magnetic resonance spectroscopy (mrs): practical 2: mrs ... · magnetic resonance spectroscopy...
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Magnetic Resonance Spectroscopy (MRS):
Practical 2: MRS analysis
SINAPSE MRS workshop
John McLean, Clinical Scientist
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