Artefact Correction in DTI
|
|
- Joshua Newton
- 5 years ago
- Views:
Transcription
1 Artefact Correction in DTI (ACID) Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, University College London Siawoosh Mohammadi
2 Motivation High-end DTI: tractography Potential problems in DTI z y x Lazar, NMR Biomed., 21 Mohammadi et al., MRM, accepted
3 Overview Diffusion Tensor Imaging (DTI) in brief Example application in DTI Three artefacts in DTI Eddy Current (EC) distortions Local Perturbation Fields (LPFs) Signal-dropout due to mechanical vibration Take home message
4 Diffusion Tensor Imaging (DTI) in brief n DW images Diffusion tensor DT represented by ellipsoid m b= images
5 Overview Diffusion Tensor Imaging (DTI) in brief Example application in DTI Three artefacts in DTI Eddy Current (EC) distortions Local Perturbation Fields (LPFs) Signal-dropout due to mechanical vibration Take home message
6 Patients (TLE) and Control Keller et al., Journal of Neuroimaging, accepted
7 7T high resolution DTI Heidemann et al., MRM, 21
8 Grey matter DTI Amygdala parcellation Variability in grey matter diffusion Bach et al., J Neurosci., 211 Nagy et al., ISMRM, 211 Cortical radial and tangential diffusivity MacNab et al., ISMRM, 211
9 High angular resolution diffusion imaging (HARDI) ODF - Orientation Distribution Function Aganj et al., MRM, 21
10 Overview Diffusion Tensor Imaging (DTI) in brief Example application in DTI Three artefacts in DTI Eddy Current (EC) distortions Local Perturbation Fields (LPFs) Signal-dropout due to mechanical vibration Take home message
11 EC distortion artefact Stejskal & Tanner, JCP, 1965 Reese et al., MRM, 23
12 EC and imaging gradients EC G z y z y Skare S., thesis, 22 EC G y EC G x x y x y
13 Whole-brain eddy current distortions original image z y y z y x x y distorted image translation in-plane shearing scaling through-plane shearing eddy current field components EC B EC G x EC G y EC G z Mohammadi et al., MRM, 21
14 Eddy currents: bright edges / blurring Without eddy current and motion correction With eddy current and motion correction
15 Less blurring leads to higher sensitivity in FA group comparison Relevance Better tensor estimates towards the cortex improves GM DTI specificity Keller et al., JON, accepted Nagy et al., ISMRM, 211 Better image quality in high resolution DTI and HARDI, where ST pulse is necessary Heidemann et al., MRM, 21 Aganj et al., MRM, 21
16 Overview Diffusion Tensor Imaging (DTI) in brief Example application in DTI Three artefacts in DTI Eddy Current (EC) distortions Local Perturbation Fields (LPFs) Signal-dropout due to mechanical vibration Take home message
17 Problem: effective gradient, e.g., due to ECs diffusion weighting period readout period expected gradients effective gradients FA original Error in B matrix FA inhomogeneity EC distortion
18 SM2 How to measure the LPFs? Mohammadi et al., Neuroimage, under review
19 Folie 18 SM2 cite zoltan Siawoosh Mohammadi;
20 Measuring LPFs on different MR systems (a) DTI1 (b) DTI2 (c) DTI3 ε11 ε22 ε11 ε ε ε22 ε 33 ε 12 ε 33 ε 12 ε 33 ε ε 13 ε ε 13 ε ε 13 ε = B δb Mohammadi et al., Neuroimage, under review B * with δ B = 2 Σ B and Σ = ε ε ε ε ε ε ε ε ε
21 LPF correction: repositioning experiment.1 z DTI3,2 = 53±3 z DTI3,1 = 41±3 number of voxel tr( δb) Measured MD MD meas DTI3,1 MD meas DTI3, MD [1-3 mm s 2 ] cor2 MD DTI3,1 number of voxel 5 cor2 MD DTI3,2 Corrected MD MD cor2 DTI3,1 MD cor2 DTI3, MD [1-3 mm s 2 ] Mohammadi et al., Neuroimage, under review
22 Relevance Improved sensitivity of group comparison of MD due to repositioning effect Keller et al., JON, accepted Better grey matter DTI due to reduced FA contrast inhomogeneity MacNab et al., ISMRM, 211
23 Overview Diffusion Tensor Imaging (DTI) in brief Example application in DTI Three artefacts in DTI Eddy Current (EC) distortions Local Perturbation Fields (LPFs) Signal-dropout due to mechanical vibration Take home message
24 Vibration artefacts in blip up and blip down DTI data sets Gallichan et al., HBM, 21
25 Problem: signal-dropout due to axial rotation Unshifted echo (blip-up PE) [arbitrary units] 1 k-space coverage echo k min k= k max k y /PE Shifted echo (blip-up PE) k y eff m1 Ω ( r) z [arbitrary units] 1 k } y Mohammadi et al., MRM, accepted k min k= k max k y /PE
26 Recover signal using phase encoding reversal Blip up Blip down Mohammadi et al., MRM, accepted
27 d Mohammadi et al., MRM, accepted Correction of vibration artefacts in DTI using phase-encoding reversal (COVIPER)
28 Relevance Robust data, e.g., avoiding false positives in FA group studies Keller et al., JON, accepted Better data quality in grey matter Less signal-dropout artefacts in HARDI MacNab et al., ISMRM, 211 Aganj et al., MRM, 21
29 Take home message Retrospective artefact correction is possible Sensitivity and robustness of DTI can be improved Three artefacts related to the diffusion weighting gradients were presented We are not finished yet
30 Acknowledgements MR physics group in WTCN, London Nikolaus Weiskopf (my supervisor and head of MR physics at the WTCN) Zoltan Nagy Oliver Josephs Chloe Hutton (special thanks for the acronym ) Antoine Lutti External collaborators Michael Deppe (University of Münster) Harald Möller (Max Plank Institute Leipzig) Dirk Müller (University of Münster) Mark Symms (Department of Clinical and Experimental Epilepsy, UCL, London) David Carmichael (Imaging and Biophysics, UCL, London) This work was supported by the Wellcome Trust.
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 informationDiffusion 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 informationDiffusion 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 informationAdvanced 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 informationBasics of Diffusion Tensor Imaging and DtiStudio
Basics of Diffusion Tensor Imaging and DtiStudio DTI Basics 1 DTI reveals White matter anatomy Gray matter White matter DTI uses water diffusion as a probe for white matter anatomy Isotropic diffusion
More informationDIFFUSION 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 informationA 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 informationHigher 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 informationDiffusion Tensor Imaging (DTI) e Neurite Orientation Dispersion and Density Imaging (NODDI)
Diffusion Tensor Imaging (DTI) e Neurite Orientation Dispersion and Density Imaging (NODDI) Claudia AM Gandini Wheeler-Kingshott, PhD Prof. of MRI Physics Overview Diffusion and microstructure NODDI theoretical
More informationCambridge 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 informationIMA 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 informationQuantitative 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 informationContrast 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 informationActive Imaging with Dual Spin-Echo Diffusion MRI
Active Imaging with Dual Spin-Echo Diffusion MRI Jonathan D. Clayden 1, Zoltan Nagy 2, Matt G. Hall 3,4, Chris A. Clark 1, and Daniel C. Alexander 3,4 1 Institute of Child Health 2 Wellcome Trust Centre
More informationApplications 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 informationDiffusion 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 informationTwo-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 informationMRI 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 informationCortical 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 informationDiffusion 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 informationFast 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 informationDiffusion 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 informationSpatial encoding in Magnetic Resonance Imaging. Jean-Marie BONNY
Spatial encoding in Magnetic Resonance Imaging Jean-Marie BONNY What s Qu est an image ce qu une? image? «a reproduction of a material object by a camera or a related technique» Multi-dimensional signal
More informationConnectomics analysis and parcellation of the brain based on diffusion-weighted fiber tractography
Connectomics analysis and parcellation of the brain based on diffusion-weighted fiber tractography Alfred Anwander Max Planck Institute for Human Cognitive and Brain Sciences Leipzig, Germany What is the
More informationAdvanced 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 informationA Novel Tensor Distribution Model for the Diffusion Weighted MR Signal
A Novel Tensor Distribution Model for the Diffusion Weighted MR Signal Baba C. UFRF Professor & Director Center for Vision, Graphics, and Medical Imaging Department of Computer & Information Science and
More informationDiffusion 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 informationSpatial encoding in Magnetic Resonance Imaging. Jean-Marie BONNY
Spatial encoding in Magnetic Resonance Imaging Jean-Marie BONNY What s Qu est an image ce qu une? image? «a reproduction of a material object by a camera or a related technique» Multi-dimensional signal
More informationRobust estimator framework in diffusion tensor imaging
The Open-Access Journal for the Basic Principles of Diffusion Theory, Experiment and Application Robust estimator framework in diffusion tensor imaging Ivan I. Maximov 1,*, Farida Grinberg 1, and N. Jon
More informationNuclear Magnetic Resonance Imaging
Nuclear Magnetic Resonance Imaging Simon Lacoste-Julien Electromagnetic Theory Project 198-562B Department of Physics McGill University April 21 2003 Abstract This paper gives an elementary introduction
More informationTissue Parametric Mapping:
Tissue Parametric Mapping: Contrast Mechanisms Using SSFP Sequences Jongho Lee Department of Radiology University of Pennsylvania Tissue Parametric Mapping: Contrast Mechanisms Using bssfp Sequences Jongho
More informationDiffusion 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 informationHow Many Gradients are Sufficient in High-Angular Resolution Diffusion Imaging (HARDI)?
How Many Gradients are Sufficient in High-Angular Resolution Diffusion Imaging (HARDI)? Liang Zhan 1, Ming-Chang Chiang 1, Alex D. Leow 1, Siwei Zhu 2, Marina Barysheva 1, Arthur W. Toga 1, Katie L. McMahon
More informationFREQUENCY 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 informationCIND 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 informationDiffusion 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 informationApplication 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 informationThe 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 informationWhat Visualization Researchers Should Know About HARDI Models
What Visualization Researchers Should Know About HARDI Models Thomas Schultz October 26, 2010 The Diffusion MRI (dmri) Signal ADC Modeling Diffusion Propagator Fiber Models Diffusion
More informationIMPROVED IMAGING OF BRAIN WHITE MATTER USING DIFFUSION WEIGHTED MAGNETIC RESONANCE IMAGING HA-KYU JEONG. Dissertation. Submitted to the Faculty of the
IMPROVED IMAGING OF BRAIN WHITE MATTER USING DIFFUSION WEIGHTED MAGNETIC RESONANCE IMAGING By HA-KYU JEONG Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial
More informationMeasuring cerebral blood flow and other haemodynamic parameters using Arterial Spin Labelling MRI. David Thomas
Measuring cerebral blood flow and other haemodynamic parameters using Arterial Spin Labelling MRI David Thomas Principal Research Associate in MR Physics Leonard Wolfson Experimental Neurology Centre UCL
More informationMRI Physics II: Gradients, Imaging. Douglas C. Noll, Ph.D. Dept. of Biomedical Engineering University of Michigan, Ann Arbor
MRI Physics II: Gradients, Imaging Douglas C., Ph.D. Dept. of Biomedical Engineering University of Michigan, Ann Arbor Magnetic Fields in MRI B 0 The main magnetic field. Always on (0.5-7 T) Magnetizes
More informationDiffusion-Weighted MRI may be used to measure the apparent diffusion coefficient of water in tissue.
Specialty Area: MR Physics for Physicists Speaker: Jennifer A. McNab, Ph.D. Assistant Professor, Radiology, Stanford University () Highlights The Bloch-Torrey equation is a generalization of the Bloch
More informationDynamic Causal Modelling for fmri
Dynamic Causal Modelling for fmri André Marreiros Friday 22 nd Oct. 2 SPM fmri course Wellcome Trust Centre for Neuroimaging London Overview Brain connectivity: types & definitions Anatomical connectivity
More informationSymmetric Positive-Definite Cartesian Tensor Orientation Distribution Functions (CT-ODF)
Symmetric Positive-Definite Cartesian Tensor Orientation Distribution Functions (CT-ODF) Yonas T. Weldeselassie 1, Angelos Barmpoutis 2, and M. Stella Atkins 1 1 School of Computing Science, Simon Fraser
More informationMorphometrics with SPM12
Morphometrics with SPM12 John Ashburner Wellcome Trust Centre for Neuroimaging, 12 Queen Square, London, UK. What kind of differences are we looking for? Usually, we try to localise regions of difference.
More informationPulse Sequences: RARE and Simulations
Pulse Sequences: RARE and Simulations M229 Advanced Topics in MRI Holden H. Wu, Ph.D. 2018.04.19 Department of Radiological Sciences David Geffen School of Medicine at UCLA Class Business Final project
More informationSpectral Graph Wavelets on the Cortical Connectome and Regularization of the EEG Inverse Problem
Spectral Graph Wavelets on the Cortical Connectome and Regularization of the EEG Inverse Problem David K Hammond University of Oregon / NeuroInformatics Center International Conference on Industrial and
More informationDiffusion 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 informationTract-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 informationExtracting Quantitative Measures from EAP: A Small Clinical Study using BFOR
Extracting Quantitative Measures from EAP: A Small Clinical Study using BFOR A. Pasha Hosseinbor, Moo K. Chung, Yu-Chien Wu, John O. Fleming, Aaron S. Field, and Andrew L. Alexander University of Wisconsin-Madison,
More informationNew 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 informationRegularization of Diffusion Tensor Field Using Coupled Robust Anisotropic Diffusion Filters
Regularization of Diffusion Tensor Field Using Coupled Robust Anisotropic Diffusion Filters Songyuan Tang a, Yong Fan a, Hongtu Zhu b, Pew-Thian Yap a Wei Gao a, Weili Lin a, and Dinggang Shen a a Department
More informationDiffusion 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 informationA 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 informationDiffusion 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 informationDeformation 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 informationLecture 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 informationGroup analysis. Jean Daunizeau Wellcome Trust Centre for Neuroimaging University College London. SPM Course Edinburgh, April 2010
Group analysis Jean Daunizeau Wellcome Trust Centre for Neuroimaging University College London SPM Course Edinburgh, April 2010 Image time-series Spatial filter Design matrix Statistical Parametric Map
More informationOn Signal to Noise Ratio Tradeoffs in fmri
On Signal to Noise Ratio Tradeoffs in fmri G. H. Glover April 11, 1999 This monograph addresses the question of signal to noise ratio (SNR) in fmri scanning, when parameters are changed under conditions
More informationIII, 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 informationUniversity of Minnesota. Kâmil Uğurbil
University of Minnesota Kâmil Uğurbil MGH CMRR, U Minn Title Kwong et al 1992 PNAS Ogawa et al PNAS 1992: Figure 2 images superimposed Submillimeter scale neuronal ensembles WHOLE BRAIN Orientation Domains
More informationOrdinary 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 informationComputing FMRI Activations: Coefficients and t-statistics by Detrending and Multiple Regression
Computing FMRI Activations: Coefficients and t-statistics by Detrending and Multiple Regression Daniel B. Rowe and Steven W. Morgan Division of Biostatistics Medical College of Wisconsin Technical Report
More informationH. 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 informationIntroduction 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 informationGeneralizing Diffusion Tensor Model Using Probabilistic Inference in Markov Random Fields
Generalizing Diffusion Tensor Model Using Probabilistic Inference in Markov Random Fields Çağatay Demiralp and David H. Laidlaw Brown University Providence, RI, USA Abstract. We give a proof of concept
More informationImproving White Matter Tractography by Resolving the Challenges of Edema
Improving White Matter Tractography by Resolving the Challenges of Edema Jérémy Lecoeur, Emmanuel Caruyer, Luke Macyszyn, Ragini Verma To cite this version: Jérémy Lecoeur, Emmanuel Caruyer, Luke Macyszyn,
More informationVelocity Images. Phase Contrast Technique. G. Reiter 1,2, U. Reiter 1, R. Rienmüller 1
Velocity Images - the MR Phase Contrast Technique G. Reiter 1,2, U. Reiter 1, R. Rienmüller 1 SSIP 2004 12 th Summer School in Image Processing, Graz, Austria 1 Interdisciplinary Cardiac Imaging Center,
More informationPhysics 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 informationMaster 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 informationSequence 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 informationMeasurement Tensors in Diffusion MRI: Generalizing the Concept of Diffusion Encoding
Measurement Tensors in Diffusion MRI: Generalizing the Concept of Diffusion Encoding Carl-Fredrik Westin 1,2, Filip Szczepankiewicz 3, Ofer Pasternak 1, Evren Özarslan1, Daniel Topgaard 4, Hans Knutsson
More informationComputational Brain Anatomy
Computational Brain Anatomy John Ashburner Wellcome Trust Centre for Neuroimaging, 12 Queen Square, London, UK. Overview Voxel-Based Morphometry Morphometry in general Volumetrics VBM preprocessing followed
More informationUnderstanding brain micro-structure using diffusion magnetic resonance imaging (dmri)
Understanding brain micro-structure using diffusion magnetic resonance imaging (dmri) Jing-Rebecca Li Equipe DEFI, CMAP, Ecole Polytechnique Institut national de recherche en informatique et en automatique
More informationHST.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 informationStatistical Analysis of Tensor Fields
Statistical Analysis of Tensor Fields Yuchen Xie Baba C. Vemuri Jeffrey Ho Department of Computer and Information Sciences and Engineering University of Florida Abstract. In this paper, we propose a Riemannian
More informationMRI in Review: Simple Steps to Cutting Edge Part I
MRI in Review: Simple Steps to Cutting Edge Part I DWI is now 2 years old... Mike Moseley Radiology Stanford DWI, b = 1413 T2wt, 28/16 ASN 21 San Francisco + Disclosures: Funding NINDS, NCRR, NCI 45 minutes
More informationDeveloping 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 informationThe 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 informationIMA Preprint Series # 2256
MULTIPLE q-shell ODF RECONSTRUCTION IN q-ball IMAGING By Iman Aganj Christophe Lenglet Guillermo Sapiro Essa Yacoub Kamil Ugurbil and Noam Harel IMA Preprint Series # 2256 ( May 2009 ) INSTITUTE FOR MATHEMATICS
More informationIntroduction to MRI Acquisition
Introduction to MRI Acquisition James Meakin FMRIB Physics Group FSL Course, Bristol, September 2012 1 What are we trying to achieve? 2 What are we trying to achieve? Informed decision making: Protocols
More informationCorrection 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 informationOrientation Distribution Function for Diffusion MRI
Orientation Distribution Function for Diffusion MRI Evgeniya Balmashnova 28 October 2009 Diffusion Tensor Imaging Diffusion MRI Diffusion MRI P(r, t) = 1 (4πDt) 3/2 e 1 4t r 2 D 1 t Diffusion time D Diffusion
More informationDecomposition of Higher-Order Homogeneous Tensors and Applications to HARDI
Decomposition of Higher-Order Homogeneous Tensors and Applications to HARDI E. Balmashnova, A. Fuster and L.M.J. Florack Eindhoven University of Technology, The Netherlands E.Balmachnova@tue.nl Abstract.
More informationA Physical Model for MR-DTI Based Connectivity Map Computation
A Physical Model for MR-DTI Based Connectivity Map Computation Erdem Yörük 1, Burak Acar 1, and Roland Bammer 1 Department of Electrical-Electronic Engineering, Bogazici University, TURKEY, erdem.yoruk@boun.edu.tr,
More informationChapter 26 Sequence Design, Artifacts and Nomenclature. Yongquan Ye, Ph.D. Assist. Prof. Radiology, SOM Wayne State University
Chapter 26 Sequence Design, Artifacts and Nomenclature Yongquan Ye, Ph.D. Assist. Prof. Radiology, SOM Wayne State University Previous classes: RF pulse, Gradient, Signal Readout Gradient echo, spin echo,
More informationFrom 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 informationMagnetic Resonance Imaging. Pål Erik Goa Associate Professor in Medical Imaging Dept. of Physics
Magnetic Resonance Imaging Pål Erik Goa Associate Professor in Medical Imaging Dept. of Physics pal.e.goa@ntnu.no 1 Why MRI? X-ray/CT: Great for bone structures and high spatial resolution Not so great
More informationApodization. Gibbs Artifact. Bioengineering 280A Principles of Biomedical Imaging. Fall Quarter 2013 MRI Lecture 5. rect(k x )
Bioengineering 280A Principles of Biomedical Imaging Fall Quarter 2013 MRI Lecture 5 GE Medical Systems 2003 Gibbs Artifact Apodization rect(k ) Hanning Window h(k )=1/2(1+cos(2πk ) 256256 image 256128
More informationA generalized CSA-ODF model for Fiber Orientation Mapping
A generalized CSA-ODF model for Fiber Orientation Mapping A THESIS SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY Amith J. Kamath IN PARTIAL FULFILLMENT OF THE REQUIREMENTS
More informationDependence of brain DTI maps of fractional anisotropy and mean diffusivity on the number of diffusion weighting directions
JOURNAL OF APPLIED CLINICAL MEDICAL PHYSICS, VOLUME 11, NUMBER 1, WINTER 2010 Dependence of brain DTI maps of fractional anisotropy and mean diffusivity on the number of diffusion weighting directions
More informationDiffusion 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 informationNMR and MRI : an introduction
Intensive Programme 2011 Design, Synthesis and Validation of Imaging Probes NMR and MRI : an introduction Walter Dastrù Università di Torino walter.dastru@unito.it \ Introduction Magnetic Resonance Imaging
More informationIntroduction 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 informationNeuroImage. The effect of finite diffusion gradient pulse duration on fibre orientation estimation in diffusion MRI
NeuroImage 51 (2010) 743 751 Contents lists available at ScienceDirect NeuroImage journal homepage: www.elsevier.com/locate/ynimg The effect of finite diffusion gradient pulse duration on fibre orientation
More informationDiffusion MRI: Mitigation of Magnetic Field Inhomogeneities
10.2478/v10048-012-0031-8 MEASUREMENT SCIENCE REVIEW, Volume 12, No. 5, 2012 iffusion MRI: Mitigation of Magnetic Field Inhomogeneities P. Marcon 1, K. Bartusek 2, Z. okoupil 2, E. Gescheidtova 1 1 epartment
More informationOverview of Spatial Statistics with Applications to fmri
with Applications to fmri School of Mathematics & Statistics Newcastle University April 8 th, 2016 Outline Why spatial statistics? Basic results Nonstationary models Inference for large data sets An example
More informationQuantitative 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