Magnetic Resonance Spectroscopy (MRS):

Practical 2: MRS analysis

SINAPSE MRS workshop

John McLean, Clinical Scientist

johnmclean@nhs.net

Overview

• JMRUI

• Viewing data

• Familiarisation with GUI

• Removing the water peak

• Pre-processing

• HLSVD

• AMARES

Open JMRUI

• JMRUI

• Open JMRUI

• Double click JMRUI-short on Desktop

• This will open the JMRUI opening screen and wizard

• Various options: 1d/time series, MRSI, batch, NMR scope, Results, set-up

Open JMRUI

Open data

• Select 1D/ time series

• Browse to

• Desktop > MRS_workshop_docs > data > 35Hipp > P50176.7.txt

• Notice water peak is @ 0ppm

• Notice water peal is >> other metabolites

• The Notice NAA to the left of H20 i.e. Not the usual way of displaying data

Open data

Viewing data

• To reverse spectra go to

– Pre-processing > Mathematics >

conjugate/reverse spectrum

• Zoom in on data

– Left-click, hold and drag

– Zoom in on metabolites of interest and H20

•

Viewing data

Viewing data

• View allow different components of the spectra to be displayed

• Options allows the axis to be labelled in different ways

• Option to File > Save as...

Preprocessing

• HLSVD peak remover

• Hankel-Lanczos singular value decomposition

• Preprocessing > Peak remover > HLSVD

• Inspect spectra post H20 removal

• Click Ok

Preprocessing

Preprocessing

Preprocessing

• Apodization

• Can be accessed via: Preprocesing > apodize

• Or through GUI shortcut middle icon that looks like a graph

• Use slides to around 5Hz or set value to 5Hz and confirm

Overview

• Pre-processing

• Apodization

– “Removing the foot”

– Change the shape of maths function

– Smooth discontinuties

• Zero-filing

– Add zero points to a dataset

– i.e. to the end of the FID

– Creates more points, interpolation

Preprocessing

Quantification

• HLSVD quantitation

• Quantitation > SVD > HLSVD

• Select number of componets

– > no. Of peaks you wish to assess (15)

• Select

•

HLSVD Quantification

HLSVD Quantification

HLSVD Quantification

HLSVD Quantification• Save results

• File > Save this > save as text

• Note that peak amplitudes are proportional to metabolite concentrations

• NB: These results should not be cited with mM units, more like Institutional Units

• Note also: JMRUI leaves T1 and T2 corrections to be done by the user

AMARES

• AMARES

• Advanced method for accurate, robust and efficient spectral fitting

• Possibility to employ prior knowledge

• Lorentz/Gauss Model fit

• Contstraints may be imposed

• Interactive

AMARES

• Define starting value

• Impose prior knowledge

– Ratios/ relationships

• Give further info

– Phase, truncation, weighting of points

• Execute quantification

AMARES

AMARES• Load pre-processed specrta

• Quantitation > AMARES

• Fix windowing

• Follow on screen instructions (blue)

• Use R or L drag to zoom in peaks

• Click on peak top (i.e. To define f)

• Click at peak ½-height for linewidth

• Right click to return to ‘previous view’

• Repeat process on other peaks

• Label NAA, Cr, Cho, mI

AMARES

AMARES

AMARES• Check other tabs

• Could establish relationships between peaks

• Quantify

• Various options for displaying results

AMARES

Other features of JMRUI

• Batch processing

• JAVA : add your own stuff

• NMR simulation with pulse sequence

• QUEST quantification

• MRSI ie multi-voxel spectro analysis

• Prior knowledge?

– Normal data

– Pilot data

– Inform larger study / power