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 sequence, performed in a GABA phantom (left) and a GSH phantom (right).

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 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).

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.

EDITINGSCHOOL feedback

Overall, it seems we did a great job:

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And prospects look good for a rerun in 2020:

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In fact, if the major criticism of EDITINGSCHOOL is that there wasn’t enough EDITINGSCHOOL…

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Thank you to (the majority of ) attendees that provided feedback. We are giving the detailed feedback consideration, and will revisit it in a year as we plan for 2020.

EDITINGSCHOOL final schedule

Day 0 (Dec 3)

     Check-in, Opening Receptiopn/ Meet-the-Faculty

Day 1 (Dec 4)

     10 - The MR Spectrum – Richard Edden

     11 - Evolution of Spin Systems – Richard Edden

          Lunch

     2 - The editable metabolites – Ashley Harris

     3 - J-difference editing explained – Georg Oeltzschner

     4 - Quantification – Paul Mullins

    5 -  Simulations and Data handling with FID-A – Jamie Near

Day 2 (Dec 5)

     10 - Practicalities of Acquisition  - Ulrike Dydak

     11 - Neurochemistry of GABA - Eric Porges & Damon Lamb

          Lunch

      2 - Advanced Editing Methods – Richard Edden

3 - Editable Metabolites in Psychiatric Disease – Laura Rowland

4 - Data Processing with Gannet – Mark Mikkelsen 

5 - Where did I go wrong? - Nick Puts     

Day 3 (Dec 6)

   Morning Career Breakouts: maximizing your postdoc; early-career challenges; TBC.

Gannet supports Siemens Hermes data

Gannet now provides support for Hermes data acquired using Siemens 3T scanner. The acceptable format is .dat. Please note that it is beneficial to acquire metabolite data and water data using the same sequence for better coil combination. Below is the GannetLoad window displaying Siemens HERMES data before and after post-processing steps in Gannet.

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HERMES of GABA and GSH at 7T

Extending the multi-metabolite editing technique at high field scanner, we have developed HERMES of GABA and GSH at ultra-high field scanner. For this, M.G. Saleh and colleagues implemented semi-LASER (sLASER) voxel localizer and Hadamard encoding scheme (Figure a) at 7T to simultaneously edit GABA (at 3 ppm) and GSH (at 2.95 ppm) in half the scan time MEGA-sLASER takes to edit these metabolites sequentially (Figure b). HERMES of GABA and GSH will be presented at 27th Joint Annual Meeting of the ESMRMB-ISMRM, Paris, France, 2018.

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Provisional EDITINGSCHOOL schedule

Day 0 (Dec 3)

     Check-in, Opening Receptiopn/ Meet-the-Faculty

Day 1 (Dec 4)

     The MR Spectrum – Richard Edden

     Evolution of Spin Systems – Richard Edden

          Lunch

     The editable metabolites – Ashley Harris

     J-difference editing explained– Georg Oeltzschner

     Quantification – Paul Mullins

     Simulations and Data handling with FID-A – Jamie Near

Day 2 (Dec 5)

     Practicalities of Acquisition  - Nick Puts

     Practicalities of Acquisition  II - TBC

          Lunch

     Editable Metabolites in Psychiatric Disease – Laura Rowland

     Advanced Editing Methods – Richard Edden

     (MRS-relevant neurochemistry of GABA - TBC)

     Data Processing with Gannet – Mark Mikkelsen 

Day 3 (Dec 6)

   Morning Career Breakouts: maximizing your postdoc; early-career challenges; TBC.

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HERMES on Siemens

We are in the late stages of implementing HERMES for GABA/GSH on Siemens.  We are actively seeking collaborators who would like to apply this sequence, so get in touch and we can start the C2P paperwork.

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Gannet now listed on NITRC!

Gannet was recently added to the software catalogue of the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).

Please follow this link to visit the page.

We will be adding to this page in the coming weeks. Stay tuned for further exciting developments....

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