Brain imaging for fun and profit <ul><li>Daniel Marcus, PhD </li></ul><ul><li>Director, Neuroinformatics Research Group @ ...
Outline <ul><li>Brain imaging 101 </li></ul><ul><li>Brain imaging & emerging technologies </li></ul><ul><li>Brain imaging ...
100 billion neurons in the human brain 100 trillion synapses in the human brain Neuron is the basic computational unit in ...
Neurons are organized into circuits in the cerebral cortex
Neuron    Network    Whole brain
Brain imaging: single neuron Misgeld &  Kerschensteiner,  2006 In vivo microscopy
Brain imaging: neuronal networks Livet, et al.  Nature  (2007) Transgenics & fluorescence microscopy
Brain imaging: whole brain <ul><li>Magnetic Resonance Imaging (MRI) </li></ul><ul><ul><li>Structural MRI </li></ul></ul><u...
Structural MRI <ul><li>Essential in clinical care. </li></ul><ul><li>Radiologists perform qualitative “lightbox” reads.  <...
Aging of the brain 20s 80s with mild Alzheimer’s 80s aging  gracefully 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 <ul><li>“ [P]ossessed a well-balanced mind, and was looked upon by those who knew him as a sh...
 
Natural History Museum, London
Another sad tale <ul><li>“ A preexisting  strong interest in pornography   dating back to adolescence ...” </li></ul><ul><...
Another sad tale
Anatomy of an fMRI study Buckner & Wheeler, 2001 Study Test (in scanner)
Anatomy of an fMRI study Buckner & Wheeler, 2001 - = Old New
Applications of fMRI <ul><li>Discovery of basic brain function </li></ul><ul><li>Discovery of brain dysfunction in disease...
http://www.noliemri.com
“ This is your brain on politics”, NY Times, Nov. 11, 2007
<ul><li>Voters sense both peril and promise in party brands.  </li></ul><ul><li>Emotions about Hillary Clinton are mixed. ...
 
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.
 
 
Functional connectivity MRI (fcMRI) requires NO task.
 
Emerging technology: quantitative radiology <ul><li>Patient visits doctor. Doctor orders fcMRI.  </li></ul><ul><li>fcMRI b...
Emerging technology: digital lab on the cloud Input:   Raw MRI scans Output:  Quantitative reports
Emerging technology: Patient-driven care Microsoft HealthVault
Google Health (prototype) Emerging technology: Patient-driven care
Brain imaging for hackers <ul><li>Get yourself some brain images </li></ul><ul><li>Get yourself some brain analysis tools ...
Get your own brain scanned <ul><li>Buy a scanner and install it in your basement </li></ul>
Get your own brain scanned <ul><li>Buy a scanner and install it in your basement </li></ul><ul><li>Inflict severe brain in...
Get your own brain scanned <ul><li>Buy a scanner and install it in your basement </li></ul><ul><li>Inflict severe brain in...
Use open access data <ul><li>Neuron: Neuron Database @ Yale Sense Lab </li></ul><ul><li>Gene expression: Allen Brain Atlas...
oasis-brains.org
brainscape.org
Get yourself some tools Neuron    Network    Whole brain Genesis Neuron Slicer, Caret, AFNI, Freesurfer, SPM, FSL, Image...
Some unsolved problems <ul><li>Automated brain extraction </li></ul><ul><li>How many networks are in the brain </li></ul><...
Start hacking.
Brain imaging: gene expression Lein et al.  Nature  (2007)
Veber den Kreislauf des Blutes in Menschlichen Gehirn (Concerning the circulation of the blood in the human brain)  Verlag...
Monday noon, September 23, 1878 From: Angelo Mosso (1881) Resting quietly Forearm Brain Arrow: room clock strikes 12 noon ...
Michael Faraday 1845 Linus Pauling 1937 The Background & Basis of the BOLD Effect in fMRI Seiji Ogawa 1990 Room Air 100% O...
fMRI depends on blood oxygenation levels ∆  Blood Flow > ∆ Oxygen Consumption fMRI BOLD Signal Difference Image “ Rest” “ ...
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  • Brain Imaging for Fun and Profit

    1. Brain imaging for fun and profit <ul><li>Daniel Marcus, PhD </li></ul><ul><li>Director, Neuroinformatics Research Group @ Washington University School of Medicine </li></ul>
    2. Outline <ul><li>Brain imaging 101 </li></ul><ul><li>Brain imaging & emerging technologies </li></ul><ul><li>Brain imaging for hackers </li></ul>
    3. 100 billion neurons in the human brain 100 trillion synapses in the human brain Neuron is the basic computational unit in the brain
    4. Neurons are organized into circuits in the cerebral cortex
    5. Neuron  Network  Whole brain
    6. Brain imaging: single neuron Misgeld & Kerschensteiner, 2006 In vivo microscopy
    7. Brain imaging: neuronal networks Livet, et al. Nature (2007) Transgenics & fluorescence microscopy
    8. Brain imaging: whole brain <ul><li>Magnetic Resonance Imaging (MRI) </li></ul><ul><ul><li>Structural MRI </li></ul></ul><ul><ul><li>Functional MRI </li></ul></ul><ul><ul><li>Functional connectivity MRI </li></ul></ul><ul><li>Computed tomography (CT) </li></ul><ul><li>Positron emission tomography (PET) </li></ul><ul><li>EEG, MEG, MRS, SPECT, DTI,… </li></ul>
    9. Structural MRI <ul><li>Essential in clinical care. </li></ul><ul><li>Radiologists perform qualitative “lightbox” reads. </li></ul><ul><li>Most psychiatric and neurological disorders are invisible to reading radiologists. </li></ul>
    10. Aging of the brain 20s 80s with mild Alzheimer’s 80s aging gracefully http://www.oasis-brains.org
    11. Brain volume declines with age Marcus et al., 2007
    12. Advanced structural methods Van Essen et al., 2006 Csernansky et al., 2005
    13. fMRI
    14. fMRI depends on functional localization
    15. The sad tale of Phineas Gage <ul><li>“ [P]ossessed a well-balanced mind, and was looked upon by those who knew him as a shrewd, smart businessman, very energetic and persistent” </li></ul><ul><li>“ 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...” </li></ul>Harlow, J.M. (1868)
    16.  
    17. Natural History Museum, London
    18. Another sad tale <ul><li>“ A preexisting strong interest in pornography dating back to adolescence ...” </li></ul><ul><li>“ An increasing interest in pornography... acquired an expanding collection of pornographic magazines and increasingly frequented Internet pornography sites.” </li></ul><ul><li>“ 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.” </li></ul><ul><li>“ Despite his strong desire to avoid prison, he could not restrain himself from soliciting sexual favors from staff at the rehabilitation center. ” </li></ul>Burns and Swerdlow, 2003
    19. Another sad tale
    20. Anatomy of an fMRI study Buckner & Wheeler, 2001 Study Test (in scanner)
    21. Anatomy of an fMRI study Buckner & Wheeler, 2001 - = Old New
    22. Applications of fMRI <ul><li>Discovery of basic brain function </li></ul><ul><li>Discovery of brain dysfunction in disease </li></ul><ul><li>Evaluation of treatment efficacy </li></ul><ul><li>Sketchy things </li></ul>
    23. http://www.noliemri.com
    24. “ This is your brain on politics”, NY Times, Nov. 11, 2007
    25. <ul><li>Voters sense both peril and promise in party brands. </li></ul><ul><li>Emotions about Hillary Clinton are mixed. </li></ul><ul><li>The gender gap may be closing. </li></ul><ul><li>Mitt Romney shows potential. </li></ul><ul><li>In Rudy Giuliani versus Fred Thompson, the latter evokes more empathy. </li></ul><ul><li>John Edwards has promise — and a problem. </li></ul><ul><li>Barack Obama and John McCain have work to do. </li></ul>
    26.  
    27. Where are the language areas? Where are the motor areas?
    28.  
    29. With fMRI, patients must perform an action, which is unreliable in clinic.
    30. Functional connectivity MRI (fcMRI) requires NO task. Highly reliable.
    31.  
    32.  
    33. Functional connectivity MRI (fcMRI) requires NO task.
    34.  
    35. Emerging technology: quantitative radiology <ul><li>Patient visits doctor. Doctor orders fcMRI. </li></ul><ul><li>fcMRI brain scan. </li></ul><ul><li>Quantitative analysis </li></ul><ul><li>Doctor receives report. </li></ul><ul><li>Doctor makes dx. and plans treatment. </li></ul>Quantitative report provides diagnostic measures, guides treatment, assesses response.
    36. Emerging technology: digital lab on the cloud Input: Raw MRI scans Output: Quantitative reports
    37. Emerging technology: Patient-driven care Microsoft HealthVault
    38. Google Health (prototype) Emerging technology: Patient-driven care
    39. Brain imaging for hackers <ul><li>Get yourself some brain images </li></ul><ul><li>Get yourself some brain analysis tools </li></ul><ul><li>Discover something, invent something </li></ul>
    40. Get your own brain scanned <ul><li>Buy a scanner and install it in your basement </li></ul>
    41. Get your own brain scanned <ul><li>Buy a scanner and install it in your basement </li></ul><ul><li>Inflict severe brain injury </li></ul>
    42. Get your own brain scanned <ul><li>Buy a scanner and install it in your basement </li></ul><ul><li>Inflict severe brain injury </li></ul><ul><li>Volunteer for a study </li></ul><ul><ul><li>Contact local research centers </li></ul></ul><ul><ul><li>Ask for your scans (“I’ve brought a blank CD with me. Will you please copy the DICOM files of my scans onto it?”) </li></ul></ul>
    43. Use open access data <ul><li>Neuron: Neuron Database @ Yale Sense Lab </li></ul><ul><li>Gene expression: Allen Brain Atlas </li></ul><ul><li>Structural MRI: Open Access Structural Imaging Series (OASIS), mBIRN Data Repository </li></ul><ul><li>Functional MRI: fMRI Data Center, fBIRN Data Repository </li></ul><ul><li>Functional connectivity MRI: Brainscape </li></ul>
    44. oasis-brains.org
    45. brainscape.org
    46. Get yourself some tools Neuron  Network  Whole brain Genesis Neuron Slicer, Caret, AFNI, Freesurfer, SPM, FSL, ImageJ See also NITRC ( http:// www.nitrc.org / ) Ed Boyden, Thursday 11:50 “ Synthetic Neurobiology: Towards Engineering Brain Circuits for Health and Human Augmentation”
    47. Some unsolved problems <ul><li>Automated brain extraction </li></ul><ul><li>How many networks are in the brain </li></ul><ul><li>Methods for distinguishing differences between populations </li></ul><ul><li>Predicting disease and aptitude </li></ul><ul><li>Data sharing </li></ul><ul><li>Individual differences in performance (“gifted”, “savant”) </li></ul><ul><li>Neuroethics </li></ul><ul><li>“ Deidentifying” images </li></ul><ul><li>Bridging the spatial divide </li></ul><ul><li>Security and privacy </li></ul><ul><li>Data mining </li></ul>
    48. Start hacking.
    49. Brain imaging: gene expression Lein et al. Nature (2007)
    50. Veber den Kreislauf des Blutes in Menschlichen Gehirn (Concerning the circulation of the blood in the human brain) Verlag von Viet & Company: Leipzig, 1881 Functional Brain Imaging and Brain Blood Flow Angelo Mosso
    51. Monday noon, September 23, 1878 From: Angelo Mosso (1881) Resting quietly Forearm Brain Arrow: room clock strikes 12 noon and of church bells heard Brain Forearm Arrow: Mosso asked Bertino if the Ave Maria should have been said Brain Forearm Arrow: “What is 8 x 12?” ω : response Brain Forearm
    52. Michael Faraday 1845 Linus Pauling 1937 The Background & Basis of the BOLD Effect in fMRI Seiji Ogawa 1990 Room Air 100% Oxygen Room Air 100% Oxygen “ BOLD” Contrast
    53. fMRI depends on blood oxygenation levels ∆ Blood Flow > ∆ Oxygen Consumption fMRI BOLD Signal Difference Image “ Rest” “ Activation”

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