Recording Excellent Phantom Spectra on the Philips platform

The purpose of this post is to describe our standard process for scanning phantoms, and describe phantom-specific parameters that we use. Acquiring excellent-quality phantom spectra on clinical scanners is a real challenge, which requires a certain amount of witchcraft.

Excellent phantom spectra have narrow lines (~1-2 Hz), so the individual lines of multiplets are resolved, and flat undisturbed baselines to enable accurate phasing and integration.

The first step of acquiring excellent phantom spectra is preparing an excellent phantom (old instructions for a good GABA phantom).

  • Relatively high concentration (~10 mM) is a great start, since phantom experiments often involve parameter series of >10 individual experiments.

  • Sodium azide helps keep the bugs down (and build-up of gunk impacts shimming).

  • Store your phantom in a dark fridge to minimize breakdown, but also know your metabolites (GABA lasts ‘forever’, GSH less well, I think).

  • Use a bottle with friendly geometry that doesn’t result in violent field distortions (we used to use old peanut jars or milk cartons, and they were a lottery on this count). The 1 liter Nalgene bottle style 2125 is fine without being perfect. Spherical containers are better and more contentrated.

  • Avoid air bubbles. It’s better to fill the phantom up (and sacrifice exact concentration) that sacrifice shimmability.

The second step is placement. Try to locate your phantom centrally within the head coil and the main B0 field. A perfect spherical phantom at isocenter in a perfect magnet shouldn’t need shimming, so the closers you can get your ‘cylindrical’ phantom aligned with the central axis of the magnet, the better. If your phantom has an air bubble (most do), it is usually worth tilting the phantom to keep it up one end (ideally in the ‘cap’ region) rather than along the full light of the bottle. Placement judgment and luck in equal measure; sometimes I spend 20 minutes trying to optimize shim and WS on a phantom and just give up. After physically moving it within the bore, I start again.

Even with good shimming, phantoms are less homogeneous than we’d like. Voxel sizes of 2x2x2 cm^3 often yield (noiser) spectra with narrower lines than 3x3x3 cm^3 voxels.

On the Philips system, we use the pb-auto projection-based shimming routine, and it performs well (and quickly) both for phantoms and in vivo. However, you don’t have the option to tweak individual shim currents to optimize the line width manually, so excellent phantom shimming involves an iterative process of slightly moving and/or rotating the voxel, re-running the prep and checking the line width. The reported line width (in the log box) is an imprecise indication, but mostly we rely upon viewing the spectra to check linewidth.

The final piece of the puzzle is water suppression (WS). We tend to use the ‘exc’ option with WS optimization ON for phantom experiments. The automated optimization does a good job of keeping baseline disturbances from residual water signal to a minimum. The quality of WS achievable is dependent on shim quality, and we tend to optimize shim and WS at the same time. Again, sometimes you just can’t get things nice enough, even after moving the voxel around, so you have to reposition the phantom in the scanner. I tend to schedule 30 minutes to get great shim and WS, and then the time to acquire experiments, so 1 hour is never enough to get a full phantom dataset (even when it is technically ‘enough’). Take you time, and get everything just right. This also helps with not mis-entering a parameter series, another common failure mode of phantom experiments!

One final note on chemical shift: your phantom is likely to be at room-temperature and ‘close-to-physiological’ pH. Chemical shifts and coupling constants can depend on temperature (and pH) and for our commonest phantoms the water line tends to come at ~4.8 ppm. For frequency-selective experiments like edited MRS, you need to account for this in setting editing pulse frequencies. This is handled in our patch via the BASING parameter ‘water freq’. The scanner tends to assume the water line comes at 4.68 ppm, so we can infer the correct water shift from a processed spectrum by checking how far off-resonance the metabolite signals appear in teh SpectroView window.

Optimizing Voxel geometry on the Philips platform

One common artifact that we see in MR spectra are unwanted water echoes. The spectrum below shows this behavior around 4 ppm. It manifests as a region of the spectrum with ‘locally increased noise’, which is more accurately considered as a broad signal with a large first-order phase error.

Screen Shot 2021-03-29 at 11.24.24 AM.png

This happens when the sequence accidentally refocuses water signals from outside of voxel OOV (or merely fails to fully suppress them with the gradient pulses), and can seriously interfere with quantification. For a given brain location and acquisition protocol, these artifacts are relatively consistent and so can be ‘optimized away ‘. This process is something we advise collaborators to do every time they set up a protocol for a new brain region.

The key parameters are the voxel orientation (transverse/coronal/sagittal) which changes the ordering of the slice-selective pulses within the PRESS sequence (or rotates the experiment 90 degrees about a cube-face) and the water-fat shifts (L/R etc) which flip the slice-selective gradients one-by-one (reflecting the experiment spatially a plane parallel to a cube-face).

Before you work on a challenging brain region, make sure your sequence works in PCC or some other ‘easy’ region with which you have experience. When you are sure the sequence is set up correctly, then you can move onto this geometric optimization.

Step 1: Run an in vivo scan in a new brain region. Use 320 averages and ~25ml volume so you know what to expect in terms of SNR. If the spectrum looks ‘clean’ with respect to these OOV echoes, then I would not continue with this process. Run a new subject and hopefully that’ll look fine too.

Step 2: If you see OOV echoes, run scans with all three options of the orientation parameter, and select the one that gives the smallest OOV echoes.

Step 3: With that orientation, start working on the water-fate shifts. One quick option is to flip all three and see if it solves your problem. Hopefully you can see the OOV echoes in the Spectroscopy tool on the scanner. For each water-fat axis, select the option that gives the smallest OOV echoes.

This process is not 100% reproducible across subjects, but it is enough to be useful.

Screen Shot 2021-03-29 at 11.23.44 AM.png

One final note: The data above were acquired from this midline ACC voxel. The orange box corresponds to the 3 ppm signal and the white to the chemical-shift-displaced water signal. When setting up a new voxel location, I tend to recommend setting the water-fat shifts to put the white box ‘inside‘ the orange box. By ‘inside’, I mean away from scalp and other challenging areas.. towards the middle of the brain….

6th International Symposium on Advanced MRS and GABA (now with added EDITINGSCHOOL)

We are really excited to announce that we are holding the 6th International Symposium on Advanced MRS and GABA at the end of the year. It will be preceded by an in-person EDITINGSCHOOL course. We are hopeful that vaccinations will continue to have an effect and that we will be able to travel by then. Go here to get your tickets booked.

EDITINGSCHOOL

EDITINGSCHOOL is a 3-day course (Nov 15-18) exclusively dedicated to edited MRS. It will cover background MRS theory, theory of editing, editable metabolites, analysis software, quantification, and practical tips on acquisition and data review.

6th International Symposium on Advanced MRS and GABA

The GABA MRS symposium (Nov 18-21) is an opportunity to present your advanced MRS study of GABA (or other metabolites), to a broad audience with a common interest in the methodology. All accepted abstracts will be orally presented, so this is a great opportunity for junior scientists to present in that format.

The two events will happen back-to-back at the beautiful XCaret Occidental Resort in Playa Del Carmen, Mexico. All tickets include food and accommodation in addition to access to the EDITINGSCHOOL and/or symposium.

Nov 15: Arrival and opening reception

Nov 16: All-day EDITINGSCHOOL PROGRAM (program TBA, but likely to follow this format)

Nov 17: All-day EDITINGSCHOOL PROGRAM (program TBA, but likely to follow this format)

Nov 18: Morning EDITINSCHOOL break-outs; departure for EDITINGSCHOOL-only attendees

Afternoon arrival for Symposium-only attendees and evening mixer

Nov 19: All-day Symposium (sessions of oral abstracts)

Nov 20: All-day Symposium (sessions of oral abstracts and break-outs)

Nov 21: Discussions and Departure

We are excited to re-open early registration for these events until the end of March. Go to https://www.eventbee.com/v/editingschool-and-gaba-mrs-symposium-2021/event?eid=164490043 to get your tickets booked.

We will have options for solo rooms or shared accommodation (we can assign you a roommate, if you don't have one). If you have a non-attendee partner that would like to attend, buy a SOLO ticket for you and a non-attendee roommate ticket for them.

FAQ

Who is this aimed at?

EDITINGSCHOOL and the Symposium will be invaluable to students, whether just starting out or preparing to write up, and postdocs using or developing MRS. Faculty, particularly those from a neuroscience/clinical background, will also find something to chew on. 

Where is this?

EDITINGSCHOOL will be at the beautiful X-Caret Occidental hotel in Playa Del Carmen, Mexico.  Flights to Cancun are relatively easy from North America and Europe, and a shuttle will take you down to the resort. 

What am I getting?

Registration will include hotel accommodation, all food, and the course itself. It is a bargain.   

How much does this cost?

There will be several rates, based on single/shared room, early/standard/late, and EDITINGSCHOOL/Symposium/both registration. To register for BOTH, early registration, running from now until March 31st will cost: $900 (shared room) and $1200 (single room).  Standard Registration, before Sep 15th will cost: $1200 (shared room) and $1600 (single room), and late registration will be $2400 (single room only).    These rates for either the Symposium or EDITINGSCHOOL only are: $540 (shared room) and $700 (single room).  Standard Registration, before Sep 15th will cost: $700 (shared room) and $900 (single room), and late registration will be $1400 (single room only).

Postdoctoral Fellowship Openings

We are looking to recruit two postdoctoral fellows to join our team developing new acquisition and analysis methods for MRS. Any prior experience with MRI or MRS is applicable, we are just looking to recruit someone curious and motivated to join our team. If you might be interested do reach out by email ( raee2 at jhu dot edu), as I am keen to talk to any interested candidates. Whatever your background, exspecially if it differs from ours, we want to hear from you.

We have active projects investigating oxidative stress in autism and are developing the tools for a large multi-site project imaging the neonatal brain. A postdoctoral fellowship in our lab is an excellent way to build up your skills for a successful independent research career. Don’t hesitate to drop us an email.

EDITINGSCHOOL Virtual

Unfortunately, we had to postpone EDITINGSCHOOL in-person, due to the pandemic, but we managed to get everything set up virtually. It has been a long and tiring week (with many people attending from a not-quite-convenient timezone) but very rewarding. Feedback so far has been positive, and the level of engagement from the floor was excellent.

Microsoft Teams proved a really great platform, allowing speakers to upload their presentations ahead of time, and to run real-time Q&A’s for each session.

Microsoft Teams proved a really great platform, allowing speakers to upload their presentations ahead of time, and to run real-time Q&A’s for each session.

82 people registered to attend, plus a dozen faculty! Given that most faculty were using Teams for the first time, it went much smoother than we might have hoped. Having real-time chat during Q&A sessions really augmented the process - often the main presenter would ask questions live and others could post links to relevant papers in the chat… I suspect we will retain the Teams framework for when we run things in-person!

Dr. Ulrike Dydak from Purdue University, running the Q&A session on Practicalities of Acquisition.

Dr. Ulrike Dydak from Purdue University, running the Q&A session on Practicalities of Acquisition.

Overall, a great week…. lots of great questions were asked and answered, new collaborations and friendships forged.

Our hotel deposit has been bounced to November 2021, when we will run the GABA symposium (18-21 November) with a special EDITINGSCHOOL re-run beforehand (15-18 November). Registration is now open! Hopefully vaccination will allow us to meet in person again in the fall.

The online format worked particularly well for live software demonstrations of Gannet by Mark Mikkelsen, Osprey by Helge Zöllner and FID-A by Jamie Near (pictured).

The online format worked particularly well for live software demonstrations of Gannet by Mark Mikkelsen, Osprey by Helge Zöllner and FID-A by Jamie Near (pictured).

A reading list on Advanced Editing

In setting up a new project, I recently wrote a reading list for someone coming new to edited MRS from outside the area. I thought it would be useful to post here for future reference and for anyone getting started.

Before you understand Advanced Editing, you need a grasp of edited MRS in general, so I’d suggest starting with a couple of reviews. There is other literature out there (including by other groups), but I reference our papers and the minimal reading.

  • Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA. Neuroimage. 2014;86:43-52.  doi: 10.1016/j.neuroimage.2012.12.004. Epub 2012 Dec 13.

    This review focuses on J-difference-edited MRS of GABA, but should be a good starting point for the basic principles.

  • Edited 1 H magnetic resonance spectroscopy in vivo: Methods and metabolites.

    Harris AD, Saleh MG, Edden RA. Magn Reson Med. 2017 Apr;77(4):1377-1389. doi: 10.1002/mrm.26619.

    This review broadens out into other metabolites that can be edited and also includes a little more detail about the mechanism of J-difference editing.

Then, moving beyond editing in general, some papers that describe editing more than one metabolite, using HERMES and HERCULES

  • HERMES: Hadamard encoding and reconstruction of MEGA-edited spectroscopy.

    Chan KL, Puts NA, Schär M, Barker PB, Edden RA. Magn Reson Med. 2016 Jul;76(1):11-9. doi: 10.1002/mrm.26233.

    This paper described the idea of Hadamard encoded editing and its application to separating signals from NAA and NAAG.

  • Simultaneous edited MRS of GABA and glutathione.

    Saleh MG, Oeltzschner G, Chan KL, Puts NAJ, Mikkelsen M, Schär M, Harris AD, Edden RAE. Neuroimage. 2016 Nov 15;142:576-582. doi: 10.1016/j.neuroimage.2016.07.056.

    We then applied the same principle to editing GABA and GSH in a single experiment.

  • Advanced Hadamard-encoded editing of seven low-concentration brain metabolites: Principles of HERCULES. Oeltzschner G, Saleh MG, Rimbault D, Mikkelsen M, Chan KL, Puts NAJ, Edden RAE. Neuroimage. 2019 Jan 15;185:181-190. doi: 10.1016/j.neuroimage.2018.10.002. 

    Next, we tried to edit everything in a single experiment HERCULES, which used a more elaborate editing scheme and multi-spectrum modeling.

In addition to editing more than one metabolite, we have also developed ways of editing more than one voxel, using PRIAM.

  • Parallel reconstruction in accelerated multivoxel MR spectroscopy.

    Boer VO, Klomp DW, Laterra J, Barker PB. Magn Reson Med. 2015 Sep;74(3):599-606. doi: 10.1002/mrm.25718.

    The original PRIAM concept was developed by Vincent Boer…

  • Dual-volume excitation and parallel reconstruction for J-difference-edited MR spectroscopy.

    Oeltzschner G, Puts NA, Chan KL, Boer VO, Barker PB, Edden RA. Magn Reson Med. 2017 Jan;77(1):16-22. doi: 10.1002/mrm.26536.

    …and it was applied to editing here. This paper includes proof-of-principle for the combination of HERMES-PRIAM for multi-voxel, multi-metabolite editing.

Universal HERMES of GABA and glutathione now includes ethanol

There is currently little understanding of the acute effects of ethanol (EtOH) on the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) and the antioxidant glutathione (GSH) levels. Previous MRS studies have demonstrated changes in GABA levels in individuals recovering from alcohol use disorder. Alcohol has also been shown to deplete GSH levels, impeding the elimination of reactive oxygen species.

Sequential MEGA-PRESS measurements of GABA, GSH, and EtOH would necessitate 30-min acquisitions, limiting the number of brain regions investigated within a typical 1-hr MR examination and the time resolution of dynamic studies. Muhammad Saleh and colleagues have extended the universal HERMES editing of GABA and GSH to include orthogonal editing of EtOH without an increase in scan time or substantial loss in spectral quality (see figure below). This new sequence is available collaboratively to the community for application in future studies.

a) The separate Experiments A-D are shown: saturated NAA signal in the ON_GABA spectra; saturated water signal in the ON_GSH spectra; and several signals saturated in the vicinity of 3.67 ppm in the ON_EtOH spectra. The saturation range of the editi…

a) The separate Experiments A-D are shown: saturated NAA signal in the ON_GABA spectra; saturated water signal in the ON_GSH spectra; and several signals saturated in the vicinity of 3.67 ppm in the ON_EtOH spectra. The saturation range of the editing pulses is shown on each spectrum as a grayscale. b) The Hadamard combinations yield GABA-edited (A+B–C–D), GSH-edited (A+C–B–D), and EtOH-edited (B+C–A–D) spectra.

Processing phantom data through Gannet

Some Gannet users have asked us whether Gannet can process phantom data. The answer is yes! Gannet can load and fit phantom data for GABA, GSH, Glx, Lac, and EtOH edited data acquired either by MEGA-PRESS or HERMES.

Note that to quantify your measurements you will need to also have an unsuppressed water signal acquisition to use as a concentration reference.

For example, the following steps would allow you to process and quantify example Lac-edited phantom data acquired on a Siemens scanner:

  1. Download the latest version of Gannet.

  2. Open GannetPreInitialise.m and make sure the settings match the screenshot in Figure 1 below, making sure MRS_struct.p.phantom is set to 1.

  3. Save your changes and enter the directory containing your phantom data.

  4. Run GannetLoad using the following command (see the output in Figure 2):

    GannetLoad({'meas_MID00380_FID11555_UNIV_Lac_TE140_22ms_1024_1khz.dat'},{'meas_MID00382_FID11557_UNIV_Lac_TE140_H20.dat'});
  5. Then run GannetFitPhantom to fit and quantify the edited Lac signal (see the output in Figure 3):

    MRS = GannetFitPhantom(MRS);

Figure 1

Figure 2

Figure 2

Figure 3

Figure 3

Live from Park City: 5th International Symposium on GABA and Advanced MRS

As it happens…

Day 1: Introduction and Welcome Speech - Richard Edden

Day 1: Introduction and Welcome Speech - Richard Edden

Plenary Lecture: A History of Edited MRS - Melissa Terpstra

Plenary Lecture: A History of Edited MRS - Melissa Terpstra

Captivated audience

Captivated audience

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Day 2: Despite the weather, the journey continues

Day 2: Despite the weather, the journey continues

Brief introductory lecture on GABA/glutamate and glutamine Biochemistry - Aaron Gudmundson

Brief introductory lecture on GABA/glutamate and glutamine Biochemistry - Aaron Gudmundson

Captivated… again

Captivated… again

Discussions on edited MRS from data acquisition to assessment

Discussions on edited MRS from data acquisition to assessment

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“Is MRS of GABA a meaningful index of inhibition?” - The Great Debate

Gannet 3.1 released

Introducing Gannet 3.1! This new version includes a number of updates and bug fixes. Notable additions include a new frequency-and-phase correction algorithm (robust spectral registration) and functionality for EtOH/GABA/GSH HERMES data.

Gannet 3.1 is available for immediate download at the following link: https://github.com/richardedden/Gannet3.1/archive/master.zip

Release notes:

MAJOR CHANGES

  • Adopted semantic versioning (see semver.org)

  • Aesthetic changes to PDF outputs throughout

  • Add functionality for processing and fitting of EtOH/GABA/GSH HERMES data

  • Introduced Robust_Spectral_Registration.m: robust correction of frequency/phase errors (recommended and default for all acquisition types)

  • If using Robust_Spectral_Registration.m, sub-spectra are averaged using weighted averaging; outlier removal is not applied in this case

  • nlinfit will no longer throw an error if peak model fitting is poor

  • GannetQuantify.m corrects metabolite measurements for partial tissue volume effects using the Gasparovic et al., 2006 (MRM) method; the Harris et al., 2015 (JMRI) method (alpha correction) is still also applied

MINOR CHANGES

  • Averaged HERMES sub-spectra are saved in MRS_struct.spec

  • HSVD water removal can be applied to all MEGA-PRESS and HERMES data (on by default)

  • Improved optimization parameters for frequency/phase alignment and peak model fitting

  • Turned off ignorable warnings that sometimes occur during peak model fitting in GannetFit.m

  • Fixed bugs in GannetMask_GE.m

  • Tissue fractions saved in MRS_struct.out renamed to fGM, fWM and fCSF

  • Text font in PDF outputs changed to Arial for cross-OS compatibility

  • More appropriate SNR thresholding in Spectral_Registration.m/Spectral_Registration_HERMES.m/Robust_Spectral_Registration.m

Finally! It's here - Universal Edited MRS

MEGA-PRESS, a spectral editing method, has gained popularity in the MRS community thanks to its ability to edit low-concentration metabolites with relative ease of implementation, allowing direct and unambiguous measurements of the inhibitory neurotransmitter GABA, the antioxidant glutathione (GSH), and the anaerobic product lactate (Lac). However, current implementations of MEGA-PRESS are diverse across vendors, differing in terms of RF pulse shapes and pulse sequence timings. Recent multi-site data revealed that ~30% of the variance in the GABA+ data is attributed to the site- and vendor-level differences in the implementation of MEGA-PRESS.

Recently, Muhammad Saleh and colleagues developed a new universal MEGA-PRESS sequence for the major MR vendors (Philips, Siemens, GE, and Canon) with common RF pulse shapes and timings, and has functionality for HERMES editing of GABA and GSH (Figure 1). Upon comparing with the existing vendor-native sequences, the universal sequence yielded edited spectra with strong correlations and low variance among vendors at both short and long TEs phantom and in vivo experiments (Figures 2 and 3). The universal sequence includes simultaneous editing of GABA and GSH with HERMES, allowing excellent separation of the edited signals in half the scan time compared with the sequentially acquired conventional MEGA editing. The universal sequence is available collaboratively to the community for application in future studies.

Exciting times ahead: Building on the universal sequence, Georg Oeltzschner and colleagues developed HERCULES sequence, capable of editing seven coupled metabolites that would usually require a single 11-min editing experiment each. This sequence is also available collaboratively to the community for application in future studies.

For more updates, stay tuned for any new developments from Edden's lab. Universal edited MRS sequences will be presented at the 27th Annual Meeting of the ISMRM, Montreal, Canada, 2019. Looking forward to meeting you all.

Figure 1: Pulse sequence diagrams indicating RF pulse shapes and timings for the vendor-native Philips, Siemens, GE and Canon sequences, and the universal sequence at TE = 68 ms.

Figure 1: Pulse sequence diagrams indicating RF pulse shapes and timings for the vendor-native Philips, Siemens, GE and Canon sequences, and the universal sequence at TE = 68 ms.

Figure 2: a) MEGA-PRESS experiment using the GABA phantom (TE = 68 ms) and Lac phantom (TE = 140 ms) from vendor-native sequences (left) and the universal sequence (right). b) Edited spectra from HERMES experiments acquired using the universal seque…

Figure 2: a) MEGA-PRESS experiment using the GABA phantom (TE = 68 ms) and Lac phantom (TE = 140 ms) from vendor-native sequences (left) and the universal sequence (right). b) Edited spectra from HERMES experiments acquired using the universal sequence, performed in a GABA phantom (left) and a GSH phantom (right).

Figure 4: In vivo experiments using the universal sequence. Spectra acquired on Philips and Siemens scanners are overlaid for each subject: a) MEGA-PRESS GABA (TE = 68 ms) and Lac (TE = 140 ms) spectra; b) GABA- and GSH-edited HERMES spectra. In viv…

Figure 4: In vivo experiments using the universal sequence. Spectra acquired on Philips and Siemens scanners are overlaid for each subject: a) MEGA-PRESS GABA (TE = 68 ms) and Lac (TE = 140 ms) spectra; b) GABA- and GSH-edited HERMES spectra. In vivo experiments using the universal sequence for GE (green) and Canon (red) scanners: c) MEGA-PRESS GABA-edited (TE = 68 ms) and Lac-edited (TE = 140 ms) spectra; d) GABA- and GSH-edited HERMES spectra. Spectra acquired are overlaid on the ± 1SD range (in gray) of the amalgamated Philips and Siemens data (6 subjects).

Gannet at Ewha Brain Institute

We are pleased to collaborate with Prof In Kyoon Loo of Ewha Brain Institute. Pictured here are graduate students Suji Lee, Myungjoo Kim, Eunji Ha, from left to right

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Note of Interest: Ewha’s scanner (pictured) originally showed some very strange sinusoidal field drift behavior, which we had not seen before. Originally we suspected the air conditioning temperature control was insufficient, but eventually it was narrowed down to a dodgy clock board … so many things you ignore until they become an issue!

5th International Symposium on MRS of GABA

We are delighted to announce that the 5th (!) International Symposium on MRS of GABA will be held from November 18-20, 2019 in Park City, Utah. More details will be posted here as they emerge (and keep an eye on https://sites.google.com/site/gabamrssymposium/ ).

In keeping with previous symposia, the meeting will include sessions of submitted abstracts, round table discussions and plenty of time to meet new collaborators. Topics covered will include methodological developments and applications of MRS of GABA, as well as other advanced MRS methods.