magnetic resonance spectroscopy (mrs): practical 2: mrs ... · magnetic resonance spectroscopy...
TRANSCRIPT
![Page 1: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/1.jpg)
Magnetic Resonance Spectroscopy (MRS):
Practical 2: MRS analysis
SINAPSE MRS workshop
John McLean, Clinical Scientist
![Page 2: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/2.jpg)
Overview
• JMRUI
• Viewing data
• Familiarisation with GUI
• Removing the water peak
• Pre-processing
• HLSVD
• AMARES
![Page 3: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/3.jpg)
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
![Page 4: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/4.jpg)
Open JMRUI
![Page 5: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/5.jpg)
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
![Page 6: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/6.jpg)
Open data
![Page 7: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/7.jpg)
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
•
![Page 8: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/8.jpg)
Viewing data
![Page 9: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/9.jpg)
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...
![Page 10: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/10.jpg)
Preprocessing
• HLSVD peak remover
• Hankel-Lanczos singular value decomposition
• Preprocessing > Peak remover > HLSVD
• Inspect spectra post H20 removal
• Click Ok
![Page 11: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/11.jpg)
Preprocessing
![Page 12: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/12.jpg)
Preprocessing
![Page 13: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/13.jpg)
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
![Page 14: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/14.jpg)
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
![Page 15: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/15.jpg)
Preprocessing
![Page 16: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/16.jpg)
Quantification
• HLSVD quantitation
• Quantitation > SVD > HLSVD
• Select number of componets
– > no. Of peaks you wish to assess (15)
• Select
•
![Page 17: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/17.jpg)
HLSVD Quantification
![Page 18: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/18.jpg)
HLSVD Quantification
![Page 19: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/19.jpg)
HLSVD Quantification
![Page 20: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/20.jpg)
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
![Page 21: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/21.jpg)
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
![Page 22: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/22.jpg)
AMARES
• Define starting value
• Impose prior knowledge
– Ratios/ relationships
• Give further info
– Phase, truncation, weighting of points
• Execute quantification
![Page 23: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/23.jpg)
AMARES
![Page 24: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/24.jpg)
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
![Page 25: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/25.jpg)
AMARES
![Page 26: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/26.jpg)
AMARES
![Page 27: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/27.jpg)
AMARES• Check other tabs
• Could establish relationships between peaks
• Quantify
• Various options for displaying results
![Page 28: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/28.jpg)
AMARES
![Page 29: Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS ... · Magnetic Resonance Spectroscopy (MRS): Practical 2: MRS analysis SINAPSE MRS workshop John McLean, Clinical Scientist](https://reader030.vdocument.in/reader030/viewer/2022040104/5ed59f1a1b7fdd786a1b59b8/html5/thumbnails/29.jpg)
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