized into circuits in the cerebral cortex
Neuron  Network  Whole brain
Brain imaging: single neuron
In vivo microscopy
Misgeld & Kerschensteiner, 2006
Brain imaging: neuronal networks
Transgenics & fluorescence microscopy
Livet, et al. Nature (2007)
Brain imaging: whole brain
‣ Magnetic Resonance Imaging (MRI)
- Structural MRI
- Functional MRI
- Functional connectivity MRI
‣ Computed tomography (CT)
‣ Positron emission tomography (PET)
‣ EEG, MEG, MRS, SPECT, DTI,…
Structural MRI
‣ Essential in clinical care.
‣ Radiologists perform
qualitative “lightbox”
reads.
‣ Most psychiatric and
neurological disorders
are invisible to reading
radiologists.
Aging of the brain
20s
80s aging
gracefully
80s with mild
Alzheimer’s
http://www.oasis-brains.org
Brain volume declines with age
Marcus et al., 2007
Advanced structural methods
Van Essen et al., 2006
Csernansky et al., 2005
fMRI
fMRI depends on functional localization
The sad tale of Phineas Gage
“[P]ossessed a well-balanced mind, and
was looked upon by those who knew him
as a shrewd, smart businessman, very
energetic and persistent”
“fitful, irreverent, indulging at times in
the grossest profanity (which was not
previously his custom), manifesting but
little deference for his fellows, impatient
of restraint or advice when it conflicts
with his desires, at times pertinaciously
obstinate, yet capricious and
vacillating...”
Harlow, J.M. (1868)
Natural History Museum, London
Another sad tale
“A preexisting strong interest in pornography dating back to
adolescence...”
“An increasing interest in pornography... acquired an expanding
collection of pornographic magazines and increasingly frequented
Internet pornography sites.”
“Much of this prurient material emphasized children and
adolescents and was specifically targeted to purveyors of child
pornography. He also solicited prostitution, which he had not
previously done.”
“Despite his strong desire to avoid prison, he could not restrain
himself from soliciting sexual favors from staff at the rehabilitation
center. ”
Burns and Swerdlow, 2003
Another sad tale
Anatomy of an fMRI study
Study
Test (in scanner)
Buckner & Wheeler, 2001
Anatomy of an fMRI study
Old
New
-
=
Buckner & Wheeler, 2001
Applications of fMRI
‣ Discovery of basic brain function
‣ Discovery of brain dysfunction in disease
‣ Evaluation of treatment efficacy
‣ Sketchy things
http://www.noliemri.com
“This is your brain on politics”, NY Times, Nov. 11, 2007
1. Voters sense both peril and promise in party brands.
2. Emotions about Hillary Clinton are mixed.
3. The gender gap may be closing.
4. Mitt Romney shows potential.
5. In Rudy Giuliani versus Fred Thompson, the latter
evokes more empathy.
6. John Edwards has promise — and a problem.
7. Barack Obama and John McCain have
work to do.
Where are the
language areas?
Where are the motor
areas?
With fMRI, patients
must perform an
action, which is
unreliable in clinic.
Functional
connectivity MRI
(fcMRI) requires NO
task. Highly reliable.
2
% BOLD Change
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Time (sec)
-1.5
200
250
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% BOLD Change
1.5
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0.5
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-0.5
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100
150
200
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300
200
250
300
-1
Time (sec)
-1.5
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% BOLD Change
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Time (sec)
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Functional
connectivity MRI
(fcMRI) requires NO
task.
Emerging technology: quantitative radiology
2. fcMRI
1. Patient visits brain
doctor.
scan.
Doctor
orders fcMRI.
3. Quantitative
analysis
4. Doctor
receives
report.
5. Doctor
makes dx.
and plans
treatment.
Quantitative report provides diagnostic measures,
guides treatment, assesses response.
Emerging technology: digital lab on the cloud
Input:
Raw MRI scans
Output:
Quantitative
reports
Emerging technology: Patient-driven care
Microsoft HealthVault
Emerging technology: Patient-driven care
Google Health (prototype)
Brain imaging for hackers
‣ Get yourself some brain images
‣ Get yourself some brain analysis tools
‣ Discover something, invent something
Get your own brain scanned
‣ Buy a scanner and install it in your basement
Get your own brain scanned
‣ Buy a scanner and install it in your basement
‣ Inflict severe brain injury
Get your own brain scanned
‣ Buy a scanner and install it in your basement
‣ Inflict severe brain injury
‣ Volunteer for a study
- Contact local research centers
- Ask for your scans (“I’ve brought a blank CD with
me. Will you please copy the DICOM files of my
scans onto it?”)
Use open access data
‣ Neuron: Neuron Database @ Yale Sense Lab
‣ Gene expression: Allen Brain Atlas
‣ Structural MRI: Open Access Structural Imaging Series
(OASIS), mBIRN Data Repository
‣ Functional MRI: fMRI Data Center, fBIRN Data
Repository
‣ Functional connectivity MRI: Brainscape
oasis-brains.org
brainscape.org
Get yourself some tools
Slicer, Caret, AFNI,
Freesurfer, SPM,
FSL, ImageJ
Neuron  Network  Whole brain
Genesis
Neuron
Ed Boyden, Thursday 11:50
“Synthetic Neurobiology: Towards Engineering Brain
Circuits for Health and Human Augmentation”
See also NITRC (http://www.nitrc.org/)
Some unsolved problems
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Automated brain extraction
How many networks are in the brain
Methods for distinguishing differences between populations
Predicting disease and aptitude
Data sharing
Individual differences in performance (“gifted”, “savant”)
Neuroethics
“Deidentifying” images
Bridging the spatial divide
Security and privacy
Data mining
Start hacking.
Brain imaging: gene expression
Lein et al. Nature (2007)
Functional Brain Imaging and Brain Blood Flow
Veber den Kreislauf des Blutes in Menschlichen Gehirn (Concerning the circulation of the blood
in the human brain) Verlag von Viet & Company: Leipzig, 1881
Angelo Mosso
Forearm
Brain
Resting quietly
Forearm
Brain
Arrow: room clock strikes 12 noon and of
church bells heard
Forearm
Brain
Arrow: Mosso asked Bertino if the Ave Maria
should have been said
Brain
Forearm
Arrow: “What is 8 x 12?”
From: Angelo Mosso (1881)
ω: response
Monday noon, September 23, 1878
fMRI depends on blood oxygenation levels
“Rest”
“Activation”
fMRI BOLD Signal
Difference Image
∆ Blood Flow > ∆ Oxygen Consumption