Introduction to MRI (structural and
diffusion)
I’ve
put together a few notes on some of the major topics for working with
structural images… Although impressive progress has been made on a variety of
scales (from just low level segmentation to working with surfaces and
connectivity), I would suggest that none of the issues is an absolutely
closed/solved field. Interesting, useful and challenging problems abound. Let
me know if this list is helpful… and please suggest other introductory
references for students approaching these fields: landman@jhu.edu
The Basics
K-Space
in the Clinic. J Magn Reson Imaging. 2004 Feb;19(2):145-59.
E-Radiography.net's MRI
Overview
Diffusion Tensor
Imaging
Diffusion
tensor imaging: concepts and applications.J Magn Reson Imaging. 2001
Apr;13(4):534-46.
Fiber Tracking Intro
with DTI
DTI and Noise
Properties
Jan Sijbers’ Notes
on MR Noise (mostly about Rician noise)
Skull-stripping/brain
extraction
A
meta-algorithm for brain extraction in MRI. Neuroimage. 2004 Oct;23(2):625-37.
Segmentation
FANTASM: http://medic.rad.jhmi.edu/projects/fantasm/
Surface Manipulation
CRUISE (JHU): http://iacl.ece.jhu.edu/projects/cruise/
Freesurfer
(MIT/Harvard/MGH): http://surfer.nmr.mgh.harvard.edu/
UCLA/LONI: New
approaches in brain morphometry. Am J Geriatr Psychiatry. 2002
Jan-Feb;10(1):13-23.
Registration/Voxel
Based Morphometry
Magnetization
Transfer Imaging (MT)
Magnetization
transfer in MRI: a review. NMR Biomed. 2001 Apr;14(2):57-64.
Skeletal Muscle DTI
Validation
of diffusion tensor MRI-based muscle fiber tracking. Magn Reson Med. 38(1):
97-104
Cardiac
Strain Measurement
Interesting Papers on
Diffusion (from CAMINO
website 2007.08.29)
|
Linear DT Fitting |
Basser PJ, Mattielo J, and Lebihan D, Estimation of the
effective self-diffusion tensor from the NMR spin echo, Journal of Magnetic
Resonance, 103, 247-54, 1994. |
|
Non-Linear and constrained DT Fitting |
Jones DK and Basser PJ, Squashing
peanuts and smashing pumpkins: How noise distorts diffusion-weighted MR data,
Magnetic Resonance in Medicine, 52(5), 979-993, 2004. |
|
RESTORE |
Chang L-C, Jones DK and Pierpaoli C, RESTORE:
Robust estimation of tensors by outlier rejection, Magnetic Resonance in
Medicine, 53(5), 1088-1095, 2005. |
|
Spherical Harmonic Fibre-Crossing Detection |
Alexander DC, Barker GJ and Arridge SR, Detection
and modelling of non-Gaussian apparent diffusion coefficient profiles in
human brain data, Magnetic Resonance in Medicine, 48, 331-340, 2002. |
|
Q-Ball |
Tuch DS, Q-Ball
Imaging, Magnetic Resonance in Medicine, 52(6), 1358-1372, 2004. |
|
PAS-MRI |
Jansons KM and Alexander DC, Persistent
angular structure: new insights from diffusion magnetic resonance imaging
data, Inverse Problems, 19, 1031-1046, 2003. |
|
Maximum Entropy Spherical Deconvolution (MESD) |
Alexander DC, Maximum entropy
spherical deconvolution for diffusion MRI, Proc. Information Processing
in Medical Imaging (IPMI), 2005. |
|
DT PICo |
Parker GJM, Haroon HA and Wheeler-Kingshott CAM, A
Framework for a Streamline-Based Probabilistic Index of Connectivity (PICo)
using a Structural Interpretation of MRI Diffusion Measurements, Journal
of Magnetic Resonance Imaging, 18, 242-254, 2003. |
|
Multi-tensor PICo |
Parker GJM and Alexander DC, Probabilistic
Monte Carlo Based Mapping of Cerebral Connections Utilising Whole-Brain
Crossing Fibre Information, Proc. IPMI 2003. |
|
PAS-PICo |
Parker GJM and Alexander DC, Probabilistic
anatomic connectivity derived from the microscopic persistent angular
structure of cerebral tissue, Philosophical Transactions of the Royal
Society B, 360, 893-902, 2005. |
|
Q-Ball PICo |
Seunarine KK, Cook PA, Hall MG, Embleton K, Parker GJM and
Alexander DC, Exploiting peak anisotropy for tracking through fanning
structures, Proc. ISMRM 2007. |
|
DT-MRI image warping |
Alexander DC, Pierpaoli C, Basser PJ and Gee JC, Spatial
Transformations of Diffusion Tensor Magnetic Resonance Images, IEEE
Trans. Medical Imaging, 20(11), 1131-1139, 2001. |
|
Electrostatic pointsets |
Jones DK, Horsfield MA and Simmons A, Optimal
strategies for measuring diffusion in anisotropic systems by MRI,
Magnetic Resonance in Medicine, 42(3), 515-525, 1999. |
|
Ordered pointsets |
Cook PA, Symms M, Boulby PA and Alexander DC, Optimal
acquisition orders of diffusion-weighted MRI measurements, Journal of
Magnetic Resonance Imaging, 25(5), 1051-1058, 2007. |
|
Model-based data synthesis |
Alexander DC and Barker GJ, Optimal
imaging parameters for fibre-orientation estimation in diffusion MRI,
NeuroImage, 27, 357-367, 2005 |
|
Monte-Carlo data synthesis |
Hall MG and Alexander DC, Finite
pulse width improve fibre orientation estimates in diffusion tensor MRI,
Proc. ISMRM 2006 |
Contributors: Issel
Lim
Last Updated: Tuesday May 27, 2008
© Copyright 2006, Bennett Landman. All rights reserved.