CMRR Spectroscopy Package

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.

If you are looking for the MRSpa Spectroscopy Analysis package, please see this page instead.

The spectroscopy package contains the following sequences:

1. Actively developed as collaboration between Edward J. Auerbach and Małgorzata Marjańska:
   • LASER (SVS and CSI): Fully-adiabatic (B₁-insensitive) excitation and refocusing^[5,11].
     • SEMI-LASER (SVS and CSI): Adiabatic refocusing, conventional sinc excitation^[2].
     • 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^[3,4].
   • STEAM (SVS): Optional ultra-short echo time STEAM (using asymmetric RF pulses)^[7].
   • FAST(EST)MAP: Automatic 1^st  and 2^nd order shimming using 2D projections^[8].
2. Actively developed as collaboration between Gülin Öz and Dinesh Deelchand:
   • SEMI-LASER (SVS): Compact short TE sLASER with interleaved adiabatic refocusing, optimized gradient scheme and 3D OVS, described in ^{[10, 12]}; harmonized across vendors ^[12].

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
• Automatic 3D OVS (not enabled for LASER, 1D only for SEMI-LASER^[2])
• 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
• Automatic calibration of reference voltage and water suppression flip angle (SEMI-LASER^{[10, 12]} only)
• Option to acquire water reference and metabolite scans in one protocol (separate DICOM with noise reference - all sequences; single DICOM - SEMI-LASER^{[10, 12]} only)
• Option to measure macromolecules using inversion-recovery technique
• 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 contact your Siemens Regional Collaboration Manager for authorization. Please ask them to use the following text in the agreement: "developed by Drs. Małgorzata Marjańska and Gülin Öz, and their colleagues (“DEVELOPER”), employees of the University of Minnesota." If you are experiencing any delays working with your Siemens Regional Collaboration Manager please contact Colin Giambrone (colin.giambrone@siemens-healthineers.com).

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.

Acknowledgement: If you publish or present results obtained using the pulse sequences in this package, please acknowledge the researchers who developed the sequences using the following language:

The MRS package was developed by ____________ (Gülin Öz and Dinesh Deelchand for the semi-LASER sequence described in ^{[10, 12]}; Edward J. Auerbach and Małgorzata Marjańska for all other sequences) and provided by the University of Minnesota under a C2P agreement.

In addition, please cite the references associated with each sequence above.

Bug reports and feature requests: If you have noticed a bug or have a request for a new feature in a future release, please contact the person listed below. Be sure to include the sequence variant, syngo version, and the model of scanner you are using when describing the issue.

• SEMI-LASER sequence described in ^{[10, 12]}: Dinesh Deelchand
• All other sequences: Małgorzata Marjańska

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 Sequences:

Spectroscopy Release 2017-07 "Tokyo" Contact person: Małgorzata Marjańska

Released 14 July 2017 Updated 26 February 2020 Release Notes 2017-07.2

Release 2017-07.1 for VB17A (build 27-Feb-2020) Release 2017-07 for VB17A-Step2.3/F37 (8Tx/16Tx F37-F40) (build 8-Oct-2018) Release 2017-07 for VB19A (build 14-Jul-2017) Release 2017-07.1 for VB19B-SP02 (build 3-Mar-2021) Release 2017-07 for VB20P (build 14-Jul-2017) Release 2017-07 for VD11D (build 21-Jul-2017) Release 2017-07 for VD13A (SP4 and newer) (build 21-Jul-2017) Release 2017-07 for VD13D (build 14-Jul-2017) Release 2017-07 for VE11A (build 24-Jul-2017) Release 2017-07 for VE11B (build 25-Jul-2017) Release 2017-07.2 for VE11C (build 2-Apr-2021) Release 2017-07.2 for VE11E (build 2-Apr-2021) Release 2017-07 for VE11K (build 29-Nov-2017) Release 2017-07 for VE11P (build 13-Jul-2017) Release 2017-07 for VE11P-SP04 (build 26-Jul-2020) Release 2017-07 for VE11R (build 25-Jul-2017) Release 2017-07 for VE11U (build 29-Nov-2017) Release 2017-07.2 for VE12U (build 2-Apr-2021) Release 2017-07.2 for VE12U-SP01 (build 1-Apr-2021) Release 2017-07.2 for VE12U-AP01-F50 (build 2-Apr-2021) Release 2017-07.2 for VE12U-AP02-F23 (build 7-Sep-2021) Release 2017-07.2 for XA20A (build 27-Apr-2023) Release 2017-07.2 for XA30A (build 1-Dec-2022) Release 2017-07.2 for XA31A (build 27-Apr-2023) Release 2017-07.2 for XA50A (build 27-Apr-2023) Release 2017-07.2 for XA60A (build 26-Apr-2024) Release 2017-07.2 for XA61A (build 26-Apr-2024)

 

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 VD13B (build 18-Sep-2014) Release 2014-09 for VD13C-SP2 (build 18-Sep-2014)

 

SEMI-LASER (MRM 2011, NMB 2019) Release 2016-12 Contact person: Dinesh Deelchand
Released December 2016 User guide (VD, VE)	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)
Released July 2017	Release 2017-07 for VE11P (build 06-Jul-2017) Release 2017-07 for VE12U-SP01 (build 08-Jun-2021)
Released August 2022	Release 2022-08 for VE11E (build 8-Aug-2022) Release 2022-08 for VE11C (build 8-Aug-2022)

 

FASTMAP Release 2016-02 Contact person: Małgorzata Marjańska

Released 5 February 2016

Release 2016-02 for VB17A-Step2.3/F37 (8Tx/16Tx F37-F40) (build 19-Oct-2017) Release 2016-02 for VB19B-SP02 (build 3-Mar-2021) Release 2016-02 for VD11D (build 19-Jun-2020) 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 2-Apr-2021) Release 2016-02 for VE11E (build 2-Apr-2021) Release 2016-02 for VE11K (build 18-Jan-2018) Release 2016-02 for VE11P (build 27-Sep-2017) Release 2016-02 for VE11P-SP04 (build 26-Jul-2020) Release 2016-02 for VE11R (build 18-Jan-2018) Release 2016-02 for VE11U (build 18-Jan-2018) Release 2016-02 for VE12U (build 2-Apr-2021) Release 2016-02 for VE12U-SP01 (build 1-Apr-2021) Release 2016-02 for VE12U-AP01-F50 (build 2-Apr-2021) Release 2016-02 for VE12U-AP02-F23 (build 7-Sep-2021) Release 2016-02 for XA20A (build 27-Apr-2023) Release 2016-02 for XA30A (build 1-Dec-2022) Release 2016-02 for XA31A (build 27-Apr-2023) Release 2016-02 for XA50A (build 27-Apr-2023) Release 2016-02 for XA60A (build 22-May-2024) Release 2016-02 for XA61A (build 21-May-2024)

 

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 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. Tkáč 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, Tkáč 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]

11. Allaïli N, Valabrègue R, Auerbach EJ, Guillemot V, Yahia-Cherif L, Bardinet E, Jabourian M, Fossati P, Lehéricy S, Marjańska M. Single-voxel ¹H spectroscopy in the human hippocampus at 3 T using the LASER sequence: characterization of neurochemical profile and reproducibility. NMR Biomed 2015;28(10):1209-1217. [PubMed]

12. Deelchand DK, Berrington A, Noeske R, Joers JM, Arani A, Gillen J, Schär M, Nielsen JF, Peltier S, Seraji-Bozorgzad N, Landheer K, Juchem C, Soher BJ, Noll DC, Kantarci K, Ratai EM, Mareci TH, Barker PB, Öz G. Across-vendor standardization of semi-LASER for single voxel MRS at 3 Tesla. NMR Biomed 2019;doi: 10.1002/nbm.4218. [PubMed]

13. Deelchand DK, Henry PG, Joers JM, Auerbach EJ, Park YW, Kara F, Ratai E, Kantarci K, Öz G. Plug-and-play advanced magnetic resonance spectroscopy. Magn Reson Med. 2022 Jun;87(6):2613-2620. doi: 10.1002/mrm.29164. Epub 2022 Jan 28. [PubMed]