MRI

General

• 🎥 Paul Callaghan explaining NMR

• 🎥 Introduction to MRI Physics

• 🎥 How MRI works / Fourier encoding (check out Parts 1, 2, 3, etc.)

• 🎥 The Insane Engineering of MRI Machines

• 🎥 Introduction to MRI by Dr. Michael Lipton (intuitive for people with a less technical background

• 🎥🇫🇷 Introduction à l’IRM (Julien Cohen-Adad, Polytechnique GBM8378

• 🌐 Peder Larson: Introduction to Principles of MRI

• 📘 Nishimura, Principles of Magnetic Resonance Imaging (1996) (NeuroPoly members only)

• 🌐 Questions and Answers in MRI

• 🌐🇫🇷 MRI Online Course (in French)

• 🌐🇫🇷 Méthodes en neurosciences cognitives

• 📄 Eills et al. Spin Hyperpolarization in Modern Magnetic Resonance. Chem. Rev. 2023

Fundamentals

• Bloch simulator for education in NMR and MRI

• Jülich Extensible MRI Simulator (JEMRIS): Sequence development and simulation environment.

RF Coils

• 📄 Roemer et al. The NMR phased array. Magn Reson Med. 1990

• 📄 Gruber et al. RF coils: A practical guide for nonphysicists. J Magn Reson Imaging. 2018

• Open source hardware at 7T from UMCU

• Open-source Console for Real-time Acquisition (OCRA)

• Open source coil design

• Birdcage builder (PennState)

B0 Shimming

• 🎥 ISMRM MR Academy - Magnetic Field B0 Shimming

• Shimming Toolbox overview

• MRI Questions

• 📄 Stockmann JP, Wald LL. In vivo B0 field shimming methods for MRI at 7T. Neuroimage. 2018 Mar;168:71–87.

• 📄 D’Astous et al. Shimming toolbox: An open-source software toolbox for B0 and B1 shimming in MRI. MRM 2023

• 📄 Breheret et al. Impact of through-slice gradient optimization for dynamic slice-wise shimming in the cervico-thoracic spinal cord. MRM 2025

• 📄 Jayadev et al. Accelerated Navigator for Rapid ∆B0 Field Mapping for Real-Time Shimming and Motion Correction of Human Brain MRI. NMR Biomed 2025

B1 Shimming

• Jupyter book covering the basics of static B1+ shimming

• Gaspard Cereza’s MSc thesis

• 🔒 VOP creation (internal documentation) @Gaspard todo: (notably list talks from UHF meeting)

• 📄 Williams et al. Ultra-high field MRI: parallel-transmit arrays and RF pulse design. Phys Med Biol 2023

Pulse Sequences

• 🕹️ SimMRI – A web-based MR Image Simulator for easy accessible MRI teaching

• Siemens IDEA programming (link is private, reserved to NeuroPoly students working on IDEA sequence. If this is your case, please contact your PI to access these documents)

• Spinbench: Pulse sequence simulator

• Open source pulse sequence programming (Matlab): http://pulseq.github.io/

• MR Pulse Sequences: What Every Radiologist Wants to Know but Is Afraid to Ask

• Understanding MRI: basic MR physics for physicians

• AAPM/RSNA Physics: Tutorial for Residents - Fundamental Physics of MR Imaging

Reconstruction

• Mark Chiew’s home page

MRI Software

• List of MRI-related software from the Open Source Imaging Initiative

• List of software from ISMRM MRHub

• Magpylib: Calculating static magnetic fields of magnets, currents, and other sources

• openEMS: Electromagnetic field solver using the FDTD method

• Reconstruction tools from NYU

• Gadgetron: Open source framework for medical image reconstruction

• ISMRM Raw data format: A proposed standard for MRI raw datasets

• MRI Unbound: Open source software for image recon and pulse seq design

• http://mrilab.sourceforge.net/

MR Spectroscopy

• Osprey

• https://mrshub.org/

  • List of other software: https://mrshub.netlify.app/software_all/

• http://www.jmrui.eu/

• http://innovation.columbia.edu/technologies/cu17130

• oxsatoolbox/oxsa

Functional MRI

• 📄 Chen JE, Glover GH. Functional Magnetic Resonance Imaging methods. Neuropsychol Rev. 2015 Sep;25(3):289–313

Diffusion MRI

• 🎥 Series of talks on diffusion MRI

Arterial Spin Labeling (ASL)

• 📄 Hernandez‐Garcia L, Aramendía‐Vidaurreta V, Bolar DS, Dai W, Fernández‐Seara MA, Guo J, Madhuranthakam AJ, Mutsaerts H, Petr J, Qin Q, Schollenberger J, Suzuki Y, Taso M, Thomas DL, van Osch MJP, Woods J, Zhao MY, Yan L, Wang Z, Zhao L, Okell TW. Recent Technical Developments in ASL: A Review of the State of the Art [Internet]. Vol. 88, Magnetic Resonance in Medicine. 2022. p. 2021–42. Available from: http://dx.doi.org/10.1002/mrm.29381

• 📄 Martín-Noguerol T, Kirsch CFE, Montesinos P, Luna A. Arterial spin labeling for head and neck lesion assessment: technical adjustments and clinical applications. Neuroradiology. 2021 Dec;63(12):1969–83.

• 📄 Hernandez-Garcia L, Lahiri A, Schollenberger J. Recent progress in ASL. Neuroimage. 2019 Feb 15;187:3–16.

• 📄 Havsteen I, Damm Nybing J, Christensen H, Christensen AF. Arterial spin labeling: a technical overview. Acta radiol. 2018 Oct;59(10):1232–8.

• 📄 Alsop DC, Detre JA, Golay X, Günther M, Hendrikse J, Hernandez-Garcia L, Lu H, MacIntosh BJ, Parkes LM, Smits M, van Osch MJP, Wang DJJ, Wong EC, Zaharchuk G. Recommended implementation of arterial spin-labeled perfusion MRI for clinical applications: A consensus of the ISMRM perfusion study group and the European consortium for ASL in dementia. Magn Reson Med. 2015 Jan;73(1):102–16.

Quality Control (QC)

• raamana/visualqc