Basics of Diffusion Tensor Imaging and DtiStudio

Size: px
Start display at page:

Download "Basics of Diffusion Tensor Imaging and DtiStudio"

Transcription

1 Basics of Diffusion Tensor Imaging and DtiStudio DTI Basics 1

2 DTI reveals White matter anatomy Gray matter White matter DTI uses water diffusion as a probe for white matter anatomy Isotropic diffusion Anisotropic diffusion 2

3 3D axonal structures can be reconstructed based on DTI What is Diffusion Imaging and How It Works RF 90 RF 90 G 3

4 Diffusion process: Concentration gradient How can we measure diffusion without perturbing the system? 4

5 Homogeneous magnetic field H O H H H O H O H B 0 / 2 e.g. B 0 = 9.4 T = 400 MHz 400 Inhomogeneous magnetic field B 0 / 2 H H O H O H H O H e.g. B 0 = 9.4 T = 400 MHz 5

6 Direction of Gradient Z X Y Z-Gradient X-Gradient Y-Gradient Strength of Gradient Z Opposite polarity +/- X Y Weak X- Gradient Strong X- Gradient Strong X- Gradient 6

7 A diagram to show the gradient application length Gx strength X Y Z how it affects spins 90 RF G Dephasing Rephasing B 0 / 2 7

8 If spins move Imperfect refocusing =Signal loss! Dephasing Rephasing Signal loss! 8

9 Signal Intensity 3/17/2012 Parameters that affect the result G D Small G Less signal loss Large G More signal loss Equation for the diffusion attenuation G ln S S G D = - bd D b-value 9

10 Signal Intensity 3/17/2012 Diffusion measurement by imaging 90 RF Imaging G b DWI and ADC 1 G/cm 6 G/cm 10 G/cm 13 G/cm b-value 10

11 Direction of the diffusion measurment Only the diffusion along a gradient direction can be measured Apparent Diffusion Constant (ADC) Map with Different Measurement Direction X Y Z 11

12 Anisotropic diffusion Free diffusion Isotropic diffusion Restricted diffusion Anisotropic diffusion Determination of diffusion ellipsoid z l 1 y l 2 x Measure diffusion along various directions (> 6) l 3 Calculate shape of the ellipsoid 12

13 Raw data of DTI S 0 S x S y S z S x+y S x+z S y+z DtiStudio Interface and DTI Data Processing 13

14 Initial data I/O window Viewing screen 14

15 Tensor calculation results 15

16 DTI-derived contrasts S 0 S x S y S z S x+y S x+z S y+z FA map Orientation map Relationships of DTI-derived maps Average STD Axial diffusivity Radial diffusivity Mean diffusivity Fractional anisotropy 16

17 Simplifications and assumptions in DTI Diffusion ellipsoid Non-tensor analysis 17

18 rotationmetric equivalent degree around x axis translation metric: mm translation score 3/17/2012 Artifact Detection and Correction Subject motion : rotationmetric : translationmetric # of DWI # of DWI 0 18

19 normalized Gx PE(Y) normalized Gy normalized Gz 3/17/2012 Uncorrectable motion problem a Eddy current distortion RO(X) b ex vs Gx, R = ey vs Gy, R = c d ez vs Gz, R = R = R = R = ex ey ez 19

20 Data corruption a b c d e f 150 g h i j k l QC Reporting Histogram of normalized absolute fitting errors before registration fitting error score 0.02 histogram eddyzmetrics a b noise 2 0 Scanner#1 Scanner#2 Scanner#3 Scanner#4 Histogram rotationmetrics equivalent degree around x axis Rotation Metric 20

21 Fiber Tracking Can axonal projections be reconstructed? At each voxel, average fiber orientation can be estimated Axonal projection reconstruction may be possible 21

22 Examples of the tracking Example of reconstruction 22

23 Fiber selection process #1 #1 #2 #3 #2 #3 Automated ROI definition and tracking 23

24 Tensor vs Non-tensor Deterministic vs Probabilistic 24

25 Pathology/ Functions/ 3/17/2012 Quantitative Data Analysis and MriStudio (DiffeoMap and RoiEditor) Scalarization is needed for image analysis Conversion to a number e.g.: FA, T2, size size 25

26 Coverage 3/17/2012 Location is the most difficult parameter to quantify Without identification of corresponding locations, quantification is meaningless Coverage and granularity of image quantification 100% Whole-brain analysis Atlas-based analysis Voxel-based analysis ROI-based analysis 1 1.5M Granularity 26

27 FA, T2 3/17/2012 Normalization of pathological brains original Normalized LDDMM: Michael I. Miller Voxel-based analysis Normalized Control Patient 27

28 Rationale of isotropic filtering Rationale of anatomical filtering: Atlas-based analysis 28

29 3D electronic brain atlas Automated segmentation of pathological brains 29

30 Automated and quantitative image analysis for population data A B DiffeoMap Interface A: Preproseccing B: Linear transformation C: LDDMM D: Transformation E: Landmark LDDMM 30

31 Choice of atlases Age-dependent 0 M 12 M 24 M Adult Multi-definition segmentation Probabilistic Structural Vascular territory Connectivity RoiEditor Interface A: ROI management B: Atlas Selection C: ROI drawing assist D: ROI list 31

Advanced Topics and Diffusion MRI

Advanced Topics and Diffusion MRI Advanced Topics and Diffusion MRI Slides originally by Karla Miller, FMRIB Centre Modified by Mark Chiew (mark.chiew@ndcn.ox.ac.uk) Slides available at: http://users.fmrib.ox.ac.uk/~mchiew/teaching/ MRI

More information

Applications of Spin Echo and Gradient Echo: Diffusion and Susceptibility Contrast

Applications of Spin Echo and Gradient Echo: Diffusion and Susceptibility Contrast Applications of Spin Echo and Gradient Echo: Diffusion and Susceptibility Contrast Chunlei Liu, PhD Department of Electrical Engineering & Computer Sciences and Helen Wills Neuroscience Institute University

More information

DIFFUSION MAGNETIC RESONANCE IMAGING

DIFFUSION MAGNETIC RESONANCE IMAGING DIFFUSION MAGNETIC RESONANCE IMAGING from spectroscopy to imaging apparent diffusion coefficient ADC-Map anisotropy diffusion tensor (imaging) DIFFUSION NMR - FROM SPECTROSCOPY TO IMAGING Combining Diffusion

More information

Contrast Mechanisms in MRI. Michael Jay Schillaci

Contrast Mechanisms in MRI. Michael Jay Schillaci Contrast Mechanisms in MRI Michael Jay Schillaci Overview Image Acquisition Basic Pulse Sequences Unwrapping K-Space Image Optimization Contrast Mechanisms Static and Motion Contrasts T1 & T2 Weighting,

More information

Correction Gradients. Nov7, Reference: Handbook of pulse sequence

Correction Gradients. Nov7, Reference: Handbook of pulse sequence Correction Gradients Nov7, 2005 Reference: Handbook of pulse sequence Correction Gradients 1. Concomitant-Field Correction Gradients 2. Crusher Gradients 3. Eddy-Current Compensation 4. Spoiler Gradients

More information

Diffusion Tensor Imaging quality control : artifacts assessment and correction. A. Coste, S. Gouttard, C. Vachet, G. Gerig. Medical Imaging Seminar

Diffusion Tensor Imaging quality control : artifacts assessment and correction. A. Coste, S. Gouttard, C. Vachet, G. Gerig. Medical Imaging Seminar Diffusion Tensor Imaging quality control : artifacts assessment and correction A. Coste, S. Gouttard, C. Vachet, G. Gerig Medical Imaging Seminar Overview Introduction DWI DTI Artifact Assessment Artifact

More information

Diffusion Tensor Imaging I: The basics. Jennifer Campbell

Diffusion Tensor Imaging I: The basics. Jennifer Campbell Diffusion Tensor Imaging I: The basics Jennifer Campbell Diffusion Tensor Imaging I: The basics Jennifer Campbell Diffusion Imaging MRI: many different sources of contrast T1W T2W PDW Perfusion BOLD DW

More information

醫用磁振學 MRM 擴散張量影像 擴散張量影像原理. 本週課程內容 MR Diffusion 擴散張量造影原理 擴散張量造影應用 盧家鋒助理教授國立陽明大學生物醫學影像暨放射科學系

醫用磁振學 MRM 擴散張量影像 擴散張量影像原理. 本週課程內容   MR Diffusion 擴散張量造影原理 擴散張量造影應用 盧家鋒助理教授國立陽明大學生物醫學影像暨放射科學系 本週課程內容 http://www.ym.edu.tw/~cflu 擴散張量造影原理 擴散張量造影應用 醫用磁振學 MRM 擴散張量影像 盧家鋒助理教授國立陽明大學生物醫學影像暨放射科學系 alvin4016@ym.edu.tw MRI The Basics (3rd edition) Chapter 22: Echo Planar Imaging MRI in Practice, (4th edition)

More information

Diffusion Tensor Imaging (DTI): An overview of key concepts

Diffusion Tensor Imaging (DTI): An overview of key concepts Diffusion Tensor Imaging (DTI): An overview of key concepts (Supplemental material for presentation) Prepared by: Nadia Barakat BMB 601 Chris Conklin Thursday, April 8 th 2010 Diffusion Concept [1,2]:

More information

DWI acquisition schemes and Diffusion Tensor estimation

DWI acquisition schemes and Diffusion Tensor estimation DWI acquisition schemes and Diffusion Tensor estimation A simulation based study Santiago Aja-Fernández, Antonio Tristán-Vega, Pablo Casaseca-de-la-Higuera Laboratory of Image Processing L A B O R A T

More information

EL-GY 6813/BE-GY 6203 Medical Imaging, Fall 2016 Final Exam

EL-GY 6813/BE-GY 6203 Medical Imaging, Fall 2016 Final Exam EL-GY 6813/BE-GY 6203 Medical Imaging, Fall 2016 Final Exam (closed book, 1 sheets of notes double sided allowed, no calculator or other electronic devices allowed) 1. Ultrasound Physics (15 pt) A) (9

More information

CIND Pre-Processing Pipeline For Diffusion Tensor Imaging. Overview

CIND Pre-Processing Pipeline For Diffusion Tensor Imaging. Overview CIND Pre-Processing Pipeline For Diffusion Tensor Imaging Overview The preprocessing pipeline of the Center for Imaging of Neurodegenerative Diseases (CIND) prepares diffusion weighted images (DWI) and

More information

Diffusion Tensor Imaging I. Jennifer Campbell

Diffusion Tensor Imaging I. Jennifer Campbell Diffusion Tensor Imaging I Jennifer Campbell Diffusion Imaging Molecular diffusion The diffusion tensor Diffusion weighting in MRI Alternatives to the tensor Overview of applications Diffusion Imaging

More information

Ordinary Least Squares and its applications

Ordinary Least Squares and its applications Ordinary Least Squares and its applications Dr. Mauro Zucchelli University Of Verona December 5, 2016 Dr. Mauro Zucchelli Ordinary Least Squares and its applications December 5, 2016 1 / 48 Contents 1

More information

Cambridge University Press MRI from A to Z: A Definitive Guide for Medical Professionals Gary Liney Excerpt More information

Cambridge University Press MRI from A to Z: A Definitive Guide for Medical Professionals Gary Liney Excerpt More information Main glossary Aa AB systems Referring to molecules exhibiting multiply split MRS peaks due to spin-spin interactions. In an AB system, the chemical shift between the spins is of similar magnitude to the

More information

Physics of MR Image Acquisition

Physics of MR Image Acquisition Physics of MR Image Acquisition HST-583, Fall 2002 Review: -MRI: Overview - MRI: Spatial Encoding MRI Contrast: Basic sequences - Gradient Echo - Spin Echo - Inversion Recovery : Functional Magnetic Resonance

More information

FREQUENCY SELECTIVE EXCITATION

FREQUENCY SELECTIVE EXCITATION PULSE SEQUENCES FREQUENCY SELECTIVE EXCITATION RF Grad 0 Sir Peter Mansfield A 1D IMAGE Field Strength / Frequency Position FOURIER PROJECTIONS MR Image Raw Data FFT of Raw Data BACK PROJECTION Image Domain

More information

A Neurosurgeon s Perspectives of Diffusion Tensor Imaging(DTI) Diffusion Tensor MRI (DTI) Background and Relevant Physics.

A Neurosurgeon s Perspectives of Diffusion Tensor Imaging(DTI) Diffusion Tensor MRI (DTI) Background and Relevant Physics. A Neurosurgeon s Perspectives of Diffusion Tensor Imaging(DTI) Kalai Arasu Muthusamy, D.Phil(Oxon) Senior Lecturer & Consultant Neurosurgeon. Division of Neurosurgery. University Malaya Medical Centre.

More information

New developments in Magnetic Resonance Spectrocopy and Diffusion MRI. Els Fieremans Steven Delputte Mahir Ozdemir

New developments in Magnetic Resonance Spectrocopy and Diffusion MRI. Els Fieremans Steven Delputte Mahir Ozdemir New developments in Magnetic Resonance Spectrocopy and Diffusion MRI Els Fieremans Steven Delputte Mahir Ozdemir Overview Magnetic Resonance Spectroscopy (MRS) Basic physics of MRS Quantitative MRS Pitfalls

More information

Diffusion Weighted MRI. Zanqi Liang & Hendrik Poernama

Diffusion Weighted MRI. Zanqi Liang & Hendrik Poernama Diffusion Weighted MRI Zanqi Liang & Hendrik Poernama 1 Outline MRI Quick Review What is Diffusion MRI? Detecting Diffusion Stroke and Tumor Detection Presenting Diffusion Anisotropy and Diffusion Tensor

More information

Introduction to MRI. Spin & Magnetic Moments. Relaxation (T1, T2) Spin Echoes. 2DFT Imaging. K-space & Spatial Resolution.

Introduction to MRI. Spin & Magnetic Moments. Relaxation (T1, T2) Spin Echoes. 2DFT Imaging. K-space & Spatial Resolution. Introduction to MRI Spin & Magnetic Moments Relaxation (T1, T2) Spin Echoes 2DFT Imaging Selective excitation, phase & frequency encoding K-space & Spatial Resolution Contrast (T1, T2) Acknowledgement:

More information

Diffusion tensor imaging (DTI):

Diffusion tensor imaging (DTI): Diffusion tensor imaging (DTI): A basic introduction to data acquisition and analysis Matthew Cykowski, MD Postdoctoral fellow Research Imaging Center UTHSCSA Room 2.320 cykowski@uthscsa.edu PART I: Acquiring

More information

Anisotropy of HARDI Diffusion Profiles Based on the L 2 -Norm

Anisotropy of HARDI Diffusion Profiles Based on the L 2 -Norm Anisotropy of HARDI Diffusion Profiles Based on the L 2 -Norm Philipp Landgraf 1, Dorit Merhof 1, Mirco Richter 1 1 Institute of Computer Science, Visual Computing Group, University of Konstanz philipp.landgraf@uni-konstanz.de

More information

Improved Correspondence for DTI Population Studies via Unbiased Atlas Building

Improved Correspondence for DTI Population Studies via Unbiased Atlas Building Improved Correspondence for DTI Population Studies via Unbiased Atlas Building Casey Goodlett 1, Brad Davis 1,2, Remi Jean 3, John Gilmore 3, and Guido Gerig 1,3 1 Department of Computer Science, University

More information

Diffusion imaging of the brain: technical considerations and practical applications

Diffusion imaging of the brain: technical considerations and practical applications Diffusion imaging of the brain: technical considerations and practical applications David G. Norris FC Donders Centre for Cognitive Neuroimaging Nijmegen Sustaining the physiologist in measuring the atomic

More information

Advanced MRI: Diffusion MRI 1: DTI and k-space

Advanced MRI: Diffusion MRI 1: DTI and k-space k y Advanced MRI: Diffusion MRI 1: DTI and k-space k X Eric Sigmund, PhD February 26th, 2013 LECTURE 1 Neuro Diffusion MRI 3-5 m White matter axons Body 15 m Renal medulla Musculoskeletal 50 m Skeletal

More information

Quantitative Neuro-Anatomic and Functional Image Assessment Recent progress on image registration and its applications

Quantitative Neuro-Anatomic and Functional Image Assessment Recent progress on image registration and its applications Quantitative Neuro-Anatomic and Functional Image Assessment Recent progress on image registration and its applications Guido Gerig Sarang Joshi Tom Fletcher Applications of image registration in neuroimaging

More information

Quantitative Susceptibility Mapping and Susceptibility Tensor Imaging. Magnetization and Susceptibility

Quantitative Susceptibility Mapping and Susceptibility Tensor Imaging. Magnetization and Susceptibility Quantitative Susceptibility Mapping and Susceptibility Tensor Imaging 1, Chunlei Liu, Ph.D. 1 Brain Imaging and Analysis Center Department of Radiology Duke University, Durham, NC, USA 1 Magnetization

More information

A Riemannian Framework for Denoising Diffusion Tensor Images

A Riemannian Framework for Denoising Diffusion Tensor Images A Riemannian Framework for Denoising Diffusion Tensor Images Manasi Datar No Institute Given Abstract. Diffusion Tensor Imaging (DTI) is a relatively new imaging modality that has been extensively used

More information

Two-step Anomalous Diffusion Tensor Imaging

Two-step Anomalous Diffusion Tensor Imaging Two-step Anomalous Diffusion Tensor Imain Thomas R. Barrick 1, Matthew G. Hall 2 1 Centre for Stroke and Dementia, Division of Cardiac and Vascular Sciences, St. Geore s University of London, 2 Department

More information

Diffusion Tensor Imaging tutorial

Diffusion Tensor Imaging tutorial NA-MIC http://na-mic.org Diffusion Tensor Imaging tutorial Sonia Pujol, PhD Surgical Planning Laboratory Harvard University DTI tutorial This tutorial is an introduction to the advanced Diffusion MR capabilities

More information

From Diffusion Data to Bundle Analysis

From Diffusion Data to Bundle Analysis From Diffusion Data to Bundle Analysis Gabriel Girard gabriel.girard@epfl.ch Computational Brain Connectivity Mapping Juan-les-Pins, France 20 November 2017 Gabriel Girard gabriel.girard@epfl.ch CoBCoM2017

More information

The effect of different number of diffusion gradients on SNR of diffusion tensor-derived measurement maps

The effect of different number of diffusion gradients on SNR of diffusion tensor-derived measurement maps J. Biomedical Science and Engineering, 009,, 96-101 The effect of different number of diffusion gradients on SNR of diffusion tensor-derived measurement maps Na Zhang 1, Zhen-Sheng Deng 1*, Fang Wang 1,

More information

Field trip: Tuesday, Feb 5th

Field trip: Tuesday, Feb 5th Pulse Sequences Field trip: Tuesday, Feb 5th Hardware tour of VUIIIS Philips 3T Meet here at regular class time (11.15) Complete MRI screening form! Chuck Nockowski Philips Service Engineer Reminder: Project/Presentation

More information

Diffusion MRI. Outline. Biology: The Neuron. Brain connectivity. Biology: Brain Organization. Brain connections and fibers

Diffusion MRI. Outline. Biology: The Neuron. Brain connectivity. Biology: Brain Organization. Brain connections and fibers Outline Diffusion MRI Alfred Anwander Download of Slides: www.cbs.mpg.de/events/ teaching/brainsignals1112 password: mpi-brain CBSWIKI: Cornet/DiffusionMRI Neuroanatomy Diffusion MRI Diffusion Tensor Imaging

More information

Quantitative Metrics for White Matter Integrity Based on Diffusion Tensor MRI Data. Stephanie Lee

Quantitative Metrics for White Matter Integrity Based on Diffusion Tensor MRI Data. Stephanie Lee Quantitative Metrics for White Matter Integrity Based on Diffusion Tensor MRI Data Stephanie Lee May 5, 2005 Quantitative Metrics for White Matter Integrity Based on Diffusion Tensor MRI Data ABSTRACT

More information

Deformation Morphometry: Basics and Applications

Deformation Morphometry: Basics and Applications Deformation Morphometry: Basics and Applications Valerie Cardenas Nicolson, Ph.D. Assistant Adjunct Professor NCIRE, UCSF, SFVA Center for Imaging of Neurodegenerative Diseases VA Challenge Clinical studies

More information

Lecture 8 Analyzing the diffusion weighted signal. Room CSB 272 this week! Please install AFNI

Lecture 8 Analyzing the diffusion weighted signal. Room CSB 272 this week! Please install AFNI Lecture 8 Analyzing the diffusion weighted signal Room CSB 272 this week! Please install AFNI http://afni.nimh.nih.gov/afni/ Next lecture, DTI For this lecture, think in terms of a single voxel We re still

More information

Tensor Visualization. CSC 7443: Scientific Information Visualization

Tensor Visualization. CSC 7443: Scientific Information Visualization Tensor Visualization Tensor data A tensor is a multivariate quantity Scalar is a tensor of rank zero s = s(x,y,z) Vector is a tensor of rank one v = (v x,v y,v z ) For a symmetric tensor of rank 2, its

More information

Image enhancement. Why image enhancement? Why image enhancement? Why image enhancement? Example of artifacts caused by image encoding

Image enhancement. Why image enhancement? Why image enhancement? Why image enhancement? Example of artifacts caused by image encoding 13 Why image enhancement? Image enhancement Example of artifacts caused by image encoding Computer Vision, Lecture 14 Michael Felsberg Computer Vision Laboratory Department of Electrical Engineering 12

More information

Tract-Specific Analysis for DTI of Brain White Matter

Tract-Specific Analysis for DTI of Brain White Matter Tract-Specific Analysis for DTI of Brain White Matter Paul Yushkevich, Hui Zhang, James Gee Penn Image Computing & Science Lab Department of Radiology University of Pennsylvania IPAM Summer School July

More information

HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis Fall 2006

HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis Fall 2006 MIT OpenCourseWare http://ocw.mit.edu HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis Fall 2006 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms.

More information

Cortical diffusion imaging

Cortical diffusion imaging Cortical diffusion imaging Alard Roebroeck Maastricht Brain Imaging Center (MBIC) Dept. of Cognitive Neuroscience Faculty of Psychology & Neuroscience Maastricht University Diffusion MRI In vivo & Ex vivo

More information

Artefact Correction in DTI

Artefact Correction in DTI Artefact Correction in DTI (ACID) Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, University College London Siawoosh Mohammadi Motivation High-end DTI: tractography Potential problems

More information

Diffusion Tensor Processing and Visualization

Diffusion Tensor Processing and Visualization NA-MIC National Alliance for Medical Image Computing http://na-mic.org Diffusion Tensor Processing and Visualization Guido Gerig University of Utah NAMIC: National Alliance for Medical Image Computing

More information

MRI beyond Fourier Encoding: From array detection to higher-order field dynamics

MRI beyond Fourier Encoding: From array detection to higher-order field dynamics MRI beyond Fourier Encoding: From array detection to higher-order field dynamics K. Pruessmann Institute for Biomedical Engineering ETH Zurich and University of Zurich Parallel MRI Signal sample: m γκ,

More information

Improved Correspondence for DTI Population Studies Via Unbiased Atlas Building

Improved Correspondence for DTI Population Studies Via Unbiased Atlas Building Improved Correspondence for DTI Population Studies Via Unbiased Atlas Building Casey Goodlett 1,BradDavis 1,2,RemiJean 3, John Gilmore 3, and Guido Gerig 1,3 1 Department of Computer Science, University

More information

Part III: Sequences and Contrast

Part III: Sequences and Contrast Part III: Sequences and Contrast Contents T1 and T2/T2* Relaxation Contrast of Imaging Sequences T1 weighting T2/T2* weighting Contrast Agents Saturation Inversion Recovery JUST WATER? (i.e., proton density

More information

IMA Preprint Series # 2298

IMA Preprint Series # 2298 RELATING FIBER CROSSING IN HARDI TO INTELLECTUAL FUNCTION By Iman Aganj, Neda Jahanshad, Christophe Lenglet, Arthur W. Toga, Katie L. McMahon, Greig I. de Zubicaray, Margaret J. Wright, Nicholas G. Martin,

More information

Application of diffusion MRI to cancer, heart and brain connectome imaging

Application of diffusion MRI to cancer, heart and brain connectome imaging Colloquium @ Department of Physics, NTU Application of diffusion MRI to cancer, heart and brain connectome imaging March 11, 2014 Wen-Yih Isaac Tseng MD, PhD Advanced Biomedical MRI Lab Center for Optoelectronic

More information

Spatial normalization of diffusion models and tensor analysis

Spatial normalization of diffusion models and tensor analysis University of Iowa Iowa Research Online Theses and Dissertations Summer 2009 Spatial normalization of diffusion models and tensor analysis Madhura Aditya Ingalhalikar University of Iowa Copyright 2009

More information

Principles of MRI EE225E / BIO265. Name That Artifact. RF Interference During Readout. RF Interference During Readout. Lecture 19

Principles of MRI EE225E / BIO265. Name That Artifact. RF Interference During Readout. RF Interference During Readout. Lecture 19 Name That Artifact Principles of MRI EE225E / BIO265 Lecture 19 Instructor: Miki Lustig UC Berkeley, EECS 1 http://mri-info.net 2 RF Interference During Readout RF Interference During Readout 1D FFT 1D

More information

Introduction to Magnetic Resonance Imaging (MRI) Pietro Gori

Introduction to Magnetic Resonance Imaging (MRI) Pietro Gori Introduction to Magnetic Resonance Imaging (MRI) Pietro Gori Enseignant-chercheur Equipe IMAGES - Télécom ParisTech pietro.gori@telecom-paristech.fr September 20, 2017 P. Gori BIOMED 20/09/2017 1 / 76

More information

Tensor Field Visualization. Ronald Peikert SciVis Tensor Fields 9-1

Tensor Field Visualization. Ronald Peikert SciVis Tensor Fields 9-1 Tensor Field Visualization Ronald Peikert SciVis 2007 - Tensor Fields 9-1 Tensors "Tensors are the language of mechanics" Tensor of order (rank) 0: scalar 1: vector 2: matrix (example: stress tensor) Tensors

More information

PhD THESIS. prepared at INRIA Sophia Antipolis

PhD THESIS. prepared at INRIA Sophia Antipolis PhD THESIS prepared at INRIA Sophia Antipolis and presented at the University of Nice-Sophia Antipolis Graduate School of Information and Communication Sciences A dissertation submitted in partial satisfaction

More information

Master of Science Thesis. Using q-space Diffusion MRI for Structural Studies of a Biological Phantom at a 3T Clinical Scanner

Master of Science Thesis. Using q-space Diffusion MRI for Structural Studies of a Biological Phantom at a 3T Clinical Scanner Master of Science Thesis Using q-space Diffusion MRI for Structural Studies of a Biological Phantom at a 3T Clinical Scanner Anna Rydhög Supervisor: Sara Brockstedt, Jimmy Lätt Medical Radiation Physics

More information

Introduction to the Physics of NMR, MRI, BOLD fmri

Introduction to the Physics of NMR, MRI, BOLD fmri Pittsburgh, June 13-17, 2011 Introduction to the Physics of NMR, MRI, BOLD fmri (with an orientation toward the practical aspects of data acquisition) Pittsburgh, June 13-17, 2001 Functional MRI in Clinical

More information

Diffusion MR Imaging Analysis (Prac6cal Aspects)

Diffusion MR Imaging Analysis (Prac6cal Aspects) Diffusion MR Imaging Analysis (Prac6cal Aspects) Jeffry R. Alger Department of Neurology Department of Radiological Sciences Ahmanson- Lovelace Brain Mapping Center UCLA (jralger@ucla.edu) Acknowledgement

More information

Electromagnetic inverse problems in biomedical engineering Jens Haueisen

Electromagnetic inverse problems in biomedical engineering Jens Haueisen Electromagnetic inverse problems in biomedical engineering Jens Haueisen Institute of Biomedical Engineering and Informatics Technical University of Ilmenau Germany Biomagnetic Center Department of Neurology

More information

Diffusion Tensor Imaging in Humans: Practical Implications for Neuroanatomy

Diffusion Tensor Imaging in Humans: Practical Implications for Neuroanatomy Diffusion Tensor Imaging in Humans: Practical Implications for Neuroanatomy Collaborators Center for Morphometric Analysis: Nikos Makris Andy Worth Verne S. Caviness George Papadimitriou MGH-NMR Center

More information

M R I Physics Course. Jerry Allison Ph.D., Chris Wright B.S., Tom Lavin B.S., Nathan Yanasak Ph.D. Department of Radiology Medical College of Georgia

M R I Physics Course. Jerry Allison Ph.D., Chris Wright B.S., Tom Lavin B.S., Nathan Yanasak Ph.D. Department of Radiology Medical College of Georgia M R I Physics Course Jerry Allison Ph.D., Chris Wright B.S., Tom Lavin B.S., Nathan Yanasak Ph.D. Department of Radiology Medical College of Georgia M R I Physics Course Spin Echo Imaging Hahn Spin Echo

More information

} B 1 } Coil } Gradients } FFT

} B 1 } Coil } Gradients } FFT Introduction to MRI Daniel B. Ennis, Ph.D. Requirements for MRI UCLA DCVI Requirements for MRI Dipoles to Images MR Active uclei e.g. 1 H in H20 Cryogen Liquid He and 2 Magnetic Field (B0) Polarizer ystem

More information

NEURONAL FIBER TRACKING IN DT-MRI

NEURONAL FIBER TRACKING IN DT-MRI NEURONAL FIBER TRACKING IN DT-MRI By TIM E. MCGRAW A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE

More information

Introduction to Biomedical Imaging

Introduction to Biomedical Imaging Alejandro Frangi, PhD Computational Imaging Lab Department of Information & Communication Technology Pompeu Fabra University www.cilab.upf.edu MRI advantages Superior soft-tissue contrast Depends on among

More information

Basic Pulse Sequences II - Spin Echoes. TE=12ms TE=47ms TE=106ms TE=153ms UCLA. Radiology

Basic Pulse Sequences II - Spin Echoes. TE=12ms TE=47ms TE=106ms TE=153ms UCLA. Radiology TE TR 90 180 90 Basic Pulse Sequences II - Spin Echoes TE=12ms TE=47ms TE=106ms TE=153ms TE=235ms Lecture #6 Summary B1(t) RF TR RF t ~M (1) (0 )= ~ M 0 = 2 4 0 0 M 0 3 5 Initial Condition ~M (1) (0 +

More information

Diffusion tensor imaging: brain pathway reconstruction

Diffusion tensor imaging: brain pathway reconstruction Neda Sepasian, Jan ten Thije Boonkkamp, Anna Vilanova Diffusion tensor imaging: brain pathway reconstruction NAW 5/6 nr. 4 december 205 259 Neda Sepasian Department of Biomedical Engineering Eindhoven

More information

Nonlinear Diffusion. 1 Introduction: Motivation for non-standard diffusion

Nonlinear Diffusion. 1 Introduction: Motivation for non-standard diffusion Nonlinear Diffusion These notes summarize the way I present this material, for my benefit. But everything in here is said in more detail, and better, in Weickert s paper. 1 Introduction: Motivation for

More information

PROTEIN NMR SPECTROSCOPY

PROTEIN NMR SPECTROSCOPY List of Figures List of Tables xvii xxvi 1. NMR SPECTROSCOPY 1 1.1 Introduction to NMR Spectroscopy 2 1.2 One Dimensional NMR Spectroscopy 3 1.2.1 Classical Description of NMR Spectroscopy 3 1.2.2 Nuclear

More information

Medical Visualization - Tensor Visualization. J.-Prof. Dr. Kai Lawonn

Medical Visualization - Tensor Visualization. J.-Prof. Dr. Kai Lawonn Medical Visualization - Tensor Visualization J.-Prof. Dr. Kai Lawonn Lecture is partially based on the lecture by Prof. Thomas Schultz 2 What is a Tensor? A tensor is a multilinear transformation that

More information

III, Diffusion, and Susceptibility. August 25, Departments of Mathematics and Applied Math and Computational Science University of Pennsylvania

III, Diffusion, and Susceptibility. August 25, Departments of Mathematics and Applied Math and Computational Science University of Pennsylvania III,, and Departments of Mathematics and Applied Math and Computational Science University of Pennsylvania August 25, 2010 Copyright Page All material in this lecture, except as noted within the text,

More information

Bayesian multi-tensor diffusion MRI and tractography

Bayesian multi-tensor diffusion MRI and tractography Bayesian multi-tensor diffusion MRI and tractography Diwei Zhou 1, Ian L. Dryden 1, Alexey Koloydenko 1, & Li Bai 2 1 School of Mathematical Sciences, Univ. of Nottingham 2 School of Computer Science and

More information

Neuroimage Processing

Neuroimage Processing Neuroimage Processing Instructor: Moo K. Chung mkchung@wisc.edu Lecture 10-11. Deformation-based morphometry (DBM) Tensor-based morphometry (TBM) November 13, 2009 Image Registration Process of transforming

More information

Rician Noise Removal in Diffusion Tensor MRI

Rician Noise Removal in Diffusion Tensor MRI Rician Noise Removal in Diffusion Tensor MRI Saurav Basu, Thomas Fletcher, and Ross Whitaker University of Utah, School of Computing, Salt Lake City, UT 84112, USA Abstract. Rician noise introduces a bias

More information

Higher Order Cartesian Tensor Representation of Orientation Distribution Functions (ODFs)

Higher Order Cartesian Tensor Representation of Orientation Distribution Functions (ODFs) Higher Order Cartesian Tensor Representation of Orientation Distribution Functions (ODFs) Yonas T. Weldeselassie (Ph.D. Candidate) Medical Image Computing and Analysis Lab, CS, SFU DT-MR Imaging Introduction

More information

The Diffusion Tensor Imaging Toolbox

The Diffusion Tensor Imaging Toolbox 7418 The Journal of Neuroscience, May 30, 2012 32(22):7418 7428 Toolbox Editor s Note: Toolboxes are intended to describe and evaluate methods that are becoming widely relevant to the neuroscience community

More information

Basic physical principles of body diffusion-weighted MRI

Basic physical principles of body diffusion-weighted MRI Chapter1 Eric E. Sigmund and Jens Jensen Basic physical principles of body diffusion-weighted MRI 1.1 Introduction The possibility of sensitizing nuclear magnetic resonance (NMR) signals to molecular diffusion

More information

Developing a Method for Distortion Correction in High b-value Diffusion-Weighted Magnetic Resonance Imaging HENRIK HANSSON

Developing a Method for Distortion Correction in High b-value Diffusion-Weighted Magnetic Resonance Imaging HENRIK HANSSON Developing a Method for Distortion Correction in High b-value Diffusion-Weighted Magnetic Resonance Imaging Master s thesis in Complex Adaptive Systems HENRIK HANSSON Department of Applied Physics Division

More information

Diffusion Imaging II. By: Osama Abdullah

Diffusion Imaging II. By: Osama Abdullah iffusion Imaging II By: Osama Abdullah Review Introduction. What is diffusion? iffusion and signal attenuation. iffusion imaging. How to capture diffusion? iffusion sensitizing gradients. Spin Echo. Gradient

More information

Basic Concepts of MR Imaging, Diffusion MR Imaging, and Diffusion Tensor Imaging

Basic Concepts of MR Imaging, Diffusion MR Imaging, and Diffusion Tensor Imaging Basic Concepts of MR Imaging, Diffusion MR Imaging, and Diffusion Tensor Imaging Eduardo H.M.S.G. de Figueiredo, BSc a, *, Arthur F.N.G. Borgonovi, BSc b,c, Thomas M. Doring, MSc d,e KEYWORDS Magnetic

More information

MRI. made. likely simplistic. Sorry, guys! We have less than one hour! Part 2: Sources of contrast. Endogenous (tissue) contrast

MRI. made. likely simplistic. Sorry, guys! We have less than one hour! Part 2: Sources of contrast. Endogenous (tissue) contrast .. made simple likely simplistic Sorry, guys! We have less than one hour! U. Himmelreich K.U.Leuven.. B. Gallez U.C.Louvain.. B. Jordan U.C.Louvain Part 2: Sources of contrast Endogenous (tissue) contrast

More information

Diffusion Magnetic Resonance Imaging Part 1: Theory & Methods

Diffusion Magnetic Resonance Imaging Part 1: Theory & Methods Diffusion Magnetic Resonance Imaging Part 1: Theory & Methods Benjamin M. Ellingson, Ph.D. Assistant Professor of Radiology, Biomedical Physics and Bioengineering Dept. of Radiological Sciences UCLA Neuro-Oncology

More information

Lab 2: Magnetic Resonance Imaging

Lab 2: Magnetic Resonance Imaging EE225E/BIOE265 Spring 2013 Principles of MRI Miki Lustig Developed by: Galen Reed and Miki Lustig Lab 2: Magnetic Resonance Imaging Introduction In this lab, we will get some hands-on experience with an

More information

H. Salehian, G. Cheng, J. Sun, B. C. Vemuri Department of CISE University of Florida

H. Salehian, G. Cheng, J. Sun, B. C. Vemuri Department of CISE University of Florida Tractography in the CST using an Intrinsic Unscented Kalman Filter H. Salehian, G. Cheng, J. Sun, B. C. Vemuri Department of CISE University of Florida Outline Introduction Method Pre-processing Fiber

More information

BNG/ECE 487 FINAL (W16)

BNG/ECE 487 FINAL (W16) BNG/ECE 487 FINAL (W16) NAME: 4 Problems for 100 pts This exam is closed-everything (no notes, books, etc.). Calculators are permitted. Possibly useful formulas and tables are provided on this page. Fourier

More information

Measuring the invisible using Quantitative Magnetic Resonance Imaging

Measuring the invisible using Quantitative Magnetic Resonance Imaging Measuring the invisible using Quantitative Magnetic Resonance Imaging Paul Tofts Emeritus Professor University of Sussex, Brighton, UK Formerly Chair in Imaging Physics, Brighton and Sussex Medical School,

More information

Eindhoven University of Technology MASTER. Assessing hypoxic ischemia in the neonatal brain accuracy of diffusion weighted imaging in MR

Eindhoven University of Technology MASTER. Assessing hypoxic ischemia in the neonatal brain accuracy of diffusion weighted imaging in MR Eindhoven University of Technology MASTER Assessing hypoxic ischemia in the neonatal brain accuracy of diffusion weighted imaging in MR van den Tillaart, J.R.M. Award date: 2004 Disclaimer This document

More information

Multivariate Statistical Analysis of Deformation Momenta Relating Anatomical Shape to Neuropsychological Measures

Multivariate Statistical Analysis of Deformation Momenta Relating Anatomical Shape to Neuropsychological Measures Multivariate Statistical Analysis of Deformation Momenta Relating Anatomical Shape to Neuropsychological Measures Nikhil Singh, Tom Fletcher, Sam Preston, Linh Ha, J. Stephen Marron, Michael Wiener, and

More information

Development of Magnetic Resonance-Based Susceptibility Imaging Applications

Development of Magnetic Resonance-Based Susceptibility Imaging Applications Development of Magnetic Resonance-Based Susceptibility Imaging Applications Sung-Min Gho The Graduate School Yonsei University Development of Magnetic Resonance-Based Susceptibility Imaging Applications

More information

Manifolds, Lie Groups, Lie Algebras, with Applications. Kurt W.A.J.H.Y. Reillag (alias Jean Gallier) CIS610, Spring 2005

Manifolds, Lie Groups, Lie Algebras, with Applications. Kurt W.A.J.H.Y. Reillag (alias Jean Gallier) CIS610, Spring 2005 Manifolds, Lie Groups, Lie Algebras, with Applications Kurt W.A.J.H.Y. Reillag (alias Jean Gallier) CIS610, Spring 2005 1 Motivations and Goals 1. Motivations Observation: Often, the set of all objects

More information

Extended Phase Graphs (EPG)

Extended Phase Graphs (EPG) Extended Phase Graphs (EPG) Purpose / Definition Propagation Gradients, Relaxation, RF Diffusion Examples 1 EPG Motivating Example: RF with Crushers RF G z Crushers are used to suppress spins that do not

More information

Sequence Overview. Gradient Echo Spin Echo Magnetization Preparation Sampling and Trajectories Parallel Imaging. B.Hargreaves - RAD 229

Sequence Overview. Gradient Echo Spin Echo Magnetization Preparation Sampling and Trajectories Parallel Imaging. B.Hargreaves - RAD 229 Sequence Overview Gradient Echo Spin Echo Magnetization Preparation Sampling and Trajectories Parallel Imaging 75 Pulse Sequences and k-space RF k y G z k x G x 3D k-space G y k y k z Acq. k x 76 Gradient

More information

Development of image processing tools and procedures for analyzing multi-site longitudinal diffusion-weighted imaging studies

Development of image processing tools and procedures for analyzing multi-site longitudinal diffusion-weighted imaging studies University of Iowa Iowa Research Online Theses and Dissertations 2014 Development of image processing tools and procedures for analyzing multi-site longitudinal diffusion-weighted imaging studies Joy Tamiko

More information

Reconstruction Algorithms for MRI. Berkin Bilgic 17 December 2012

Reconstruction Algorithms for MRI. Berkin Bilgic 17 December 2012 Reconstruction Algorithms for MRI Berkin Bilgic 17 December 2012 Outline Magnetic Resonance Imaging (MRI) 2 Outline Magnetic Resonance Imaging (MRI) Non-invasive imaging, great versatility structural imaging

More information

NMR/MRI examination (8N080 / 3F240)

NMR/MRI examination (8N080 / 3F240) NMR/MRI examination (8N080 / 3F240) Remarks: 1. This test consists of 3 problems with at total of 26 sub-questions. 2. Questions are in English. You are allowed to answer them in English or Dutch. 3. Please

More information

Tensor fields. Tensor fields: Outline. Chantal Oberson Ausoni

Tensor fields. Tensor fields: Outline. Chantal Oberson Ausoni Tensor fields Chantal Oberson Ausoni 7.8.2014 ICS Summer school Roscoff - Visualization at the interfaces 28.7-8.8, 2014 1 Tensor fields: Outline 1. TENSOR FIELDS: DEFINITION 2. PROPERTIES OF SECOND-ORDER

More information

Extended Phase Graphs (EPG)

Extended Phase Graphs (EPG) Extended Phase Graphs (EPG) Purpose / Definition Propagation Gradients, Relaxation, RF Diffusion Examples 133 EPG Motivating Example: RF with Crushers RF G z Crushers are used to suppress spins that do

More information

CHEM / BCMB 4190/6190/8189. Introductory NMR. Lecture 10

CHEM / BCMB 4190/6190/8189. Introductory NMR. Lecture 10 CHEM / BCMB 490/690/889 Introductory NMR Lecture 0 - - CHEM 490/690 Spin-Echo The spin-echo pulse sequence: 90 - τ - 80 - τ(echo) Spins echoes are widely used as part of larger pulse sequence to refocus

More information

Spin Echo Imaging Sequence

Spin Echo Imaging Sequence 1 MRI In Stereotactic Procedures Edward F. Jackson, Ph.D. The University of Texas M.D. Anderson Cancer Center Houston, Texas 2 RF G slice G phase G freq Signal k-space Spin Echo Imaging Sequence TE 1st

More information

Principles of Nuclear Magnetic Resonance Microscopy

Principles of Nuclear Magnetic Resonance Microscopy Principles of Nuclear Magnetic Resonance Microscopy Paul T. Callaghan Department of Physics and Biophysics Massey University New Zealand CLARENDON PRESS OXFORD CONTENTS 1 PRINCIPLES OF IMAGING 1 1.1 Introduction

More information

Fast and Accurate HARDI and its Application to Neurological Diagnosis

Fast and Accurate HARDI and its Application to Neurological Diagnosis Fast and Accurate HARDI and its Application to Neurological Diagnosis Dr. Oleg Michailovich Department of Electrical and Computer Engineering University of Waterloo June 21, 2011 Outline 1 Diffusion imaging

More information