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Tools, Sequences and Datasets

​​​​​​​​I​​f you are developing or supplying tools, seqeunces or datasets to WIN 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 WIN Protocols Database: https://open.win.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.

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.

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.

Multiband sequence

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. 

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

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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