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10 tips for spectroscopy

Application Tip
de Kok, Wendy Philips Healthcare Philips Global
Alberts, Eveline Philips Healthcare Philips Global

Introduction

Spectroscopy is a technique that collects chemical shift information of the tissue of interest. Performing a spectroscopy scan requires different skills than MR-imaging.
This document provides general tips and hints for proton spectroscopy examinations and processing in all applications.

 

All information in this document is valid for 1.5T, unless specifically mentioned.

 

Tip 1: Selecting a spectroscopy scan

Spectroscopy acquisitions are usually part of a comprehensive examination, performed in ExamCards. The spectroscopy protocol database is only accessible from within the Scan List.

 

Workflow:

  • Acquire all required imaging scans in ExamCards.
  • Make sure scans in orthogonal directions are available, to be used for planning spectroscopy.
  • Select System in the main menu bar.
  • Select Switch Acquisition context.
  • Select Scan List.
  • Switch to Spectro in the Scan List.
  • Select the required anatomy and subanatomy.
  • Select the required preset procedure for planning.

 

Note: Switch to Spectro in Scan control before Start Scan is selected to ensure that the spectroscopy scanlist is executed instead of the imaging Scan List.

Main menu Spectro switch in Scan List.
Main menu "System"
Spectro switch in Scan List.
Switch to Scan list is accessed via main menu "system".

Tip 2: Planning a spectroscopy scan

Planning of a spectroscopy scan is critical. Accurate planning of the volume must be performed and the volume position should be controlled in at least two orthogonal directions. Avoid inclusion of air-tissue interfaces for optimized shimming and linewidths.

 

Workflow:

  • Load anatomical images in three orthogonal directions in the planscan viewports.
  • Adapt the size of the volume such that it includes only tissue of interest to avoid partial volume effects.
  • Scroll through all slices that intersect the spectroscopy volume to check the planning.
  • Display the most important image intersecting the volume before the planning is confirmed: these images will be displayed in SpectroView or in Review PlanScan in post-processing.

 

For spectroscopic imaging:

It is important that the spectroscopic imaging slice has equal geometry settings to one of the imaging slices to allow a correct grid display or ROI contour in post-processing. This can easily be achieved by copying the planscan settings from imaging:

 

Workflow:

  • Select Imaging in the Scan List.
  • Select Repeat to display the list of all imaging scans from the examination.
  • Select the preset procedure of which the geometry settings are to be repeated: this scan is listed in the Imaging scan list.
  • Planscan the selected preset and Proceed to confirm its planning.
  • Select Spectro in the Scan List.
  • Select the required preset procedure for spectroscopic imaging for planning: the geometry settings are copied from the imaging preset procedure.
  • Scroll to the required imaging slice in one of the Planscan viewports.
  • Position the VOI without changing its angulation: the SI-slice will follow.
  • Adapt the in-plane VOI-size (and possibly its in-plane angulation)
  • If multiple REST slabs are used for outer volume suppression, make sure that these slabs suppress all unwanted signals.
  • Use cone-angle to adapt REST slab positions orthogonal to the scan plane.

 

Instead of repeating the planning from an anatomical scan, three points planscan can be used for planning. Workflow:

  • Load required anatomical slice in large viewport.
  • Select preset procedure from spectro database.
  • Hide stack and slab display, to make sure VOI is active.
  • Select three points planscan: 3PPS and enable P1.
  • Left-mouse click in the image to define point 1.
  • Repeat this step to define point 2 and 3.
  • Compute plane. The geometry is defined by a plane through the 3 points: in-plane with slice.
  • Show stack and slabs again, and adapt REST slabs as described above.
Planning single voxel in hippocampus The small volume doesn't include air-tissue interfaces.Planning TSI Multiple REST slabs are used for outer volume suppression.
Planning single voxel in hippocampus
Planning TSI
The small volume doesn't include air-tissue interfaces.
Multiple REST slabs are used for outer volume suppression.

Tip 3: More planning tips

As mentioned in tip 2, planning is critical and has great effect on the outcome of the spectra.

This section provides a collection of points that have an effect on the spectral quality.

 

  • Angulation of the anatomy:

Can have an effect on the appearance of susceptibility artifacts. Hotspots caused by susceptibility are projected in the spectroscopic image in the direction of the main magnetic field.

A well-known example is the hotspot that is seen in regions above the sinus in 2DSI of the brain:

Tilting the patient's head slightly more backwards can move the position of the hotspot more to the edge of the chemical shift images.

 

  • Angulation of the coil:

Related to the previous remark, coil angulation can have the same effect. Use of the Quadrature Head coil for spectroscopy leads to good results, but do not use that coil on the base plate of the Synergy Head-neck coil.

 

  • Angulation of the volume:

Is used to make the volume cover the anatomy of interest, but should be kept to a minimum. Avoid high angulations for sharpest volume definition and optimized signal.

Planning example CSI The head is slightly tilted backward. A possible hotspot of the sinus will be projected in the direction of the main magnetic field on the edge of the SI-FOV.Planning example CSI The head is slightly tilted forward. A possible hotspot of the sinus will be projected closer to the area of interest.Choline metabolite map A susceptibility hotspot is visible in the region of the left orbit. It doesn't reduce the quality of the metabolite map.
Planning example CSI
Planning example CSI
Choline metabolite map
The head is slightly tilted backward. A possible hotspot of the sinus will be projected in the direction of the main magnetic field on the edge of the SI-FOV.
The head is slightly tilted forward. A possible hotspot of the sinus will be projected closer to the area of interest.
A susceptibility hotspot is visible in the region of the left orbit. It doesn't reduce the quality of the metabolite map.

Tip 4: Volume selection

The volume of interest needs to be defined in spectroscopy. The method of choice for proton spectroscopy is the echo volume selection method (also known as PRESS). This is a double-spin echo sequence with slice selective gradients applied around the three RF-pulses. The intersection area of the three slice selective gradients defines a block-shaped volume that generates an echo signal.

 

The volume displayed in planscan represents the volume of signals at +/- 2 ppm (~NAA-volume). As the precession frequency for the other metabolites is different, the slice selective gradients select a shifted volume for those other metabolites. This chemical shift occurs in all directions in which the slice selective gradients are applied. The size of the shift depends on field strength and on the coil used.

 

For spectroscopic imaging it is possible to use change volume selection that results in real slice selection, where slice selective gradients are applied in only one direction. Chemical shift will not occur in-plane. This is the preferred method for 2DSI if the selected FOV is larger than the covered anatomy as foldover must not occur.

To suppress signals at the edge of the anatomy, circular REST slabs can be applied.

Full volume selection Choline and creatine volume are displaced with regards to NAA.Spectral display The left arrow in the spectral display indicates that Cho/Cre signals are not present as they were not selected. The right arrow reveals presence of Cho/Cre: signals were selected.Full volume selection vs slice selection Chemical shift displacement is detected in the upper row, where full volume selection is used. It is not seen in the lower row, where slice selection is used.
Full volume selection
Spectral display
Full volume selection vs slice selection
Choline and creatine volume are displaced with regards to NAA.
The left arrow in the spectral display indicates that Cho/Cre signals are not present as they were not selected. The right arrow reveals presence of Cho/Cre: signals were selected.
Chemical shift displacement is detected in the upper row, where full volume selection is used. It is not seen in the lower row, where slice selection is used.

Tip 5: Echo acquisition

The echo signal in a spectroscopy examination is sampled to detect the various precession frequencies that compose the signal. Two methods for echo acquisition can be selected:

 

Half echo:

Signal sampling starts at time=TE. A possible phase difference of this signal can be corrected automatically if a phase corrected measurement is performed. Display of real spectra is possible.

This is the preferred method for single voxel spectroscopy and for regular 2DSI where acquisition time can be long.

Note that only phase corrected single voxel spectra can be processed in SpectroView, see tip 10

Maximum echo:

Signal sampling starts as soon as possible to sample as much as possible of the echo signal. The possible phase difference at echotop position is not known and the spectrum can not be phase corrected. Only modulus display is possible.

This method is used for Turbo Spectroscopic imaging where the acquisition time is always smaller than the echo spacing.

More info on acquisition time is found in tip 6: spectral resolution

2DSI half echo Real spectra are displayed, phase correction is applied.TSI maximum echo Modulus spectra are displayed, phase correction is not possible. Spectral separation is slightly lower as can be seen from the Cho/Cre separation in the upper right corner.SVS and 2DSI Upper window: single voxel spectra, TE 144 ms, half echo: real signal aspect. Lactate signal at 1.3ppm is negative.
Lower window: 2DSI image guided spectra, TE 144 ms, maximum echo: modulus signal aspect. Lactate at 1.3ppm is positive.
2DSI half echo
TSI maximum echo
SVS and 2DSI
Real spectra are displayed, phase correction is applied.
Modulus spectra are displayed, phase correction is not possible. Spectral separation is slightly lower as can be seen from the Cho/Cre separation in the upper right corner.
Upper window: single voxel spectra, TE 144 ms, half echo: real signal aspect. Lactate signal at 1.3ppm is negative. Lower window: 2DSI image guided spectra, TE 144 ms, maximum echo: modulus signal aspect. Lactate at 1.3ppm is positive.

Tip 6: Spectral resolution

The spectral resolution is the minimal frequency difference that can be detected in a spectrum and should be small enough to differentiate the signals of the metabolites. It is determined by the spectral bandwidth and by the number of samples:

 

        BW/nr.samples = spectral resolution (Hz)

 

The bandwidth should be large enough to include the entire range of frequencies of interest. A good default for proton spectroscopy is +/- 1000 Hz.

To separate choline and creatine, the required spectral resolution is +/- 4 Hz. The minimal number of samples to achieve that is 256. It is more common to use 512 samples.

Like in imaging, the following is true: Higher resolution results in lower signal-to-noise ratio!

 

The time required for sampling the echo signal is inversely related to the spectral resolution, the acquisition time is determined by:

 

       nr.samples/BW = acquisition time (sec)

 

The repetition time in spectroscopy is generally long, so a long acquisition time will easily fit in. Even increasing the number of samples to 1024 (acq. time +/- 1 sec) doesn't lead to problems in single voxel and CSI.

 

This is different for Turbo Spectroscopic imaging (TSI): The acquisition time must fit in the echo spacing, that is usually 288ms in brain spectroscopy. The maximum sample time in this case is limited to +/- 256 ms, and the maximum achievable spectral resolution is limited to +/- 4 Hz.

 

Position of image guided spectra 256 samples, spectral res ~ 4 Hz Choline and creatine resonances are separated.128 samples, spectral res ~ 8 Hz Choline and creatine resonances cannot be separated.
Position of image guided spectra
256 samples, spectral res ~ 4 Hz
128 samples, spectral res ~ 8 Hz
Choline and creatine resonances are separated.
Choline and creatine resonances cannot be separated.

Tip 7: Shimming

Two shimming methods are available:

 

Autoshim optimizes the T2-decay of the water signal. It requires a few minutes, but gives very good results, especially in other body parts than brain.

 

HOS-shimming acquires several pencil beam excitations through the volume to collect phase information. Both first order (1.5T + 3.0T) and second order (3.0T only) can be calculated. Preparation time is +/- 30 seconds. The method method works particularly well in the brain.

 

The minimum HOS-shim volume size is 25 x 25 x 25 mm and has equal off-centers and angulations as the spectroscopy volume.

 

In general, use:

  • HOS first in SVS in the brain: short preparation time, good result
  • autoshim in SVS, close to air-tissue boundaries in the brain: risk of including susceptibility in shim volume, HOS could give less desirable results
  • HOS first (1.5T) or second (3.0T) in CSI in the brain
  • autoshim in body parts other than the brain
TSI autoshim vs second order shim Image guided spectra are displayed from a TSI sequence. Upper window: autoshim, only 1 spectrum is of good quality. Lower window: second order shim, all spectra show good quality.SVS shim comparison in brain A small volume is planned in the cingulum. Autoshim, first order shim and second order shim are compared. In this homogeneous region of the brain, second order shim gives best results, even though the shim volume is very small.SVS in prostate Upper window: autoshim. Lower window: first order shim. The resulting linewidth is more narrow when autoshim is used.
TSI autoshim vs second order shim
SVS shim comparison in brain
SVS in prostate
Image guided spectra are displayed from a TSI sequence. Upper window: autoshim, only 1 spectrum is of good quality. Lower window: second order shim, all spectra show good quality.
A small volume is planned in the cingulum. Autoshim, first order shim and second order shim are compared. In this homogeneous region of the brain, second order shim gives best results, even though the shim volume is very small.
Upper window: autoshim. Lower window: first order shim. The resulting linewidth is more narrow when autoshim is used.

Tip 8: Water (and/or fat) suppression optimization

Water suppression is most often performed with spectral selective excitation. Two selective excitation pulses and crusher gradients destroy the water signal before the acquisition starts.

 

Optimization is performed in the preparation phases:

  • Several water spectra are acquired with increasing excitation angle (nr. of steps).
  • The start excitation angle is a value of a sweeping adiabatic pulse, the end result is +/- 90 degrees.
  • The step size determines the increase of the WS exc angle in the next spectrum.
  • To cover a large range of flip angles, use a low start angle (+/- 200) and a large step (50).
  • The linewidth and the base on the right of the residual water peak are important criteria: narrow line with flat base will not interfere with the spectrum.
  • Switch to modulus display to judge amplitude of the spectrum.
  • Also judge time domain signals to detect the lowest amplitude.

 

Spectral selective inversion is also performed. The water magnetization is inverted and acquisition starts when water signal is nulled. For brain spectroscopy, a dual-inversion technique is used to optimize signal nulling for both water in CSF and in gray/white matter. Minimal TR increases when using dual inversion, and is therefore not often used for CSI.

 

Optimization is performed in the preparation phases:

  • Several water spectra are acquired with decreasing inversion delay time (nr. of steps).
  • The start inversion delay time is the value of the second inversion pulse. The first value is fixed in the preset.
  • The step size determines the decrease of the inversion delay time in the next spectrum.
  • To cover a large range of delay times, use a high start value (+/- 500) and a large step (35 - 40).
  • The linewidth and the base on the right of the residual water peak are important criteria: narrow line with flat base will not interfere with the spectrum.
  • Switch to modulus display to judge amplitude of the spectrum.
  • Also judge time domain signals to detect the lowest amplitude.

 

Fat suppression is performed by spectral selective inversion.

The workflow is equal to what is described for water suppression with inversion.

The optimal inversion delay time for fat suppression can also be estimated from the T1-relaxation time of fat, which is quite short. The expected value can be set in the preset procedure, and optimization can be skipped.

Water suppression monitoring Upper display: time domain signals. lower display: corresponding residual water signals.Zoomed portion of monitoring Spectrum 5 is selected. The linewidth is most narrow, residual water signal will not interfere with the metabolite signals in the resulting spectrum.Fat suppression monitoring Markers indicate the residual fat signal. Upper window: time domain signals. Lower window: modulus spectra of the residual water signals.
Water suppression monitoring
Zoomed portion of monitoring
Fat suppression monitoring
Upper display: time domain signals. lower display: corresponding residual water signals.
Spectrum 5 is selected. The linewidth is most narrow, residual water signal will not interfere with the metabolite signals in the resulting spectrum.
Markers indicate the residual fat signal. Upper window: time domain signals. Lower window: modulus spectra of the residual water signals.

Tip 9: Repetition time and echo time

Repetition time must be long to:

  • allow sufficient signal sampling time to obtain the required spectral resolution.
  • allow good T1-relaxation of the metabolite signals for good signal to noise ratio.

Ideally, the TR must be at least 5 x T1-relaxation constant for full T1-relaxation, but this will lead to unacceptable long scan time. A TR of 1500-2000 ms is usually used as a good compromise between SNR and scan time. Use of shorter TR's should be compensated with higher number of NSA.

 

Echo time is either short, to detect metabolite signals with short T2-values, or long to detect only those metabolites with long T2-values. These spectra will have sharper lines and are easier to interpret, but will not reveal all metabolite information.

 

Secondly, it is important that the echo time is optimized for J-coupled systems. Some metabolite signals split into more peaks, and these peaks will be in-phase with each other at very specific echo times only.

An example is lactate, that splits up into a doublet peak with a frequency difference of +/- 7 Hz. The two peaks of lactate are best detected at TE = 144 or 288 ms. The lactate signal will not be detected if the two peaks are in opposed phase (at TE = 216 ms).

 

Effect of TE on lactate Lactate signal is negative in a spectrum at TE = 144 ms, and positive at TE = 288 ms. The diagram shows the evolution of the lactate signal at t=0, t=72, t=144, t=216 and t=288 ms.Effect of TR on SNR in prostate spectroscopy Upper spectrum: TR = 1500 ms, relative SNR citrate 30,8. Lower spectrum: TR = 1200 ms, relative SNR citrate 24,1. SNR increases almost linearly with increasing TR since TR is relatively short in relation to the T1-relaxation constant.
Effect of TE on lactate
Effect of TR on SNR in prostate spectroscopy
Lactate signal is negative in a spectrum at TE = 144 ms, and positive at TE = 288 ms. The diagram shows the evolution of the lactate signal at t=0, t=72, t=144, t=216 and t=288 ms.
Upper spectrum: TR = 1500 ms, relative SNR citrate 30,8. Lower spectrum: TR = 1200 ms, relative SNR citrate 24,1. SNR increases almost linearly with increasing TR since TR is relatively short in relation to the T1-relaxation constant.

Tip 10: SpectroView post-processing

SpectroView is used to present spectroscopy data. It will generate fitted spectra and tables of results for SVS, and metabolite and ratio maps for CSI.

 

More information on SpectroView can be found on NetForum: Education and Training/Product training.

 

Workflow single voxel:

  • double-click the dataset in the pictoral index: spectrum and planscan images are loaded.
  • Select the proper script, if not already selected.
  • Edit script if required.
  • Run script to create the fitted spectrum and table of results.
  • Create DICOM screen capture to save the results to the database.

 

Workflow CSI:

  • double-click the dataset in the pictorial index: spectral grid and corresponding anatomical slices are loaded.
  • Select the proper script, if not already selected.
  • Edit script if required.
  • Enable voxel selection mode and select all required voxels for processing.
  • Run script to create specified color maps.
  • Select voxels to display corresponding spectra.
  • Create DICOM screen capture to save the results to the database.
SVS in SpectroView Planscan images, fitted spectrum and table of results are displayed.Main menu Screen capture pop-up Upon Proceed, a DICOM screen capture is stored in the database.
SVS in SpectroView
Main menu "Tools"
Screen capture pop-up
Planscan images, fitted spectrum and table of results are displayed.
Screen capture functionality is accessed via Tools in Main Menu.
Upon Proceed, a DICOM screen capture is stored in the database.
Toolbar button voxel selection mode Activate the button to allow voxel selection in the spectral grid by left-mouse clicking.2DSI in SpectroView 2DSI is processed in SpectroView. Two spectra are selected from the grid for display after processing all spectra.
Toolbar button voxel selection mode
2DSI in SpectroView
Activate the button to allow voxel selection in the spectral grid by left-mouse clicking.
2DSI is processed in SpectroView. Two spectra are selected from the grid for display after processing all spectra.


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Application Tip
Achieva 1.5T, Achieva 3.0T, Intera 1.0T, Intera 1.5T, Intera 3.0T
Neuro, Spectroscopy
 

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