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Tools, Sequences and Datasets

​​​​​​​​I​​f you are developing or supplying tools, seqeunces or datasets to Centre and you want to be included on this page, or to suggest other updates, please contact stuart.clare@ndcn.ox.ac.uk​​.

Analysis tools

FSL

To quote the relevant references for FSL tools you should look in the individual tools' manual pages, and also please reference one or more of the FSL overview papers:

  • M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
  • ​S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004
  • M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012​​

Other tools

These are typically recent developments that are not yet part of, or have just been added to, FSL.  If you are using these tools you are advised to discuss their use with the developer listed below, and discuss whether co-authorship is appropriate.​

  • SWE: Longitudinal inference in collaboration with Tom Nichols​
  • PALM - any new features not citable with a paper listed in PALM references; contact Anderson Winkler if not sure​
  • Oxford_ASL/basil recent features in collaboration with Michael Chappell
  • VEMAP: VEASL analysis in collaboration with Michael Chappell
  • MMORF (registration): in collaboration with Rick Lange and Jesper Andersson
  • TIRL (histo-MRI reg): in collaboration with Istvan Huszar, Karla Miller, Mark Jenkinson
  • FSL-MRS: in collaboration with Saad Jbabdi and William Clarke
  • XTRACT: in collaboration with Saad Jbabdi, Rogier Mars, Stam Sotiropoulos
  • BIANCA recent features: in collaboration​ with Ludovica Griffanti and Mark Jenkinson​

Compute Cluster

If analysis was carried out on the BMRC clusters then the suggested form of acknowledgement is:

Analysis was carried out on the clusters at the Oxford Biomedical Research Computing (BMRC) facility and FMRIB (part of the Wellcome Centre for Integrative Neuroimaging). BMRC is a joint development between the Wellcome Centre for Human Genetics and the Big Data Institute, supported by Health Data Research UK and the NIHR Oxford Biomedical Research Centre.

 

Pulse sequences and protocols

Protocols

Referencing and usage requirements for MRI protocols are principally found in the OxCIN Protocols Database: https://open.oxcin.ox.ac.uk/protocols/ 

UK7T protocol

  • Clarke WT, Mougin O, Driver ID, Rua C, Morgan AT, Asghar M, Clare S, Francis S, Wise RG, Rodgers CT, Carpenter A, Muir M, Bowtell RW. Multi-site harmonization of 7 tesla MRI neuroimaging protocols. NeuroImage 2020; 206(116335) https://doi.org/10.1016/j.neuroimage.2019.116335.

SPECTROSCOPY (MRS)

WIN MRS sequences come from a variety of sources, and it is a condition of use for some sequences that the developer is involved.  To assist users, any study that plans to use a WIN written MRS sequence should contact william.clarke@ndcn.ox.ac.uk, both for help with selecting the appropriate sequence and analysis pipeline and so that the conditions of use can be discussed before the study starts. 

Purdue: Sequences developed by Uzay Emir

For projects using sequences developed by Uzay Emir (Purdue University), the developer must be

  1. informed of any use of his sequence in a specific project,
  2. invited to tell the researcher what citations and acknowledgements should be included, and
  3. invited to contact the authors if he desires to become more involved, which then could warrant authorship.

CMRR: Spectroscopy

Please acknowledge the use of this package as follows: “We would like to acknowledge Edward J. Auerbach, Ph.D. and Małgorzata Marjańska, Ph.D. (Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota, USA) for the development of the pulse sequences for the Siemens platform which were provided by the University of Minnesota under a C2P agreement.”  

All manuscripts, abstracts and presentations must acknowledge the receipt of the Software from the Center for Magnetic Resonance Research, University of Minnesota in the acknowledgments section. Specifically, if results obtained using the pulse sequences in this package are published or presented, the researchers who developed the sequences should be acknowledged using the following language: 

“The MRS package was developed by ____________ (Gülin Öz and Dinesh Deelchand for the semi-LASER sequence described in the Öz & Tkáč, MRM 2011 paper; Edward J. Auerbach and Małgorzata Marjańska for all other sequences) and provided by the University of Minnesota under a C2P agreement.” 

In addition, the references associated with each component of the package need to be cited, as indicated at the following webpage: https://www.cmrr.umn.edu/spectro/. 

Co-authorship (depending on involvement in the project) for development of the software for Gulin Oz and Dinesh Deelchand (when using semi-LASER MRM 2011 sequence), and Malgorzata Marjanska and Edward Auerbach (for all other sequences), is to be discussed at the time of manuscript preparation.  

For motion-corrected semi-LASER and MEGA sequences, consult Dinesh Deelchand regarding citation and co-authorship. Please cite https://doi.org/10.1002/mrm.29950  and https://doi.org/10.1002/mrm.30151. 

MGH: MRS-fMRI (hybrid spectroscopy-EPI)

First author  

EPI

CMRR: EPI and DWI

All manuscripts, abstracts and presentations must acknowledge the receipt of the Software from the University of Minnesota Center for Magnetic Resonance Research in the acknowledgments section.

In all manuscripts, abstracts, and presentations the following papers should be cited:

  • Moeller S, Yacoub E, Olman CA, Auerbach E, Strupp J, Harel N, Ugurbil K. Multiband multislice GE-EPI at 7 tesla, with 16-fold acceleration using partial parallel imaging with application to high spatial and temporal whole-brain fMRI. Magn Reson Med 2010;63(5):1144-1153.
  • Feinberg DA, Moeller S, Smith SM, Auerbach E, Ramanna S, Glasser MF, Miller KL, Ugurbil K, Yacoub E. Multiplexed Echo Planar Imaging for Sub-Second Whole Brain FMRI and Fast Diffusion Imaging. PLoS One 2010;5(12):e15710.
  • Xu, J., S. Moeller, E. J. Auerbach, J. Strupp, S. M. Smith, D. A. Feinberg, E. Yacoub and K. Ugurbil. Evaluation of slice accelerations using multiband echo planar imaging at 3 T. Neuroimage 2013;83: 991-1001. 

MGH: vNav - motion corrected and ABCD protocols

Check with Aaron Hess (aaron.hess@ndcn.ox.ac.uk)  

Recipient shall acknowledge in the publication(s) that the Software was provided to Recipient by MGH. Recipient agrees that it will not use the name or logo of MGH or any of its affiliates, or of any trustee, director, officer, staff member, employee, student or agent thereof, or any adaptation thereof in any advertisement or press release without prior written permission from MGH. 

DZNE: 3D EPI

Update who to acknowledge for specific pulse sequences 

DZNE 3D EPI: Please cite Stirnberg, R. and Stöcker, T. (2021), if you use data acquired with this sequence for your publication. We are also happy to collaborate and optimize your protocol, if we can. 

Stirnberg R., Stöcker, T. (2021). Segmented K-Space Blipped-Controlled Aliasing in Parallel Imaging for High Spatiotemporal Resolution EPI. Magnetic Resonance in Medicine. https://doi.org/10.1002/mrm.28486  

Structural Scanning

CEA: Pasture MPRAGE

Sequence name: cea_MPRAGE_UP 

If you are publishing data that have been acquired with this sequence, please cite the corresponding publication, i.e. some of the following: 

All sequences: 

Gras, V., Vignaud, A., Amadon, A., Bihan, D. and Boulant, N. (2017), `Universal pulses: A new concept for calibration free parallel transmission', Magnetic Resonance in Medicine 77(2), 635-643. 

MPRAGE: 

Gras, V., Boland, M., Vignaud, A., Ferrand, G., Amadon, A., Mauconduit, F., Le Bihan, D., Stöcker, T. and Boulant, N. (2017), `Homogeneous non-selective and slice-selective parallel-transmit excitations at 7 Tesla with universal pulses: A validation study on two commercial RF coils', PLOS ONE 12(8), e0183562. 

T2 and SPACE: 

Gras, V., Mauconduit, F., Vignaud, A., Amadon, A., Le Bihan, D., Stöcker, T. and Boulant, N. (2018), `Design of universal parallel-transmit refocusing kt-point pulses and application to 3D T 2 -weighted imaging at 7T: Universal Pulse Design of 3D Refocusing Pulses', Magnetic Resonance in Medicine 80(1), 53-65. 

Gras, V., Pracht, E. D., Mauconduit, F., Le Bihan, D., Stöcker, T. and Boulant, N. (2019), `Robust nonadiabatic T 2 preparation using universal parallel-transmit kt-point pulses for 3D FLAIR imaging at 7 T', Magnetic Resonance in Medicine 81(5), 3202-3208. 

Van Damme, L., Mauconduit, F., Chambrion, T., Boulant, N. and Gras, V. (2021),  `Universal nonselective excitation and refocusing pulses with improved robustness to off resonance for Magnetic Resonance Imaging at 7 Tesla with parallel transmission', Magnetic Resonance in Medicine 85(2), 678-693. 

Other: 

Wu, X., Gras, V., Vignaud, A., Mauconduit, F., Boland, M., Stoecker, T., Ugur- bil, K. and Boulant, N. (2018), The travelling pulses: multicenter evaluation of universal pulses at 7T., in `Proceedings of the International Society for Magnetic Resonance in Medicine', Paris, France.  

B1 Mapping

FMRIB: Sandwich B1+ map

Please reference: 

Kent et al, MRM 2022 

“Rapid 3D absolute B1+ mapping using a sandwiched train presaturated TurboFLASH sequence at 7 T for the brain and heart” 

Where multi voltage maps are used to acknowledge Matthijs H. S. de Buck and cite DOI: 10.1002/mrm.29845 

ThreeDREAM

  • Ehses et al. Whole-brain B1-mapping using three-dimensional DREAM. Magn Reson Med 2019;82:924-34. doi: 10.1002/mrm.27773.  

  • Nehrke et al. Volumetric B1+ Mapping of the Brain at 7T using DREAM. Magn Reson Med 2014;71:246-56. doi: 10.1002/mrm.24667.  

  • Nehrke and Börnert. DREAM–a novel approach for robust, ultrafast, multislice B1 mapping. Magn Reson Med 2012;68:1517-26. doi: 10.1002/mrm.24158.  

  • Brunner et al. B1(+) interferometry for the calibration of RF transmitter arrays. Magn Reson Med 2009 Jun;61(6):1480-8. doi: 10.1002/mrm.21893.   

ASL

Multi-PLD pseudocontinuous ASL with an EPI readout (with or without vessel-encoding)

Sequence/protocol names: 

    • to_ep2d_VEPCASL
    • to_ep2d_PCASL
    • to_VEPCASL_perf_ep2d_pasl_BGS_Arb_mPLD
    • to_VEPCASL_perf_ep2d_bold_BGS_inc
    • fmrib_PCASL

Reference

    • Okell, T.W., Chappell, M.A., Kelly, M.E., Jezzard, P., 2013. Cerebral blood flow quantification using vessel-encoded arterial spin labeling. J Cereb Blood Flow Metab 33, 1716–1724. https://doi.org/10.1038/jcbfm.2013.129

Multi-PLD pseudocontinuous ASL with an EPI readout with time-encoding:

​Sequence name:

    • ​jw_ep2d_VEPCASL

Usage:

    • Please contact Tom Okell to discuss before use.

​Reference:

    • Woods, J.G., Chappell, M.A., Okell, T.W., 2019. A general framework for optimizing arterial spin labeling MRI experiments. Magnetic Resonance in Medicine 81, 2474–2488. https://doi.org/10.1002/mrm.27580

Multi-PLD pseudocontinuous ASL with a 3D-GRASE readout (with or without time-encoding)

Sequence name:

    • ​​jw_tgse_VEPCASL

Usage:

    • Please contact Tom Okell to discuss before use.

Reference:

    • Woods, J.G., Chappell, M.A., Okell, T.W., 2020. Designing and comparing optimized pseudo-continuous Arterial Spin Labeling protocols for measurement of cerebral blood flow. NeuroImage 223, 117246. https://doi.org/10.1016/j.neuroimage.2020.117246

Multi-phase pseudocontinuous ASL with an EPI readout

​Sequence/protocol names:

    • OX_MPPCASL
    • to_jam_mpPCASL

Usage:

    • Please contact Tom Okell to discuss before use

​Reference:

    • Okell, T.W., Chappell, M.A., Kelly, M.E., Jezzard, P., 2013. Cerebral blood flow quantification using vessel-encoded arterial spin labeling. J Cereb Blood Flow Metab 33, 1716–1724. https://doi.org/10.1038/jcbfm.2013.129

Pseudocontinuous ASL dynamic angiography (including Combined Angiography and Perfusion using Radial Imaging and ASL [CAPRIA])

Sequence names:

    • to_CV_VEPCASL
    • to_CAPIASL_CV_nce_angio
    • to_VEPCASL_3D_CV_nce_angio

Usage:

    • Please contact Tom Okell to discuss before use​

References:

    • Okell, T.W., Chappell, M.A., Woolrich, M.W., Günther, M., Feinberg, D.A., Jezzard, P., 2010. Vessel-encoded dynamic magnetic resonance angiography using arterial spin labeling. Magn Reson Med 64, 698–706. https://doi.org/10.1002/mrm.22458
    • Okell, T.W., Schmitt, P., Bi, X., Chappell, M.A., Tijssen, R.H.N., Sheerin, F., Miller, K.L., Jezzard, P., 2016. Optimization of 4D vessel-selective arterial spin labeling angiography using balanced steady-state free precession and vessel-encoding. NMR in Biomedicine 29, 776–786. https://doi.org/10.1002/nbm.3515
    • Okell, T.W., 2019. Combined angiography and perfusion using radial imaging and arterial spin labeling. Magnetic Resonance in Medicine 81, 182–194. https://doi.org/10.1002/mrm.27366

PulseQ

MRDAC - Freibug: Pulseq

This package being a substantial commitment from our side is provided free of charge for everybody to benefit. In order to encourage the continued development of the package feel free to reference the following paper(s) in your publications:  

Layton KJ, Kroboth S, Jia F, Littin S, Yu H, Leupold J, Nielsen JF, Stocker T, Zaitsev M (2017). "Pulseq: A rapid and hardware-independent pulse sequence prototyping framework." Magn Reson Med 77(4): 1544-1552.  

Depending on the Pulseq design tool you use, you may choose to reference further works, e.g. some from the References section below.  

 

Datasets

WIN Open Data Project

Referencing and usage requirements for data from the WIN Open Data project are available on the WIN Open Science pages: https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/​​

Biobank

Studies using the Biobank data should reference:

  • Miller K, Alfaro-Almagro F, Bangerter N, Thomas DL, Yacoub E, Xu J, Bartsch AJ, Jbabdi S, Sotiropoulos SN, Andersson JLR, Griffanti L, Douaud G, Okell TW, Weale P, Dragonu I, Garratt S, Hudson S, Collins R, Jenkinson M, Matthews PM, Smith SM. Multimodal population brain imaging in the UK Biobank prospective epidemiological study. Nature Neuroscience 2016;19(1523–1536) https://doi.org/10.1038/nn.4393
  • Alfaro-Almagro F, Jenkinson M, Bangerter NK, Andersson JLR, Griffanti L, Douaud G, Sotiropoulos SN, Jbabdi S, Hernandez-Fernandez M, Vallee E, Vidaurre D, Webster M, McCarthy P, Rorden C, Daducci A, Alexander DC, Zhang H, Dragonu I, Matthews PM, Miller KL, Smith SM. Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank. Neuroimage 2018;166(400-424) https://doi.org/10.1016/j.neuroimage.2017.10.034.​

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