EduNMRSoft

Dear Spinlanders,

Because blogsome will close down its’ site very soon we will move the blog EduNMRSoft from blogsome to wordpress. New address:

EduNMRSoft.wordpress.com

Stay tuned!

 73, Peter 

Some historic notes on the developments of magnetic resonance.

Free.

http://www.youtube.com/watch?v=NiCuIIuvNSc

http://www.youtube.com/watch?v=369yd2rGqH4

http://www.youtube.com/watch?v=fICkha04o6A

http://www.youtube.com/watch?v=eeYpInEhoiM 

http://www.youtube.com/watch?v=S4yzmYW8PjQ 

http://www.youtube.com/watch?v=40qRrV8xxxk

http://www.youtube.com/watch?v=RXEoETrS4RY

http://www.youtube.com/watch?v=tM3QgSobMLs

http://www.youtube.com/watch?v=9sPuIEy7tRM&feature=related 

http://www.youtube.com/watch?v=yBsRNxh0mTM

http://www.youtube.com/watch?v=UrLyWZpV71U

http://youtu.be/m4bxZimYVyA

http://youtu.be/TLBrUMl4pxY

http://youtu.be/4AIrMW0WrXY 

http://www.youtube.com/watch?v=tq-ghKkLRDI 

http://youtu.be/PcDIYYMD9Gg 

http://www.youtube.com/watch?v=_zSgrN_jRaA 

This is a collection of lecture notes, handouts and animations for teaching MR-principles. By D. Topgaard.

Free 

http://www.kemi.lu.se/utbildning/avancerad/kemm17/handouts 

This is a series of videos in which Paul Callaghan explains the basic principles behind NMR and MRI.

Free 

1. Precession and resonance: http://www.youtube.com/watch?v=7aRKAXD4dAg

2. Introduction to NMR: http://www.youtube.com/watch?v=jUKdVBpCLHM

3. How the Terra-Nova MRI works: http://www.youtube.com/watch?v=GjLvu1hOAAA

4. Acquiring an FID: http://www.youtube.com/watch?v=MPXbDDRumwM&feature=related

5. Field Homogeneity: http://www.youtube.com/watch?v=o8PzreUSbVE&feature=related

6. Spin echo, CPMG, and T2-relaxation: http://www.youtube.com/watch?v=B2HMAJQJ7ok

7. Measuring T1 and T2-relaxation: http://www.youtube.com/watch?v=753GoKV1F4Y

8. MRI in 1D: http://www.youtube.com/watch?v=RlsM__mz3bk

9. Introduction to k-space: http://www.youtube.com/watch?v=XJvVnlMv1LQ

10. k-space in multiple dimensions: http://www.youtube.com/watch?v=SrG_w5v3R8A

11. 2D MRI: http://www.youtube.com/watch?v=MdyvLYdxXqo

There is a range of NMR and MRI demonstrations, as well as related phenomena, available as YouTube movies. Here is a collection of useful films.

Free

MRI 

http://www.youtube.com/watch?v=0YBUSOrH0lw&feature=related

http://www.youtube.com/watch?v=Z3ofp4i6RD4&feature=related

http://www.youtube.com/watch?v=wrjYlVJSvC4&feature=related 

http://www.youtube.com/watch?v=6_2D3Lh1v74&feature=related

http://www.youtube.com/watch?v=IGk3NAziVWs&feature=related

http://www.youtube.com/watch?v=AwXJNXNcLNs&feature=related

http://www.youtube.com/watch?v=H5q79R9C-mk 

http://www.youtube.com/watch?v=M2wvFTpmSKc&feature=related 

MRI-safety 

http://www.youtube.com/watch?v=1R7KsfosV-o&feature=related 

http://www.youtube.com/watch?v=tKj39eWFs10 

http://www.youtube.com/watch?v=6BBx8BwLhqg&feature=related 

http://www.youtube.com/watch?v=p9T6m21AZ80&feature=related 

NMR

http://www.youtube.com/watch?v=vT8eN3A5zPY&feature=related

http://youtu.be/b2n1-nvo7d4 

http://www.youtube.com/watch?v=KtWnmFg-u5g&feature=related 

http://www.youtube.com/watch?v=uNM801B9Y84 

http://www.youtube.com/watch?v=BirHLLz3aXc 

PHYSICS

http://www.youtube.com/watch?v=7aRKAXD4dAg 

http://www.youtube.com/watch?v=XJvVnlMv1LQ 

http://www.youtube.com/watch?v=EUfU95fCSkw&feature=related 

http://www.youtube.com/watch?v=liDjr439-fY&feature=related 

http://www.youtube.com/watch?v=4nTewAjhGsY&feature=related  

http://www.youtube.com/watch?v=w-ST7CshK20

http://www.youtube.com/watch?v=Be3qiux6Dow

http://www.youtube.com/watch?v=ekmhJo7fjqA

http://www.youtube.com/watch?v=m-Al7GAnH8Q

Explaining the principle for Magnetic Resonance using a compass needle as a model system, by Lars G. Hansen.

Free, for any web browser with Java. 

http://www.drcmr.dk/JavaCompass

There is also a companion YouTube demonstration available at:

http://www.youtube.com/watch?v=1OrPCNVSA4o 

Demonstration software of different MRI-related phenomena such as contrast, SNR etc by P-G Bjorklund.

CONTRAST: Vary TR, TE and TI and observe the effect on image contrast for SE and IR-pulse sequences.

SLICESELECT: Visual description of how slice selection depends on gradient strengths, frequency and bandwidth.

SNR: Description of how SNR depends on matrix parameters and bandwidth.

SPINWARP: Visual presentation of what happens during a simple MRI-sequence.

SPINDEMO Visualization of excitation, relaxation etc using the vector model.

MRI: A textbook by P-G Bjorklund on MRI (in swedish) 

For web browsers such as Safari, IE, Firefox etc. Requires Java 1.6.

Free.

www.bjopg.se.

Electronic textbook by Joseph Hornak on the basics of MRI

Any web reader.

Free 

http://www.cis.rit.edu/htbooks/mri/

A versatile application suite called VeSPA which contains three MR-spectroscopy applications: (S) spectral simulation, (P) RFPulse (pulse design), and (A) spectral data processing and analysis. It also allows control of GAMMA via a GUI.

Free, open source, MacOS, Linux, Windows. 

http://scion.duhs.duke.edu/vespa/ 

Article on GAVA http://www.sciencedirect.com/science/article/pii/S1090780707000080 

This is an MRI sequence development and simulation environment for the MRI community. Including simulations of 3D MRI experiments on modern MRI systems hardware, covering aspects such as parallel transmit and receive, off-resonance effects, non-linear gradients, and arbitrary spatiotemporal parameter variations at different levels. MRI sequences with arbitrary waveforms and complex inter-dependent modules are modelled in a GUI-based environment.

Binaries are available for several operating systems.

Free.

http://www.jemris.org/index.shtml 

Software for calculation of chemical exchange.

C.

Free.  

http://www.chemistry.mcmaster.ca/bain/exchange.html 

More software is available at

http://www.chemistry.mcmaster.ca/bain/ 

The NMR course presents explanations on how the various pulse sequences work using the vector model and animations.  

Any web-browser.

Free. 

http://www.chem.queensu.ca/FACILITIES/NMR/nmr/webcourse/index1.htm

Lectures by James Keeler on NMR spectroscopy.

PDF.

Free. 

http://www-keeler.ch.cam.ac.uk/lectures/index.html

Simulations of composite pulse trains.

Any webbrowser.

Free.

http://www.mhl.soton.ac.uk/public/Main/research/topics/CompositePulses/index.html 

NMR simulations and spectral data processing.

Windows.

Free.

http://www.chemistry.vt.edu/chem-dept/hbell/simulation/hb2/TESTPAGE.htm 

A computer program for simulation of modern NMR experiments (COSY, HSQC, HNCO, etc). 

Any platform running Matlab.

Free. 

http://gandalf.umd.edu/

An on-line database and depository that is dedicated to the omics of small biomolecules. It is intended to facilitate access to NMR parameters of small metabolites in liquid phase (aqueous solution). NMR-parameters such as chemical shift. multiplicity, isotope are accompanied by acquisition parameters such as the field strength. temperature and pH.

Any webbrowser.

Free. 

http://www.liu.se/hu/mdl/

PULSAR is a simulation program for solid-state nuclear magnetic resonance spectroscopy (pyPULSAR is a user-friendly version of this program with a graphical interface and Python scripting capabilities).

Windows.

Free. 

http://www-lcs.ensicaen.fr/pyPulsar/index.php/Home

GSim is a visualisation and processing tool for solid-state NMR data. 

Windows.

Free. 

http://www.dur.ac.uk/vadim.zorin/soft.htm

For analyzing and visualizing first-order NMR coupling patterns.

All platforms.

Free. 

http://jvisualizer.sourceforge.net/

 The Bloch simulator illustrates fundamental aspects of MRI such as precession, resonance, excitation, inhomogeneity and relaxation. Important concepts such as rotating frames, weightings, spoilers, spin-echoes, stimulated echoes and driven equilibrium can also be demonstrated using the program. Finally, the fundamentals of MR imaging can be shown, i.e. how the similarity between induced phase roll patterns and the structure of the imaged object is reflected in the MR signal. By Lars G. Hanson.

For all platforms.

Free. 

http://www.drcmr.dk/main/content/view/33/74/

There are companion YouTube-demonstrations available. 

Processing, analysis, and simulation of NMR spectra.

OS X.

Commercial. 

http://www.inmr.net/

Graphical NMR spin system simulation program, or SSS for short, for PC (Windows). Shows a tool for executing pulses (any phase), and delays, the complex density matrix in graphical form, the macroscopic vectors, and the populations. Homo- or heteronuclear experiments or a single spin simulation.

Windows 98.

Free. 

http://www.spectroscopynow.com/FCKeditor/UserFiles/File/specNOW/HTML%20files/Spin_System_Simulator_1005a.htm

For processing and displaying chemical shift imaging data (CSI). 3DiCSI combines data visualization, spectral processing, spectral localization and estimation, spectral quantification together with multi-variate analytical procedures, such as Principal Component Analysis (PCA) and constrained non-negative matrix factorization (cNMF). 

Windows.

Free. 

http://hatch.cpmc.columbia.edu/software.html

This is a toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB. 

For any platform supporting Matlab.

Free. 

http://matnmr.sourceforge.net/

SpinBench is a software environment designed for the rapid prototyping and analysis of magnetic resonance imaging experiments. MRI pulse sequences can be easily defined and simulated in a variety of ways, all through the graphical user interface. SpinBench is also useful as a teaching tool for courses covering MRI spin physics.

OS X.

Free. 

http://www-mrsrl.stanford.edu/SpinBench/index.html

POMA = Product Operator Formalism in Mathematica. It is a very handy tool for product operator formalism calculation for NMR pulse program development.

Any platform supporting Mathematica.

Free. 

http://www.nmr.chem.uu.nl/~hsu/NMR/POMA/poma.html 

GAMMA is a computer package designed to facilitate construction of programs that simulate magnetic resonance phenomena. It is a platform upon which one can easily build programs.

Any platform.

Free. 

http://scion.duhs.duke.edu/vespa/gamma 

This page will introduce to you the auditory presentation of free induction decay (FID) signals obtained by NMR spectrometers (NMR=Nuclear Magnetic Resonance).

Any webreader.

Free. 

http://www.chemie.uni-erlangen.de/oc/research/NMR/music.html

Greg Crowther’s science songs.

MP3, any webreader

http://faculty.washington.edu/crowther/Misc/Songs/music.shtml