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
- 3. Brains, the Final Frontier! Neuroimaging Informatics
- 4. Neuroimaging Informatics computational methods and infrastructure for understanding the structure and function of the brain
- 5. Neuroinformatics FTW! I have burning… questions! Neuroscience! tools and databases methods for analysis computational models
- 6. I’ll take any question to prove my method! I just want to understand the visual system
- 7. I will build you a new spaceship! I just discovered a new nebula!
- 8. Captain’s Log A Brief History 1989 What to do with this data?
- 9. Captain’s Log A Brief History 1989 What to do with this data? Here are some ideas! 1991
- 10. Captain’s Log A Brief History 1989 What to do with this data? Here are some ideas! 1991 Fine! Here’s grant $$$ 1993 Neuroinformatics!
- 11. Captain’s Log A Brief History 1989 What to do with this data? Here are some ideas! 1991 Fine! Here’s grant $$$ 1993 Neuroinformatics! 2006 INCF
- 12. 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
- 13. Mission • The Human Brain • How do we image brains? • How do we build tools? UNCHARTED TERRITORY HOW TO EXPLORE NEUROINFORMATICS
- 14. Mission • The Human Brain • How do we image brains? • How do we build tools? BACKGROUND DATA METHODS
- 15. The Uncharted Territory: The Human Brain
- 16. The Uncharted Territory BACKGROUND DATA METHODS Central Nervous System (CNS) Peripheral Nervous System (CNS)
- 17. The Human Brain BACKGROUND DATA METHODS
- 18. The Human Brain BACKGROUND DATA METHODS 3 pounds <> 109 neurons <> 1015 synaptic connections
- 19. BACKGROUND DATA METHODS The Human Brain
- 20. Anatomical Directions BACKGROUND DATA METHODS ANTERIOR POSTERIOR SUPERIOR INFERIOR ROSTRAL CAUDAL VENTRAL DORSAL DORSAL
- 21. Slice it up! BACKGROUND DATA METHODS CORONAL SAGITTAL AXIAL
- 22. How to Explore: Neuroimaging Methods
- 23. We study brains with Neuroimaging BACKGROUND DATA METHODS TEMPORAL RESOLUTION SPATIALRESOLUTION
- 24. We don’t want to cut people open! BACKGROUND DATA METHODS Oh?
- 25. 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
- 26. structure and function BACKGROUND DATA METHODS We collect data to answer a biological question ? Population Protocol Data Public Repository
- 27. 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?
- 28. We measure structure and function BACKGROUND DATA METHODS Invasive Non-invasive Structure sMRI CT DTI Function fMRI PET EEG MEG
- 29. 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
- 30. What imaging modalities do we use to measure structure?
- 31. Computed Tomography BACKGROUND DATA METHODS CT tumors bones! infarction calcifications
- 32. Magnetic Resonance Imaging BACKGROUND DATA METHODS sMRI gray matter white matter cerebrospinal fluid T2 T1
- 33. Diffusion Tensor Imaging BACKGROUND DATA METHODS DTI white matter integrity
- 34. What imaging modalities do we use to measure function?
- 35. Functional Magnetic Resonance Imaging BACKGROUND DATA METHODS fMRI neural activity blood flow oxyhemoglobin MR signal
- 36. Positron Emission Tomography BACKGROUND DATA METHODS PET
- 39. 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
- 40. What does my data look like?
- 42. What does my data look like? BACKGROUND DATA METHODS TIME
- 43. What does my data look like? BACKGROUND DATA METHODS SLICE VOXEL
- 44. 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
- 45. What are those numbers?! • Structural – Gray and white matter volume – White Matter Integrity – Cortical Thickness • Functional – Functional connectivity – Blood flow
- 46. How we build tools: Neuroimaging Informatics Methods
- 47. 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!”
- 48. BACKGROUND DATA METHODS IMAGE ACQUISITION PREPROCESSING PROCESSING ANALYSIS Neuroimaging Informatics Pipeline Data + Knowledge Representation + Infrastructure = Sharing, Knowledge, Tools 1 2 3
- 49. BACKGROUND DATA METHODS IMAGE ACQUISITION PREPROCESSING PROCESSING ANALYSIS Neuroimaging Informatics Pipeline Data + Knowledge Representation + Infrastructure = Sharing, Knowledge, Tools 1 2 3
- 50. Segment Realign and Reslice Coregister Normalize Smooth Segment BACKGROUND DATA METHODS Pre/Processing Prepares for Analysis
- 51. Realign and Reslice Coregister Normalize Smooth Segment METHODS Realignment for Motion Correction DATABACKGROUND translation rotation zooming shearingtranslation rotation
- 52. Realign and Reslice Coregister Normalize Smooth Segment METHODS Coregistration DATABACKGROUND
- 53. Realign and Reslice Coregister Normalize Smooth Segment METHODS Normalization DATABACKGROUND
- 54. Realign and Reslice Coregister Normalize Smooth Segment METHODS Smoothing DATABACKGROUND No smoothing 4 mm kernel
- 55. Realign and Reslice Coregister Normalize Smooth Segment METHODS Segmentation DATABACKGROUND Brain/skullCSFWMGM Priors Tissue Types
- 56. Realign and Reslice Coregister Normalize Smooth Segment METHODS Segmentation DATABACKGROUND
- 57. BACKGROUND DATA METHODS IMAGE ACQUISITION PREPROCESSING PROCESSING ANALYSIS Neuroimaging Informatics Pipeline Data driven approaches Hypothesis drive approaches 1 2 3
- 58. ? I’m getting bigger! BACKGROUND DATA METHODS Two Analysis Approaches Can we address my burning question now?
- 59. What are commonly used apriori methods?
- 60. 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
- 61. BACKGROUND DATA METHODS How are two or more brain regions of interest connected anatomically in a subject population? ? TRACTOGRAPHY (DTI)
- 62. 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
- 63. 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
- 64. What are commonly used data- driven methods?
- 65. 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
- 66. BACKGROUND DATA METHODS How and which set of brain regions cumulatively represent an experimental stimuli? ? MULTI VOXEL PATTERN ANALYSIS (MVPA) fMRI
- 67. How do I use informatics to extend my analyses?
- 68. 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
- 69. Atlas: Terms for Spatial Characteristics BACKGROUND DATA METHODS Brodmann Atlas ICBM Atlas
- 70. Knowledge Representation BACKGROUND DATA METHODS FMA NIFSTD XCEDE
- 71. Challenges, Captain! BACKGROUND DATA METHODS Complex, noisy data! Arg! Take that, poor resolution! Where are the standards?!
- 72. BACKGROUND DATA METHODS The Journey Continues… PRESENTPAST FUTURE