Magnetic Resonance Spectroscopy (MRS):

Overview of MRS software

SINAPSE MRS workshop

John McLean, Clinical Scientist

johnmclean@nhs.net

Content of presentation

• Overview of MRS software

• LCmodel

• JMRUI

• Proprietary

• Interpret Decision support system

• Spectral Classifier (SC)

• Others : 3Dcsi

LCModel aim / overview

• The Linear Combination Model

• Website: http://s-provencher.com/pages/lcmodel.shtml

• Current version: 6.2

• LCmodel analyses in-vivo spectra as a linear combination of Modelled In-vitro spectra from individual metabolite solutions

• Automatic quantification of in-vivo proton MRS data

• GUI

• Phasing, referencing, quantitation done automatically

• A constrained non-linear least-squares analysis estimates metabolite concentrations and their uncertainties

• Absolute quantification via calibration phantom or water scalingbut check LCmodel manual and your hardware

LCModel Pros & Cons

• Pros

• Quick analysis of SV and MV* MRS data

• Fully automatic, wide range of basis sets available

• Operator independent

• Published info on methods in literature

• Extensive manual

• Good support

• Used widely

• One-page output

• Accepts most manufacturer data

• Cons

• Linux based

• Commercial ~ 6-10k £

• Limited customisation

LCModel Interface

LC model overview

• Residuals

• Metabolite concentration

and ratios

• Confidence levels (< 20%)

• Data vs. model plot

• FWHM (<0.1ppm)

LCModel Comments

• Try before you buy

• Read manual

• Consider purpose

• Contact S Provencher

• Check quantification options in manual for your scanner manufacturer & Hardware

JMRUI aim / overview• Java Magnetic resonance user interface• Web address:

http://www.mrui.uab.es/mrui/mrui_Overview.shtml

• Current version is: v4.0

• MRUI is a Graphical User Interface that allows MR spectroscopists to easily perform time-domain analysis of in vivo MR data: 1D spectra, time-series and 3D-MRSI datasets.

• Various algorithms included

• frequency selective filtering of signals

• correction of eddy-currents artefacts

• Cadzow enhancement of the FID

• Linear Prediction

• non-linear fitting in the time-domain (AMARES, QUEST)

• quantum-mechanics simulation of spectra (NMR-SCOPE)

JMRUI Pros & Cons

• Pros• Free

• Customisable

• Interface is simple and easy to use

• Various options for pre-processing / quantification

• Analysis of SV and MV MRS data

• Published info on methods in literature

• Extensive manual

• Used widely

• Accepts most manufacturer data

• Other useful MRS modules: e.g. simulation

• Cons• Inputting data may require some customisation

• Potential for user variability

JMRUI Interaface

JMRUI Interaface

JMRUI Comments

• It’s free so a good place to start

• Licence/ approval necessary

• Go on the JMRUI course

• Pre-processing with JMRUI can lead to use of SC / Interpret

• Algorithms are published

• Potential to incorporate additional modules to aid quantification

• What about T1 or T2 correction?

INTERPRET aim / overview

• INTERPRET Decision support system

• http://gabrmn.uab.es/dss

• Current version: v.3.0.2

• Aim to facilitate the use of MRS for improved diagnosis and therapy of patients with brain tumours

• Standard acquisition/ processing

• A database of cases

• Implementation of classifiers

INTERPRET Pros & Cons

• Pros• Free

• Built in data

• GUI can present a lot of info at once

• Use of multi-variate spectra classifier

• Reads JMRUI data

• Customisable with use of sister SC program

• Methods published in literature

• Multi-platform

• Incorporate imaging data/ clinical report Info

• Cons• Be aware of deviations in practice

• GUI presentation of cases not immediately intuitive

INTERPRET

Patient Information

Mean Spectra

All data in database

Image

Spectra for comparison

INTERPRET Examples

Spectral Classifier overview

• SC

• http://gabrmn.uab.es/sc

• Current version: v.2.0

• Java based tool for implementing MRS spectra classifiers

• Only minimal knowledge of statistics necessary

• Modular based program

• Interactive GUI

SC Pros & Cons

• Pros• Free

• Customisable

• GUI

• Can integrate with JMRUI/ INTERPRET

• Good manual

• Published methods

• Simple implementation of advanced statistics

• Training data can be used

• Cons• Requires cases / time / consistency

SC Examples

SC Examples

Closing comments

• Various frameworks already exist

• No need to re-invent the wheel

• Understand processes, appreciate limitations

• Customise to your needs

• Decide on quantification method before you

start and test it out on pilot data/ normal volunteer

• Consistency of practice is key!

• As far as possible, check your assumptions