Awesome Magnetic Resonance Imaging (MRI)
A curated list of delightful Magnetic Resonance (MR) courses, books, lectures, papers, blogs and free resources.
Table of Contents
Courses
- Interactive online course on NMR and MRI
- Comprehensive material on the fundamentals of MRI. Course designed for radiologists, but fit for beginners in general. Limited, but existent, support for other languages.
- Questions and Answers in MRI
- Though not strictly a course, contains high quality introductory material and lots of references for further study.
Books
- Handbook of MRI Pulse Sequences
- A through overview of imaging fundamentals, and details of pulse design in general. Published in 2004.
- Echo-Planar Imaging
- Theory of EPI. Relevant for all diving into FMRI and Diffusion Imaging. By Schmitt et al., 1998.
- Spin Dynamics. Basics of Nuclear Magnetic Resonance
- Fundamentals of NMR from a QM perspective. Focus on clarity and consistence. Published in 2008.
- MRI: Physical Principles and Sequence Design
- A comprehensive overview of the physics of MRI.
Tutorials
- A K-Space Odissey
- An interactive iOS app to explore k-space. The help section may contain inexact information, though.
- Is Quantum Mechanics Necessary for Understanding MR?
- A manifesto against possibly misleading and outdated NMR teachings.
Historical Papers
MR Physics
- The Nuclear Induction Experiment
- The first publication describing the phenomenon of NMR and relaxation times, by F. Bloch et al.
- Spin Echoes
- The seminal paper describing the discovery of Spin Echoes, by Erwin Hahn.
- CPMG Sequence
- A convenient variation of Hahn’s Spin Echoes is described.
- Extended Phase Graphs
- Algorithm to recognize all echoes ocurring in a multipulse sequence, by J. Hennig.
- The role of magnetic susceptibility in MRI
- Comprehensive discussion on MRI magnetic compatibility and the basic physics of magnetization and magnetic susceptibility.
Fundamentals of MRI
- Echo Planar Imaging
- Not the first publication, but the first describing the promises of EPI.
- MRI
- Famous P. Lauterbur Nature seminal paper introducing MRI, at the time called zeugmatography.
- MRI in vivo
- First demonstration of MRI in vivo, by P. Mansfield, showing finger images.
Image Reconstruction
- The NMR phased array
- The first reference publication on multiple coil acquisition and signal combination, by P. Roemer.
- Generalized Autocalibrating Partially Parallel Acquisitions (GRAPPA)
- The GRAPPA paper, by Mark Griswold.
- SENSE: Sensitivity Encoding for Fast MRI
- “New theoretical and practical concepts are presented for considerably enhancing the performance of magnetic resonance imaging (MRI) by means of arrays of multiple receiver coils.”
- Compressed Sensing
- Describes the theory for acquisition and reconstruction of sparse MRI data using Compressed Sensing. By M. Lustig, 2007.
MR Techniques
- FMRI, BOLD Contrast
- What is considered the first observation of Blood Oxygenation Level-Dependent Contrast, by Ogawa et al.
- Magnetization Transfer
- First demonstration of the MTC effect in vivo.
- Resting State FMRI
- The first report on functional connectivity measured with BOLD, without any FMRI task.
Blogs
- Practical FMRI
- Education, tips and tricks to help conduct better fMRI experiments. Focus on acquisition, not on post-processing.
- Layer FMRI
- Renzo Huber’s blog on high resolution cortical-depth fMRI analysis. Talks about details from the acquisition to the pre-processing and analysis of high res. functional data.
Resources
General
- ISMRM Community
- Website of the International Society for Magnetic Resonance in Medicine. Provides educational resources, video recordings of previous conferences, job boards, links to social media, a blog and a member section.
- Open Source Imaging
- An initiative from the community to provide an open hardware and open software MR system.
- MR Hub
- A platform to share resources and projects within the MR community. Sponsored by the International Society for Magnetic Resonance in Medicine (ISMRM).
MR Simulation
- MRILab: A numerical MRI simulator
- MRiLab is a rapid and versatile numerical MRI simulator with Matlab interface and GPU parallel acceleration on Windows and Linux. High simulation accuracy is achieved by simulating discrete spin evolution at small time interval using the Bloch-equation and appropriate tissue model.
- BlochBuster
- A nuclear magnetic resonance Bloch equation simulator written in Python. It simulates magnetization vectors based on the Bloch equations, including precession, relaxation, and excitation. Takes yaml-config files as inputs and saves simulation results as videos.
Pulse Sequence Development
- ODIN: Object-oriented Development Interface for NMR
- Full featured, GPL licensed software framework to develop and simulate magnetic resonance sequences.
- Pulseq: Open Source Framework for Pulse Sequences
- Pulseq is an open source framework for the development, representation and execution of magnetic resonance (MR) sequences. A central contribution of the project is an open file format to compactly describe MR sequences suitable for execution on an MRI scanner or NMR spectrometer. MATLAB and C++ source code is provided for reading and writing sequence files.
Data Reconstruction
- Gadgetron
- Open Source Framework for Image Reconstruction. With Gadgetron raw data can be reconstructed offline and sent back to the MR scanner. For the end-user it looks like the data were reconstructed online.
- BART: Berkeley Advanced Reconstruction Toolbox
- “The library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms.”. In very active development as of 2017.
Data Analysis
License
To the extent possible under law, Daniel Gomez has waived all copyright and related or neighboring rights to this work.