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.

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.

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).

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.

OSPREY: An introductory video

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 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);

View fullsize

Figure 1

Figure 2

Figure 3

EDITINGSCHOOL 2020

We are excited to announce that EDITINGSCHOOL2020 will be running December 8-12 2020 at XCaret Occidental, Playa Del Carmen. Registration is now open here.

XCaret Occidental is a great place with lots of wildlife to keep things interesting.