Historical Information

Older methods and literature references will go here...

Processing and Analyzing GABA Data - non-Flywheel methods

(1) Analysis of GABA Data collected with the MEGA-PRESS sequence with Gannet

To analyze the data from MEGA-PRESS experiments, we recommend Gannet, a batch-analysis tool for GABA-edited MRS data. The Gannet code and instruction manual can be downloaded from here gabamrs.blogspot.com Additional and newer information can be found here www.gabamrs.com and here www.gabamrs.com/about/ Note that Matlab with Optimization and Statistics Toolboxes must be installed on your computer prior to downloading the Gannet2.0 code.

Note that following change needs to be made to the Gannet code in order to correctly analyze data obtained the CNI MEGA-PRESS sequence gabamrs.blogspot.com (When Gannet goes wrong section)

From gabamrs blogspot - Solution 2: ON and OFF are incorrectly identified. If the creatine stripe is correct (red on blue; spectra phased positively) and the difference spectra are still negative, then the issue is the ordering of ON and OFF spectra. The simple solution is to change the MRS_struct.p.onofforder parameter in GannetPreInitialise.m. It is either 'onfirst' or 'offfirst' depending on the acquisition order. So here's the summary: "Gannet makes my GABA difference spectra negative". "Are your creatine signals phased positively?". If yes, change MRS_struct.p.onofforder; if no, change MRS_struct.p.WaterPositive.

Spectroscopy

For users who are totally new to spectroscopy a good basic reference is MRI From Picture to Proton Donald W. McRobbie, Elizabeth A. Moore, Martin J. Graves, and Martin Prince, Cambridge University Press, Second Edition 2007, Chapter 15 (It's not just squiggles: in vivo spectroscopy). This chapter describes spectroscopy from the clinical side, but covers the basics for both data acquisition and processing.

Books:

In Vivo NMR Spectroscopy, 2nd Edition, Author: Robin de Graaf, Wiley Online Library

A recently published book Magnetic Resonance Spectroscopy - Tools for Neuroscience Research and Emerging Clinical Applications

An excellent spectroscopy resource website is https://mrshub.org/ The MRSHub is a curated collection of resources for the analysis of magnetic resonance spectroscopy data. It is maintained by the Committee for MRS Code and Data Sharing of the MR Spectroscopy Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM).

Papers presented at the ISMRM MR Spectroscopy Study Group Virtual Meeting: NMR in Biomedicine Special Issue Experts' Recommendations: Where Consensus Was Reached and Where Dissent Prevailed, Part 1 (November 12, 2020)

Advanced methodology for in vivo magnetic resonance spectroscopy In‐Young Choi Roland Kreis https://doi.org/10.1002/nbm.4504 Editorial

B0 shimming for in vivo magnetic resonance spectroscopy: Experts' consensus recommendations Christoph Juchem, Cristina Cudalbu, Robin A. de Graaf, Rolf Gruetter, Anke Henning, Hoby P. Hetherington, Vincent O. Boer NMR in Biomedicine 2020;e4350 https://doi.org/10.1002/nbm.4350

Advanced magnetic resonance spectroscopic neuroimaging: Experts' consensus recommendations Andrew A. Maudsley, Ovidiu C. Andronesi, Peter B. Barker, Alberto Bizzi, Wolfgang Bogner, Anke Henning, Sarah J. Nelson, Stefan Posse, Dikoma C. Shungu, Brian J. Soher NMR in Biomedicine 2020;e4309 https://doi.org/10.1002/nbm.4309

Motion correction methods for MRS: experts' consensus recommendations Ovidiu C. Andronesi, Pallab K. Bhattacharyya, Wolfgang Bogner, In‐Young Choi, Aaron T. Hess, Phil Lee, Ernesta M. Meintjes, M. Dylan Tisdall, Maxim Zaitzev, André van der Kouwe NMR in Biomedicine 2020;e4364 https://doi.org/10.1002/nbm.4364

Preprocessing, analysis and quantification in single‐voxel magnetic resonance spectroscopy: experts' consensus recommendations Jamie Near Ashley D. Harris Christoph Juchem Roland Kreis Małgorzata Marjańska Gülin Öz Johannes Slotboom Martin Wilson Charles Gasparovic NMR in Biomedicine 2020;e4257 https://doi.org/10.1002/nbm.4257

Proton magnetic resonance spectroscopy in skeletal muscle: Experts' consensus recommendations Martin Krššák, Lucas Lindeboom, Vera Schrauwen‐Hinderling, Lidia S. Szczepaniak, Wim Derave, Jesper Lundbom, Douglas Befroy, Fritz Schick, Jürgen Machann, Roland Kreis, Chris Boesch NMR in Biomedicine 2020;e4266 https://doi.org/10.1002/nbm.4266

31P magnetic resonance spectroscopy in skeletal muscle: Experts' consensus recommendations Martin Meyerspeer, Chris Boesch, Donnie Cameron, Monika Dezortová, Sean C. Forbes, Arend Heerschap, Jeroen A.L. Jeneson, Hermien E. Kan, Jane Kent, Gwenaël Layec, Jeanine J. Prompers, Harmen Reyngoudt, Alison Sleigh, Ladislav Valkovič, Graham J. Kemp, Experts' Working Group on 31P MR Spectroscopy of Skeletal Muscle NMR in Biomedicine 2020;e4246 https://doi.org/10.1002/nbm.4246

Other review papers in the special issue now online

Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: Background and experts' consensus recommendations Roland Kreis, Vincent Boer, In‐Young Choi, Cristina Cudalbu, Robin A. de Graaf, Charles Gasparovic,,Arend Heerschap, Martin Krššák, Bernard Lanz, Andrew A. Maudsley, Martin Meyerspeer, Jamie Near, Gülin Öz, Stefan Posse, Johannes Slotboom, Melissa Terpstra, Ivan Tkáč, Martin Wilson, Wolfgang Bogner, Experts' Working Group on Terminology for MR Spectroscopy NMR in Biomedicine 2020;e4347 https://doi.org/10.1002/nbm.4347

Spectral editing in 1H magnetic resonance spectroscopy: Experts' consensus recommendations In‐Young Choi, Ovidiu C. Andronesi, Peter Barker, Wolfgang Bogner, Richard A. E. Edden, Lana G. Kaiser, Phil Lee, Małgorzata Marjańska, Melissa Terpstra, Robin A. de Graaf NMR in Biomedicine 2020;e4411 https://doi.org/10.1002/nbm.4411

Magnetic resonance spectroscopy in the rodent brain: Experts' consensus recommendations Bernard Lanz, Alireza Abaei, Olivier Braissant, In‐Young Choi, Cristina Cudalbu, Pierre‐Gilles Henry, Rolf Gruetter, Firat Kara, Kejal Kantarci, Phil Lee, Norbert W. Lutz, Małgorzata Marjańska, Vladimír Mlynárik, Volker Rasche, Lijing Xin, Julien Valette, the Experts' Working Group on Magnetic resonance spectroscopy in the rodent brain NMR in Biomedicine 2020;e4325 https://doi.org/10.1002/nbm.4325

Advanced single voxel 1H magnetic resonance spectroscopy techniques in humans: Experts' consensus recommendations Gülin Öz Dinesh K. Deelchand Jannie P. Wijnen Vladimír Mlynárik Lijing Xin Ralf Mekle Ralph Noeske Tom W.J. Scheenen Ivan Tkáč the Experts' Working Group on Advanced Single Voxel 1H MRS https://doi.org/10.1002/nbm.4236 NMR in Biomedicine. 2020;e4236

Representative Research Studies

Examples of studies at CNI using in-vivo spectroscopy techniques include characterization of biomarkers following transcranial magnetic stimulation, and metabolite characterization for conditions such as substance addiction, pain, depression, and various forms of dementia. These studies illustrate integrated data acquisition and data processing tools accessible to the CNI user community which simplify the use and sharing of spectroscopy results in neuroimaging applications.

Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability DeSouza DD, Stimpson K, Baltusis L, Sacchet MD, Gu M, Hurd R, Wu H, Yeomans DC, Williams N, Spiegel D. Association between anterior cingulate neurochemical concentration and individual differences in hypnotizability. Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3644–3654, https://doi.org/10.1093/cercor/bhz332

New Methods and Techniques

The CNI continues to support the research of its user community by developing and incorporating for general use new data acquisition and data analysis capabilities.

GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence Gu M, Hurd R, Noeske R, Baltusis L, Hancock R, Sacchet MD, Gotlib IH, Chin FT, Spielman DM (2018) GABA editing with macromolecule suppression using an improved MEGA-SPECIAL sequence, Magnetic Resonance in Medicine 79:41-47 https://doi.org/10.1002/mrm.26691

Additional review and research papers

Across‐vendor standardization of semi‐LASER for single‐voxel MRS at 3T Dinesh K. Deelchand Adam Berrington Ralph Noeske James M. Joers Arvin Arani Joseph Gillen Michael Schär Jon‐Fredrik Nielsen Scott Peltier Navid Seraji‐Bozorgzad Karl Landheer Christoph Juchem Brian J. Soher Douglas C. Noll Kejal Kantarci Eva M. Ratai Thomas H. Mareci Peter B. Barker Gülin Öz NMR in Biomedicine.2019;e4218 https://doi.org/10.1002/nbm.4218

Multi-vendor standardized sequence for edited magnetic resonance spectroscopy Muhammad G.Saleh Daniel Rimbault Mark Mikkelsen Georg Oeltzschner Anna M.Wang Dengrong Jiang Ali Alhamud Jamie Near Michael Schär Ralph Noeske James B.Murdoch Lars Ersland Alexander R.Craven Gerard Eric Dwyer Eli Renate Grüner LiPann Sinyeob Ahnn Richard A.E.Edden Neuroimage 189 (2019) 425-431 https://doi.org/10.1016/j.neuroimage.2019.01.056

Big GABA II: Water-referenced edited MR spectroscopy at 25 research sites MarkMikkelsen Daniel L.Rimbault Peter B.Barker Pallab K.Bhattacharyya Maiken K.Brix Pieter F.Buur Kim M.Cecil Kimberly L.Chanab David Y.-T.Chen Alexander R.Craven KoenCuypers MichaelDacko Niall W.Duncan UlrikeDydak David A.Edmondson GabrieleEnde LarsErsland Megan A.Forbes FeiGao IanGreenhouse Ashley D.Harris NayingHe StefanieHeba NigelHoggard Tun-WeiHsu Jacobus F.A.Jansen AlayarKangarlu ThomasLang R. MarcLebel YanLi Chien-Yuan E.Lin Jy-KangLiou Jiing-FengLirng FengLiu Joanna R.Long RuoyunMaq CelineMaes MartaMoreno-Ortega Scott O.Murray SeanNoah RalphNoeske Michael D.Noseworthy GeorgOeltzschner Eric C.Porges James J.Prisciandaro Nicolaas A.J.Puts Timothy P.L.Roberts MarkusSack NapaponSailasuta Muhammad G.Saleh Michael-PaulSchallmo NicholasSimard DiederickStoffers Stephan P.Swinnen MartinTegenthoff PeterTruong GuangbinWang Iain D.Wilkinson Hans-JörgWittsack Adam J.Woods HongminXu FuhuaYan ChenchengZhang VadimZipunnikov Helge J.Zöllner Richard A.E.Edden https://doi.org/10.1016/j.neuroimage.2019.02.059

Validation of in vivo MRS measures of metabolite concentrations in the human brain Elvisha Dhamala Ines Abdelkefi Mavesa Nguyen T. Jay Hennessy Hélène Nadeau Jamie Near NMR in Biomedicine. 2019;32:4058 https://doi.org/10.1002/nbm.4058

In vivo diffusion‐weighted MRS using semi‐LASER in the human brain at 3 T: Methodological aspects and clinical feasibility Guglielmo Genovese, Małgorzata Marjańska, Edward J. Auerbach, Lydia Yahia Cherif, Itamar Ronen, Stéphane Lehéricy, Francesca Branzoli NMR in Biomedicine 2020;e4206 https://doi.org/10.1002/nbm.4206

Correcting frequency and phase offsets in MRS data using robust spectral registrationMark Mikkelsen, Sofie Tapper, Jamie Near, Stewart H. Mostofsky, Nicolaas A. J. Puts, Richard A. E. Edden NMR in Biomedicine 2020;e4368 https://doi.org/10.1002/nbm.4368

In vivo Glx and Glu measurements from GABA‐edited MRS at 3 TTiffany Bell, Elodie S. Boudes, Rachelle S. Loo, Gareth J. Barker, David J. Lythgoe, Richard A.E. Edden, R. Marc Lebel, Martin Wilson, Ashley D. Harris NMR in Biomedicine 2020;e4245 https://doi.org/10.1002/nbm.4245

Influence of fitting approaches in LCModel on MRS quantification focusing on age‐specific macromolecules and the spline baseline Małgorzata Marjańska, Melissa Terpstra NMR in Biomedicine 2019;e4197 https://doi.org/10.1002/nbm.4197

Localized MRS reliability of in vivo glutamate at 3 T in shortened scan times: A feasibility study – Efforts to improve rigor and reproducibility Randy P. Auerbach, Diego A. Pizzagalli NMR in Biomedicine 2019;e4093 https://doi.org/10.1002/nbm.4093

Insights into brain microstructure from in vivo DW-MRS Marco Palombo, Noam Shemesh, Itamar Ronen, Julien Valette Neuroimage Volume 182, 15 November 2018, Pages 97-116 https://doi.org/10.1016/j.neuroimage.2017.11.028

Several new publications here on advanced editing techniques - http://www.gabamrs.com/

Voxel placement publication

AutoVOI: real‐time automatic prescription of volume‐of‐interest for single voxel spectroscopy Young Woo Park Dinesh K. Deelchand James M. Joers Brian Hanna Adam Berrington Joseph S. Gillen Kejal Kantarci Brian J.Soher Peter B. Barker HyunWook Park Gülin Öz Christophe Lenglet Magn Reson MEd. 2018;80:1787-1798 https://doi.org/10.1002/mrm.27203

New open-source processing package currently under evaluation -

Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data Georg Oeltzschner Helge J.Zöllner Steve C.N.Hui Mark Mikkelsen Muhammad G.Saleh Sofie Tapper Richard A.E. Edden Journal of Neuroscience Methods Volume 343, 1 September 2020, 108827 https://doi.org/10.1016/j.jneumeth.2020.108827

Presentation at 2020 ENC Meeting - Accelerated MR spectroscopic imaging—a review of current and emerging techniques

Accelerated MR spectroscopic imaging—a review of current and emerging techniques Wolfgang Bogner Ricardo Otazo Anke Henning NMR in Biomedicine.2020;e4314 https://doi.org/10.1002/nbm.4314

WIPs Information:

[1] J. Star-Lack et al., In Vivo Lactate Editing with Simultaneous Detection of Choline, Creatine, NAA, and Lipid Singlets at 1.5 T Using PRESS Excitation with Applications to the Study of Brain andHead and Neck Tumors, J Magn Reson, 133: 243 – 254 (1998) https://doi.org/10.1006/jmre.1998.1458

[2] M. Mikkelsen et al., Big GABA: Edited MR spectroscopy at 24 research sites, NeuroImage, 159, 32 – 45, (2017) https://doi.org/10.1016/j.neuroimage.2017.07.021

[3] M.G. Saleh et al., Multi-vendor standardized sequence for edited magnetic resonance spectroscopy, NeuroImage, (2019) https://doi.org/10.1016/j.neuroimage.2019.01.056

[1] G. Öz et al., Short-Echo, Single-Shot, Full-Intensity Proton Magnetic Resonance Spectroscopy for Neurochemical Profiling at 4 T: Validation in the Cerebellum andBrainstem, Magn Reson Med, 65: 901 – 910 (2011) https://doi.org/10.1002/mrm.22708

[2] VO. Boer et al., 7-T 1H MRS with adiabatic refocusing at short TE using radiofrequency focusing with a dualchannel volume transmit coil, NMR Biomed, 24(9), 1038 – 1046, (2011) https://doi.org/10.1002/nbm.1641

[3] TW. Scheenen et al., Short Echo Time 1H-MRSI of the Human Brain at 3T With Minimal Chemical Shift Displacement Errors Using Adiabatic Refocusing Pulses, Magn Reson Med, 59: 1 – 6 (2008) https://doi.org/10.1002/mrm.21302

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Automated magnetic resonance spectroscopy voxel placement tools

Typically MRS data is collected within a single voxel that needs to be manually prescribed. To improve data collection quality, there has been anincreased interest and development of real-time single voxel automated prescription placement methods8. Researchers can now acquire MRS data in a routine way using a variety of automated voxel placement procedures. The procedures are used in real-time during data acquisition and have been streamlined for efficient usage and low time cost.

• One procedure uses non-linear warping between native subject space and template space (i.e., Montreal Neurological Institute [MNI] space) to identify precise voxel locations in scanner space that are based on MNI neuroanatomy.

• A second procedure is for the real-time in-scan session identification of precise coordinates from prior scanning sessions for MRS voxel placement based on person-specific coordinates. For example, if an initial scan session includes a functional task, information from that data can be used for subsequent voxel placement.

• A third procedure that is similar to second procedure above is using the central coordinate of an MRS voxel collected previously for placement in the same individual during a second scan session.

Extra section to be removed

Bottomley PA. Spatial localization in NMR spectroscopy in vivo. Ann NY Acad Sci 1987;508:333–48 https://doi.org/10.1111/j.1749-6632.1987.tb32915.x

PRESS1

PRESS2

PRESS Broadband

The product refocusing pulses within PRESS can be replaced by broadband refocusing pulses described in M. Janich et al., Slice-selective broadband refocusing pulses for the robust generation of crushed spin-echoes, J Magn Reson, 223: 129 – 137 (2012) https://doi.org/10.1016/j.jmr.2012.08.003 to reduce the CSDE.

PRESS-Broadband-1

PRESS-Broadband-2

CV 0 5000

CV0: spectral width The total spectral frequency width in Hz.

CV 1 4096

CV1: number of points The number of complex data points acquired per excitation.

CV 4 128 (1.5T) 64 (3T)

CV4: total number of scans The total number of excitations acquired per echo (cycle) when signal averaging. The value of CV4 must be an integer multiple of NEX.

CV 14 0

CV14: JPRESS Mode

0 (PRESS) standard PRESS acquisition, TE1 is set by sequence to minimum

1 (asym. PRESS) TE1 is set by user

2 (half-echo) standard JPRESS acquisition mode, echo acquired from echo top

3 (max-echo) maximum-echo mode described in [6]. For shortest echo time echo is acquired from echo top, for longer echo times data acquisition starts before the echo top.

CV 18 7

CV18: ROI edge sat/gradient mask There are three pairs of VSS RF pulses available at the edge of the Spectroscopy VOI. The VSS can be selected or deselected.

0 – no VSS RF pulses;

1 – S/I the superior and inferior pulses only;

2 – A/P the anterior and posterior pulses only;

3 – S/I and A/P, two pulse pairs;

4 – R/L the right and the left pulses only;

5 – R/L and S/I, two pulse pairs;

6 - R/L and A/P, two pulse pairs;

7 – R/L, A/P and S/I, three pulse pairs, this is the default value

This bitmask determines the polarity of the slice gradients of the three PRESS excitation/refocusing pulses and therefore the direction of the fat-water chemical shift. The corresponding bit set to 1 is negative polarity, 0 is positive.

0 – S/I, A/P and R/L all positive, this is the default value

8 – S/I negative, A/P and R/L positive

16 – A/P negative, S/I and R/L positive

24 – S/I and A/P negative, R/L positive

32 – R/L negative, S/I and A/P positive

40 – R/L and S/I negative, A/P positive

48 - R/L and A/P negative, S/I positive

56 – R/L, A/P and S/I all negative

CV 23 20

CV23: Refocusing Pulse Shape: PRESS refocusing pulse shape

20 – S-BREBOP-7500.rho, pw = 7.5ms

26 – flip_1803.rho, non-linear phase refocusing pulse used for CPRESS

-1 – default pulse set by PSD

CV 24 1

CV24: Feature flag

1 (no add) Store each single data acquisition in pfile.

2 (Bloch-Siegert) Bloch-Siegert TG calibration

PRESS FatSat

The dual BASING technique can be used for additional metabolite suppression, e.g. fat.

J. Star-Lack et al., Improved Water and Lipid Suppression for 3D PRESS CSI Using RF Band Selective Inversion with Gradient Dephasing (BASING), Magn Reson Med, 38, 311 – 321, (1997) https://doi.org/10.1002/mrm.1910380222

CPRESS

CPRESS is a modified PRESS spectroscopic localization pulse sequence that replaces each of the two refocusing RF pulses with a pair of non-linear phase refocusing pulses. The non-linear phase refocusing pulses has been designed to operate at a lower maximum B1 requirement (0.15 G) while keeping the pulse width short (4.3 ms) and maintaining adequate bandwidth for spectroscopy application at 3T (1.2 kHz). At a TE of 42 ms, the short inter pulse delay (10.5 ms) between the refocusing pulses has a potential to provide improved sensitivity for J-coupled metabolites such as myoinositol (mI) and glutamate / glutamine (Glx) over conventional short TE (35 ms) PRESS sequence.

I. Hancu, Which pulse sequence is optimal for myo-inositol detection at 3T? NMR Biomed, 22: 426 – 435 (2009) https://doi.org/10.1002/nbm.1353

I. Hancu et al, Improved Myo-inositol Detection Through Carr–Purcell PRESS: A Tool for More Sensitive Mild Cognitive Impairment Diagnosis, Magn Reson Med, 65: 1515 – 1521 (2011) https://doi.org/10.1002/mrm.22749

JPRESS

The two-dimensional J-resolved spectroscopy sequence consists of a series of spin-echo experiments with different echo times defined by the average echo time (TE) and the delta of echo times (User CV 16) employing PRESS localization. Adding the spectra gives a TEA-PRESS spectrum.

L. Ryner et al., Localized 2D J-resolved H-1 MR spectroscopy – strong coupling effects in vitro and in vivo, Magn Reson Imaging, 13: 853 – 869 (1995) https://doi.org/10.1016/0730-725x(95)00031-b

R. Schulte, Improved two-dimensional J-resolved spectroscopy, NMR Biomed, 19: 264 – 270 (2006) https://doi.org/10.1002/nbm.1027

mBREASE

mBREASE is a TEA-PRESS sequence with enabled STIR fat suppression, storage of each aquired FID to correct for frequency shifts and acquisition of reference data with different echo times to correct for water T2. It includes quantification of the choline signal using a voigt-lineshape model function in time domain and linear baseline in frequency domain. T2 corrected water signal is used as internal reference.

Editing

Spectral j-difference editing describes an advanced spectroscopy acquisition technique which is generally necessary to detect j-coupled markers and separate from co-resonant metabolite peaks. The implemented editing technique is based on the BASING technique described.

J. Star-Lack et al., Improved Water and Lipid Suppression for 3D PRESS CSI Using RF Band Selective Inversion with Gradient Dephasing (BASING), Magn Reson Med, 38, 311 – 321, (1997) https://doi.org/10.1002/mrm.1910380222

J. Star-Lack et al., In Vivo Lactate Editing with Simultaneous Detection of Choline, Creatine, NAA, and Lipid Singlets at 1.5 T Using PRESS Excitation with Applications to the Study of Brain and Head and Neck Tumors, J Magn Reson, 133: 243 – 254 (1998) https://doi.org/10.1006/jmre.1998.1458

BS-PRESS

BS-PRESS is a voxel based TG calibration method described in [8]. The phase-based B1+ mapping technique using the Bloch-Siegert shift method encodes the B1 information into a signal phase resulting from off-resonant RF pulses within the sequence [9-11].

8. R. Noeske et al., Voxel Based Transmit Gain Calibration using Bloch-Siegert Shift Method for MR Spectroscopy, Proc 20th Annual Meeting ISMRM, Melbourne: 1733 (2012)

9. Sacolick et al., B1 Mapping by Bloch-Siegert Shift, Magn Reson Med, 63: 1315 - 1322 (2010)

10. Sacolick et al., Fast Radiofrequency Flip Angle Calibration by Bloch–Siegert Shift, Magn Reson Med, 66: 1333 - 1338 (2011)

11. Sacolick et al., Fast Spin Echo Bloch-Siegert B1 Mapping, Proc 19th Annual Meeting ISMRM, Montreal: 2927 (2011)

GABA

Older protocols (and sequences):

The CNI GABA spectroscopy MEGA PRESS protocol (CNI 32ch Participant GABA Spectroscopy) (located in CNI/Head), which can be run independently or added to an fMRI protocol.

There is now also the CNI-PRESS-SPECIAL (located in CNI/Head) protocol for GABA data collection, which can be run independently or added to an fMRI protocol. This is the latest protocol and the one to use.

Key Parameters for sequences:

This section (in the process of being updated) includes:

• parameters that require adjustment or checking prior to collecting spectroscopy data.
• additional setup sequences prior to running the spectroscopy sequence (example - shims) with setup details.

PRESS1

PRESS2

SPECIAL1

SPECIAL2

SPECIAL3

SPECIAL4

SPECIAL5

SPECIAL6

SPECIAL7

Automated voxel placement tools:

Typically MRS data is collected within a single voxel that needs to be manually prescribed. Manual prescription can lead to systematic bias and low data quality that may be caused by inexperienced users or inter-individual placement variability. To avoid these issues, and improve data collection quality, Matthew Sacchet has developed an automated voxel placement tool. It uses non-linear warping between native subject space and template space to identify precise voxel locations in scanner space. The tool is used in real-time during data acquisition and has been streamlined for efficient usage and low time cost.

Review papers of MRS of GABA:

In vivo magnetic resonance spectroscopy of GABA: A methodological review Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60, January 2012, Pages 29-41, Nicolaas A. J. Puts, Richard A. E. Edden

Current practice in the use of MEGA-PRESS spectroscopy for the detection of GABA NeuroImage Volume 86, 1 February 2014, Pages 43–52, Paul G. Mullins, David J. McGonigle, Ruth L. O'Gormand, Nicolaas A.J. Puts, Rishma Vidyasagar, C. John Evans, Cardiff Symposium on MRS of GABA, Richard A.E. Edden

Methods Papers for the detection of GABA:

Localized 1H NMR measurements of gamma-aminobutyric acid in human brain in vivo Proc. Natl. Acad. Sci. USA Vol.90, pp.5662-5666 June 1993 D L Rothman, O A Petroff, K L Behar, and R H Mattson

Simultaneous in vivo spectral editing and water suppression NMR in Biomedicine Vol 11 Issue 6 pp.266-272 October 1998 M. Mescher, H. Merkle, J. Kirsch, M. Garwood and R. Gruetter

Brain GABA editing without macromolecule contamination Magnetic Resonance in Medicine Volume 45 Issue 3 pp.517-520 March 2001 Pierre-Gilles Henry, Caroline Dautry, Philippe Hantraye and Gilles Bloch

Efficient γ-aminobutyric acid editing at 3T without macromolecule contamination: MEGA-SPECIAL NMR in Biomedicine Volume 24 Issue 10 pp.1277-1285 December 2011 Jamie Near, Robin Simpson, Philip Cowen and Peter Jezzard

Macromolecule-suppressed GABA-edited magnetic resonance spectroscopy at 3T Magnetic Resonance in Medicine 68:657-661 (2012) Richard A. E. Edden, Nicolaas A. J. Puts and Peter B. Barker

Spectral-editing measurements of GABA in the human brain with and without macromolecule suppression Magnetic Resonance in Medicine Volume 74, Issue 6, pages 1523–1529, December 2015 Ashley D. Harris, Nicolaas A.J. Puts, Peter B. Barker and Richard A.E. Edden

Data Collection and Analysis of GABA MRS:

Subtraction artifacts and frequency (Mis-)alignment in J-difference GABA editing JOURNAL OF MAGNETIC RESONANCE IMAGING 38:970–975 (2013) C. John Evans, Nicolaas A.J. Puts, Sian E. Robson, Frederic Boy,David J. McGonigle, Petroc Sumner, Krish D. Singh, and Richard A.E. Edden

Long-term reproducibility of GABA Magnetic Resonance Spectroscopy Neuroimage Volume 99 October 2014 Pages 191–196 Jamie Near, Yi-Ching Lynn Hoc, Kristian Sandberg, Chathura Kumaragamage, Jakob Udby Blicher

Impact of frequency drift on gamma-aminobutyric acid-edited MR spectroscopy Magnetic Resonance in Medicine 72:941–948 (2014) Ashley D. Harris, Benjamin Glaubitz, Jamie Near, C. John Evans, Nicolaas A.J. Puts, Tobias Schmidt-Wilcke, Martin Tegenthoff, Peter B. Barker, Richard A.E. Edden

Tissue correction for GABA-edited MRS: Considerations of voxel composition, tissue segmentation, and tissue relaxations. J Magn Reson Imaging 2015 Nov;42(5):1431-40 Ashley D. Harris, Nicolaas A.J. Puts, and Richard A.E. Edden

Gannet: A Batch-Processing Tool for the Quantitative Analysis of Gamma-Aminobutyric Acid-Edited MR Spectroscopy Spectra J Magn Reson Imaging (2014) 40,1445-1452, Richard Edden, Nicolaas A.J. Puts, Ashley D. Harris, Peter Barker, and C. John Evans

Applications Papers:

Learning Studies:

Local GABA Concentration Predicts Perceptual Improvements After Repetitive Sensory Stimulation in Humans Cerebral Cortex, 2015, 1–7 Stefanie Heba1, Nicolaas A. J. Puts, Tobias Kalisch, Benjamin Glaubitz1, Lauren M. Haag, Melanie Lenz, Hubert R. Dinse, Richard A. E. Edden, Martin Tegenthoff and Tobias Schmidt-Wilcke

Aging Related Studies:

Edited magnetic resonance spectroscopy detects an age-related decline in brain GABA levels NeuroImage Volume 78, September 2013, Pages 75–82 Fei Gaoa, Richard A.E. Edden, Muwei Li, Nicolaas A.J. Puts, Guangbin Wang, Cheng Liu, Bin Zhao, Huiquan Wang, Xue Bai, Chen Zhao, Xin Wang, Peter B. Barker

Autism Studies:

GABA estimation in the brains of children on the autism spectrum: Measurement precision and regional cortical variation NeuroImage Volume 86, 1 February 2014, Pages 1–9, W. Gaetz, L. Bloy, D.J. Wang, R.G. Port, L. Blaskey, S.E. Levy, T.P.L. Roberts

Decreased left perisylvian GABA concentration in children with autism and unaffected siblings NeuroImage Volume 86, 1 February 2014, Pages 28–34 Donald C. Rojas, Debra Singel, Sarah Steinmetz, Susan Hepburn, Mark S. Brown

Tourette Syndrome:

Reduced GABAergic inhibition and abnormal sensory symptoms in children with Tourette syndrome Journal of Neurophysiology Published 1 August 2015 Vol. 114 no. 2, 808-817 Nicolaas A. J. Puts, Ashley D. Harris, Deana Crocetti, Carrie Nettles, Harvey S. Singer, Mark Tommerdahl, Richard A. E. Edden, Stewart H. Mostofsky

Motor-cortical plasticity:

Magnetic Resonance Spectroscopy as a tool to study the role of GABA in motor-cortical plasticity NeuroImage 86 (2014) 19–27, Charlotte J. Stagg

(2) Analysis of GABA Data collected with the MEGA-PRESS sequence and using a compiled version of Gannet on your own machine with docker application

Download the docker application - home page (https://www.docker.com/ www.docker.com), links for downloading are here (https://www.docker.com/products/docker#/ www.docker.com/products/docker#) Compiled code is here (https://hub.docker.com/r/huawu02/gannet/) Data analysis is currently done via a terminal interface - Instructions for this are in progress.

(3) Analysis of MEGA-PRESS data with SMAL

To analyze the data from MEGA-PRESS experiments, an older processing package is here the Stanford MRS Analysis Library (SMAL) Use the navigation bar on the right hand side of the landing page to explore processing options.

(4) Typically metabolites identified using MRS are primarily localized to grey matter. Because of this, it is desirable to know how much of a given MRS voxel includes grey matter. This information can then be included in regressions to control for inter-individual differences in voxel gray matter content. Matthew Sacchet has developed a segmentation protocol for the precise quantification of gray, white, and CSF proportions of the MRS voxel.