CMRR Spectroscopy and FASTMAP Pulse Sequences

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The following spectroscopy & shimming sequences and tools developed at CMRR are now available for use at other institutions on compatible Siemens scanners by C2P agreement with CMRR and Siemens:

These sequences and the accompanying reconstructions are being actively developed as a collaboration between Edward J. Auerbach and Małgorzata Marjańska.

Spectroscopy Sequences Package:

  • LASER (SVS & CSI): Fully-adiabatic (B1-insensitive) excitation and refocusing.
    • SEMI-LASER (SVS & CSI): Adiabatic refocusing, conventional sinc excitation.
    • MEGA-SEMI-LASER (SVS & CSI): SEMI-LASER with MEGA spectral editing.
  • PRESS (SVS & CSI): Standard 3D localized spectroscopy with short TE (~11 ms).
    • MEGA-PRESS (SVS): PRESS with MEGA spectral editing. Optional PRESS+4.
  • STEAM (SVS): Optional ultra-short echo time STEAM (using asymmetric RF pulses).

FASTMAP Package:

  • FAST(EST)MAP: Automatic 1st and 2nd order shimming using 2D projections.

All of the above spectroscopy sequences include the following options, which can be enabled and disabled on a per-protocol basis by the user:

  • VAPOR water suppression with optimized timing and RF for 3 T & 7 T
  • Optimized channel combination for multi-channel RF coils using an integrated reference scan
  • Optional output of integrated water and noise reference scans to DICOM
  • Automatic 3D OVS (not enabled for LASER, 1D only for SEMI-LASER)
  • Dual-banded simultaneous water & fat suppression
  • User-defined RF pulse durations (all variants) & R factors (LASER/SEMI-LASER only)
  • User-defined gradient ramp times & spoiler gradient definitions
  • 3D RF pulse selection profile readout with online display
  • Optional output to DICOM of unsummed averages (for offline processing)
  • Calibration loops (for optimizing flip angles, delays, water suppression, frequency offsets, et al.) with online display
  • MEGA: interleaved editing frequencies (up to 4)
  • MEGA: optional dual-banded editing pulses with simultaneous water/fat suppression

If you are interested in obtaining these sequences, the CMRR C2P instructions and agreement can be found on the web page of the University of Minnesota Office for Technology Commercialization. Once you have executed a C2P agreement and have been given an access password, the sequence binaries can be downloaded here.

Note to users: If you have noticed a bug or have a request for a new feature in a future release, please email Małgorzata Marjańska. Be sure to include the sequence variant, syngo version, and the model of scanner you are using when describing the problem.

Security concerns: The sequences and software are developed in a firewalled environment, the web server is regularly checked for network vulnerabilities, and the downloadable files here are regularly scanned for viruses. To detect unexpected changes, the downloads available here are regularly checked remotely against baseline checksums stored on the remote machine. Also, Siemens provides virus software for their scanners. You can confirm that you have downloaded a valid version correctly by comparing a md5sum of the downloaded file with these checksums.


Download Spectroscopy Sequences:

Spectroscopy Release 2016-06
Released 15 June 2016
Release 2016-06 for VE11B (build 15-Jun-2016)
Release 2016-06 for VE11C (build 19-Oct-2016)

Spectroscopy Release 2014-09
Released 24 September 2014
Release 2014-09 for VB15A (build 18-Sep-2014)
Release 2014-09 for VB17A (build 18-Sep-2014)
Release 2014-09 for VB19A (build 20-Oct-2014)
Release 2014-09 for VB20P (build 20-Oct-2014)
Release 2014-09 for VD11D (build 18-Sep-2014)
Release 2014-09 for VD13A-SP4 (build 18-Sep-2014)
Release 2014-09 for VD13B (build 18-Sep-2014)
Release 2014-09 for VD13C-SP2 (build 18-Sep-2014)
Release 2014-09 for VD13D (build 18-Sep-2014)
Release 2014-09 for VE11A (build 1-Jun-2015)


Download FASTMAP:

FASTMAP Release 2016-02
Released 5 February 2016
Release 2016-02 for VD13D (build 5-Feb-2016)
Release 2016-02 for VE11A (build 5-Feb-2016)
Release 2016-02 for VE11B (build 5-Feb-2016)
Release 2016-02 for VE11C (build 19-Oct-2016)

FASTMAP Release 2014-09
Released 24 September 2014
Release 2014-09 for VB15A (build 18-Sep-2014)
Release 2014-09 for VB17A (build 18-Sep-2014)
Release 2014-09 for VB19A (build 20-Oct-2014)
Release 2014-09 for VB20P (build 20-Oct-2014)
Release 2014-09 for VD11D (build 18-Sep-2014)
Release 2014-09 for VD13A-SP4 (build 18-Sep-2014)
Release 2014-09 for VD13B (build 23-Sep-2014)
Release 2014-09 for VD13C-SP2 (build 18-Sep-2014)

Selected References:

  1. Marjańska M, Auerbach EJ, Valabrègue R, Van de Moortele P-F, Adriany G, Garwood M. Localized 1H NMR spectroscopy in different regions of human brain in vivo at 7 T: T2 relaxation times and concentrations of cerebral metabolites. NMR Biomed. 2012 Feb;25(2):332-9. [PubMed]

  2. Marjańska M, Lehéricy S, Valabrègue R, Popa T, Worbe Y, Russo M, Auerbach EJ, Grabli D, Bonnet C, Gallea C, Coudert M, Yahia-Cherif L, Vidailhet M, Meunier C. Brain dynamic neurochemical changes in dystonic patients: a magnetic resonance spectroscopy study. Mov Disord. 2013 Feb;28(2):201-9. [PubMed]

  3. Garwood M, DelaBarre L. The return of the frequency sweep: designing adiabatic pulses for contemporary NMR. J Magn Reson. 2001 Dec;153(2):155-77. [PubMed]

  4. Mescher M, Merkle H, Kirsch J, Garwood M, Gruetter R. Simultaneous in vivo spectral editing and water suppression. NMR Biomed. 1998 Oct;11(6):266-72. [PubMed]

  5. Tkác I, Starcuk Z, Choi IY, Gruetter R. In vivo 1H NMR spectroscopy of rat brain at 1 ms echo time. Magn Reson Med. 1999 Apr;41(4):649-56. [PubMed]

  6. Gruetter R, Tkác I. Field mapping without reference scan using asymmetric echo-planar techniques. Magn Reson Med. 2000 Feb;43(2):319-23. [PubMed]

  7. Klomp DW, Bitz AK, Heerschap A, Scheenen TW. Proton spectroscopic imaging of the human prostate at 7 T. NMR Biomed. 2009 Jun;22(5):495-501. [PubMed]

  8. Kaiser LG, Young K, Matson GB. Elimination of spatial interference in PRESS-localized editing spectroscopy. Magn Reson Med. 2007 Oct;58(4):813-8. [PubMed]



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