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Introduction to Neuroimaging Informatics

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Lecture to introduce neuroimaging informatics for BMI 260, Stanford University, 5/8/2013

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Introduction to Neuroimaging Informatics

  1. 1. Neuroimaging Informatics Vanessa Sochat 05/08/2013
  2. 2. Brains, the Final Frontier! Neuroimaging Informatics
  3. 3. Neuroimaging Informatics computational methods and infrastructure for understanding the structure and function of the brain
  4. 4. Neuroinformatics FTW! I have burning… questions! Neuroscience! tools and databases methods for analysis computational models
  5. 5. I’ll take any question to prove my method! I just want to understand the visual system
  6. 6. I will build you a new spaceship! I just discovered a new nebula!
  7. 7. Captain’s Log A Brief History 1989 What to do with this data?
  8. 8. Captain’s Log A Brief History 1989 What to do with this data? Here are some ideas! 1991
  9. 9. Captain’s Log A Brief History 1989 What to do with this data? Here are some ideas! 1991 Fine! Here’s grant $$$ 1993 Neuroinformatics!
  10. 10. Captain’s Log A Brief History 1989 What to do with this data? Here are some ideas! 1991 Fine! Here’s grant $$$ 1993 Neuroinformatics! 2006 INCF
  11. 11. Captain’s Log A Brief History 1989 What to do with this data? Here are some ideas! 1991 Fine! Here’s grant $$$ 1993 Neuroinformatics! 2006 2013
  12. 12. Mission • The Human Brain • How do we image brains? • How do we build tools? UNCHARTED TERRITORY HOW TO EXPLORE NEUROINFORMATICS
  13. 13. Mission • The Human Brain • How do we image brains? • How do we build tools? BACKGROUND DATA METHODS
  14. 14. The Uncharted Territory: The Human Brain
  15. 15. The Uncharted Territory BACKGROUND DATA METHODS Central Nervous System (CNS) Peripheral Nervous System (CNS)
  16. 16. The Human Brain BACKGROUND DATA METHODS
  17. 17. The Human Brain BACKGROUND DATA METHODS 3 pounds <> 109 neurons <> 1015 synaptic connections
  18. 18. BACKGROUND DATA METHODS The Human Brain
  19. 19. Anatomical Directions BACKGROUND DATA METHODS ANTERIOR POSTERIOR SUPERIOR INFERIOR ROSTRAL CAUDAL VENTRAL DORSAL DORSAL
  20. 20. Slice it up! BACKGROUND DATA METHODS CORONAL SAGITTAL AXIAL
  21. 21. How to Explore: Neuroimaging Methods
  22. 22. We study brains with Neuroimaging BACKGROUND DATA METHODS TEMPORAL RESOLUTION SPATIALRESOLUTION
  23. 23. We don’t want to cut people open! BACKGROUND DATA METHODS Oh?
  24. 24. structure and function BACKGROUND DATA METHODS We collect data to answer a biological question ? Population Protocol Data What happens to the structure of region X as we get older? What is my brain doing when I see pictures of cats? Which regions are working together? Public Repository
  25. 25. structure and function BACKGROUND DATA METHODS We collect data to answer a biological question ? Population Protocol Data Public Repository
  26. 26. BACKGROUND DATA METHODS We like to identify biomarkers in our images ? Feature Extraction Public Data Process Analysis / Machine Learning Disorder diagnosis Classification of subtypes of disease Improved filtering methods Understanding human connectome Why?
  27. 27. We measure structure and function BACKGROUND DATA METHODS Invasive Non-invasive Structure sMRI CT DTI Function fMRI PET EEG MEG
  28. 28. We measure structure and function BACKGROUND DATA METHODS Invasive Non-invasive Structure sMRI CT DTI Function fMRI PET EEG MEG sMRI DTI CT fMRI EEG PET MEG
  29. 29. What imaging modalities do we use to measure structure?
  30. 30. Computed Tomography BACKGROUND DATA METHODS CT tumors bones! infarction calcifications
  31. 31. Magnetic Resonance Imaging BACKGROUND DATA METHODS sMRI gray matter white matter cerebrospinal fluid T2 T1
  32. 32. Diffusion Tensor Imaging BACKGROUND DATA METHODS DTI white matter integrity
  33. 33. What imaging modalities do we use to measure function?
  34. 34. Functional Magnetic Resonance Imaging BACKGROUND DATA METHODS fMRI neural activity   blood flow   oxyhemoglobin   MR signal
  35. 35. Positron Emission Tomography BACKGROUND DATA METHODS PET
  36. 36. Electroencephalography BACKGROUND DATA METHODS EEG
  37. 37. Magnetoencephalography BACKGROUND DATA METHODS MEG
  38. 38. What data do I need to measure… BACKGROUND DATA METHODS I want to measure… Imaging Modality Some tissue volume sMRI (T1) Tumor, bone, or fluid CT, sMRI (T2) Cortical Thickness sMRI (T1) White Matter Integrity DTI Brain Function fMRI, with sMRI (T1) for registration Superficial Activity EEG, MEG Neurotransmitter-specific Activity PET
  39. 39. What does my data look like?
  40. 40. What does my data look like? BACKGROUND DATA METHODS TIME
  41. 41. What does my data look like? BACKGROUND DATA METHODS SLICE VOXEL
  42. 42. What does my data look like? BACKGROUND DATA METHODS P Files Imaging Data Header Nifti • .nii (one file) • .img / .hdr combo 3D • .nii.gz (compressed file) • .nii (uncompressed) • .img/.hdr combos 4D
  43. 43. What are those numbers?! • Structural – Gray and white matter volume – White Matter Integrity – Cortical Thickness • Functional – Functional connectivity – Blood flow
  44. 44. How we build tools: Neuroimaging Informatics Methods
  45. 45. computational methods and infrastructure for understanding the structure and function of the brain develop and apply new methods for acquisition, representation, and analysis of neuroimaging data and knowledge BACKGROUND DATA METHODS “What I want!” “What I do!”
  46. 46. BACKGROUND DATA METHODS IMAGE ACQUISITION PREPROCESSING PROCESSING ANALYSIS Neuroimaging Informatics Pipeline Data + Knowledge Representation + Infrastructure = Sharing, Knowledge, Tools 1 2 3
  47. 47. BACKGROUND DATA METHODS IMAGE ACQUISITION PREPROCESSING PROCESSING ANALYSIS Neuroimaging Informatics Pipeline Data + Knowledge Representation + Infrastructure = Sharing, Knowledge, Tools 1 2 3
  48. 48. Segment Realign and Reslice Coregister Normalize Smooth Segment BACKGROUND DATA METHODS Pre/Processing Prepares for Analysis
  49. 49. Realign and Reslice Coregister Normalize Smooth Segment METHODS Realignment for Motion Correction DATABACKGROUND translation rotation zooming shearingtranslation rotation
  50. 50. Realign and Reslice Coregister Normalize Smooth Segment METHODS Coregistration DATABACKGROUND
  51. 51. Realign and Reslice Coregister Normalize Smooth Segment METHODS Normalization DATABACKGROUND
  52. 52. Realign and Reslice Coregister Normalize Smooth Segment METHODS Smoothing DATABACKGROUND No smoothing 4 mm kernel
  53. 53. Realign and Reslice Coregister Normalize Smooth Segment METHODS Segmentation DATABACKGROUND Brain/skullCSFWMGM Priors Tissue Types
  54. 54. Realign and Reslice Coregister Normalize Smooth Segment METHODS Segmentation DATABACKGROUND
  55. 55. BACKGROUND DATA METHODS IMAGE ACQUISITION PREPROCESSING PROCESSING ANALYSIS Neuroimaging Informatics Pipeline Data driven approaches Hypothesis drive approaches 1 2 3
  56. 56. ? I’m getting bigger! BACKGROUND DATA METHODS Two Analysis Approaches Can we address my burning question now?
  57. 57. What are commonly used apriori methods?
  58. 58. BACKGROUND DATA METHODS What are structural characteristics (e.g. gray matter volume, density) within a brain region of interest in a subject population? ? VOXEL BASED MORPHOMETRY (VBM) SEGMENT NORMALIZE MODULATE SMOOTH VOXEL-WISE STATISTICS sMRI
  59. 59. BACKGROUND DATA METHODS How are two or more brain regions of interest connected anatomically in a subject population? ? TRACTOGRAPHY (DTI)
  60. 60. BACKGROUND DATA METHODS Which brain regions show neural activity during a function of interest? ? GENERAL LINEAR MODEL (GLM) Brain regions responding “active” to biological motion REALIGN AND RESLICE SEGMENT REGISTER NORMALIZE FIT to GLM sMRI and fMRI
  61. 61. BACKGROUND DATA METHODS What is the brain network underlying a function of interest? ? CORRELATIONS Brain network underlying hand movement IDENTIFY ROI EXTRACT SIGNAL NETWORK CONNECTIVITY
  62. 62. What are commonly used data- driven methods?
  63. 63. BACKGROUND DATA METHODS What is the brain network underlying a function of interest? ? INDEPENDENT COMPONENT ANALYSIS (ICA) X = A SX n x m n x n n x m S = A-1 XX
  64. 64. BACKGROUND DATA METHODS How and which set of brain regions cumulatively represent an experimental stimuli? ? MULTI VOXEL PATTERN ANALYSIS (MVPA) fMRI
  65. 65. How do I use informatics to extend my analyses?
  66. 66. Databases to Distribute Resources BACKGROUND DATA METHODS Publicly available Brain DBs: fMRIDC Allen Brain Atlas BIRN Neurosynth ADNI NDAR Human Connectome Demographics Imaging Protocol Raw Images Processed Images
  67. 67. Atlas: Terms for Spatial Characteristics BACKGROUND DATA METHODS Brodmann Atlas ICBM Atlas
  68. 68. Knowledge Representation BACKGROUND DATA METHODS FMA NIFSTD XCEDE
  69. 69. Challenges, Captain! BACKGROUND DATA METHODS Complex, noisy data! Arg! Take that, poor resolution! Where are the standards?!
  70. 70. BACKGROUND DATA METHODS The Journey Continues… PRESENTPAST FUTURE
  71. 71. I have questions… vsochat@stanford.edu

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