CMRR Spectroscopy Package

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The CMRR Spectroscopy Package contains spectroscopy and shimming sequences, and the accompanying reconstructions developed at the CMRR. This package is now available for use at other institutions on compatible Siemens scanners by C2P agreement with CMRR and Siemens.

The spectroscopy package contains following sequences:

  • actively developed as collaboration between Edward J. Auerbach and Małgorzata Marjańska:
    • LASER (SVS and CSI): Fully-adiabatic (B1 -insensitive) excitation and refocusing.
      • SEMI-LASER (SVS and CSI): Adiabatic refocusing, conventional sinc excitation.
      • MEGA-SEMI-LASER (SVS and CSI): SEMI-LASER with MEGA spectral editing.
    • PRESS (SVS and 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).
    • FAST(EST)MAP: Automatic 1st  and 2nd order shimming using 2D projections.
  • actively developed as collaboration between Gülin Öz and Dinesh Deelchand:
    • SEMI-LASER (SVS): described in Öz and Tkáč, MRM, 2011; 65: 901.

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 and 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 and fat suppression
  • User-defined RF pulse durations (all variants) and R factors (LASER/SEMI-LASER only)
  • User-defined gradient ramp times and 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

To obtain sequences: The available supported software versions are listed below. If you are interested in obtaining these sequences, please download a template of the authorization form (L083 Global_C2P_20130826_UMN_MRS_final.docx) and obtain authorization from your Siemens Regional Collaboration Manager. Please send completed authorization form to either Małgorzata Marjańska or Gülin Öz, who will send you instructions on how to complete the licensing agreement with the University of Minnesota. Once you have executed a C2P agreement and have been given an access password, the sequence binaries can be downloaded here by selecting the desired release number.

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.

Note to users: If you have noticed a bug or have a request for a new feature in a future releases of:

Be sure to include the sequence variant, syngo version, and the model of scanner you are using when describing the problem.

 

Download Sequences:

Spectroscopy Release 2016-06
Contact person: Małgorzata Marjańska
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
Contact person: Małgorzata Marjańska
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)

 

SEMI-LASER (MRM 2011) Release 2016-12
Contact person: Dinesh Deelchand
Released December 2016
Release 2016-12 for VB15ClinScan (build 15-Jun-2015)
Release 2016-12 for VB17A (build 24-Sep-2015)
Release 2016-12 for VB19A (build 24-Oct-2016)
Release 2016-12 for VB20P (build 14-Jul-2015)
Release 2016-12 for VD13A (build 22-Sep-2015)
Release 2016-12 for VD13B (build 07-Dec-2015)
Release 2016-12 for VD13D (build 28-Mar-2015)
Release 2016-12 for VE11A (build 05-Dec-2016)
Release 2016-12 for VE11B (build 05-Oct-2016)
Release 2016-12 for VE11C (build 05-Sep-2016)

 

FASTMAP Release 2016-02
Contact person: Małgorzata Marjańska
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
Contact person: Małgorzata Marjańska
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;25:332-9. [PubMed]

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

  3. Tremblay S, Beaulé V, Proulx S, Lafleur LP, Doyon J, Marjańska M, Théoret H. The use of magnetic resonance spectroscopy as a tool for the measurement of bi-hemispheric transcranial electric stimulation effects on primary motor cortex metabolism. J Vis Exp 2014;93,e51631. [PubMed]

  4. 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;28:201-9. [PubMed]

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

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

  7. 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;41:649-56. [PubMed]

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

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

  10. Öz G, Tkáč I. Short-echo, single-shot, full-intensity proton magnetic resonance spectroscopy for neurochemical profiling at 4 T: validation in the cerebellum and brainstem. Magn Reson Med. 2011;65:901-10. [PubMed]