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@incollection{Boudreau2019,
title = {Chapter 2 - Quantitative T1 and T1ρ Mapping},
editor = {Nicole Seiberlich and Vikas Gulani and Fernando Calamante and Adrienne Campbell-Washburn and Mariya Doneva and Houchun Harry Hu and Steven Sourbron},
series = {Advances in Magnetic Resonance Technology and Applications},
publisher = {Academic Press},
volume = {1},
pages = {19-45},
year = {2020},
booktitle = {Quantitative Magnetic Resonance Imaging},
issn = {2666-9099},
doi = {10.1016/B978-0-12-817057-1.00004-4},
author = {Mathieu Boudreau and Kathryn E. Keenan and Nikola Stikov},
keywords = {, , Relaxometry, Inversion recovery, Variable flip angle, VFA, DESPOT1, MP2RAGE},
abstract = {The spin-lattice relaxation time (T1) is one of the fundamental parameters of Magnetic Resonance Imaging (MRI). It characterizes the rate at which the longitudinal magnetization component recovers to its equilibrium state. T1 has been established as a sensitive biomarker for tissue characterization, and is also an important consideration in pulse sequence development and optimization. The development of T1 mapping techniques has been an active field of research since the early days of NMR, and a wide range of strategies have emerged for measuring T1, each with unique benefits and pitfalls. This chapter covers several strategies for measuring the T1 parameter. First, we introduce the inversion recovery (IR) T1 mapping technique. Limited by its long acquisition time, IR is widely used as a reference measure due to its high accuracy and robustness. The second section is on the variable flip angle (VFA, a.k.a. DESPOT1) technique, which leverages the steady-state signal sensitivity with respect to the excitation flip angles and T1. Capable of rapid 3D imaging, VFA is dependent on another quantitative MRI map, the radio-frequency transmit field (B1+, or B1). The third section presents a widely used dictionary-based T1 mapping technique, MP2RAGE. Boasting rapid acquisition and reconstruction times, MP2RAGE is a promising technique to get T1 maps used in the clinic. The final section presents an overview of spin-lattice relaxation time in the rotating frame (T1ρ) and its acquisition techniques. T1ρ is more sensitive to molecular motion in the kHz range, and has been extensively used to study the musculoskeletal system.}
}

@article{Karakuzu2020-ul,
    author = {Karakuzu, Agah and Boudreau, Mathieu and Duval, Tanguy and
Boshkovski, Tommy and Leppert, Ilana and Cabana, Jean-Fran{\c
c}ois and Gagnon, Ian and Beliveau, Pascale and Pike, G and
Cohen-Adad, Julien and Stikov, Nikola},
    copyright = {http://creativecommons.org/licenses/by/4.0/},
    doi = {10.21105/joss.02343},
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@article{Boudreau2023, 
        doi = {10.55458/neurolibre.00014}, 
        year = {2023}, 
        publisher = {NeuroLibre}, 
        author = {Mathieu Boudreau and Agah Karakuzu and Julien Cohen-Adad and Ecem Bozkurt and Madeline Carr and Marco Castellaro and Luis Concha and Mariya Doneva and Seraina Dual and Alex Ensworth and Alexandru Foias and Véronique Fortier and Refaat E. Gabr and Guillaume Gilbert and Carri K. Glide-Hurst and Matthew Grech-Sollars and Siyuan Hu and Oscar Jalnefjord and Jorge Jovicich and Kübra Keskin and Peter Koken and Anastasia Kolokotronis and Simran Kukran and Nam. G. Lee and Ives R. Levesque and Bochao Li and Dan Ma and Burkhard Mädler and Nyasha Maforo and Jamie Near and Erick Pasaye and Alonso Ramirez-Manzanares and Ben Statton and Christian Stehning and Stefano Tambalo and Ye Tian and Chenyang Wang and Kilian Weis and Niloufar Zakariaei and Shuo Zhang and Ziwei Zhao and Nikola Stikov}, 
        title = {Results of the ISMRM 2020 joint Reproducible Research & Quantitative MR study groups reproducibility challenge on phantom and human brain T1 mapping}, 
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@article{Stikov2015,
    abstract = {Purpose There are many T1 mapping methods available, each of them validated in phantoms and reporting excellent agreement with literature. However, values in literature vary greatly, with T1 in white matter ranging from 690 to 1100 ms at 3 Tesla. This brings into question the accuracy of one of the most fundamental measurements in quantitative MRI. Our goal was to explain these variations and look into ways of mitigating them. Theory and Methods We evaluated the three most common T1 mapping methods (inversion recovery, Look-Locker, and variable flip angle) through Bloch simulations, a white matter phantom and the brains of 10 healthy subjects (single-slice). We pooled the T1 histograms of the subjects to determine whether there is a sequence-dependent bias and whether it is reproducible across subjects. Results We found good agreement between the three methods in phantoms, but poor agreement in vivo, with the white matter T1 histogram peak in healthy subjects varying by more than 30\% depending on the method used. We also found that the pooled brain histograms displayed three distinct white matter peaks, with Look-Locker consistently underestimating, and variable flip angle overestimating the inversion recovery T1 values. The Bloch simulations indicated that incomplete spoiling and inaccurate B1 mapping could account for the observed differences. Conclusion We conclude that the three most common T1 mapping protocols produce stable T1 values in phantoms, but not in vivo. To improve the accuracy of T1 mapping, we recommend that sites perform in vivo validation of their T1 mapping method against the inversion recovery reference method, as the first step toward developing a robust calibration scheme. Magn Reson Med 73:514–522, 2015. © 2014 Wiley Periodicals, Inc.},
    author = {Stikov, Nikola and Boudreau, Mathieu and Levesque, Ives R. and Tardif, Christine L. and Barral, Joëlle K. and Pike, G. Bruce},
    doi = {10.1002/mrm.25135},
    eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.25135},
    journal = {Magnetic Resonance in Medicine},
    keywords = {relaxometry, T1 mapping, quantitative MRI, accuracy, precision, inversion recovery, Look-Locker, variable flip angle, B1 mapping},
    number = {2},
    pages = {514-522},
    title = {On the accuracy of T1 mapping: Searching for common ground},
    volume = {73},
    year = {2015}
}

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@misc{Karakuzu2022-nlwf,
 title={NeuroLibre : A preprint server for full-fledged reproducible neuroscience},
 url={osf.io/h89js},
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 author={Karakuzu, Agah and DuPre, Elizabeth and Tetrel, Loic and Bermudez, Patrick and Boudreau, Mathieu and Chin, Mary and Poline, Jean-Baptiste and Das, Samir and Bellec, Pierre and Stikov, Nikola},
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@article{Harding2023-conp,
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	abstract = {The Canadian Open Neuroscience Platform (CONP) takes a multifaceted approach to enabling open neuroscience, aiming to make research, data, and tools accessible to everyone, with the ultimate objective of accelerating discovery. Its core infrastructure is the CONP Portal, a repository with a decentralized design, where datasets and analysis tools across disparate platforms can be browsed, searched, accessed, and shared in accordance with FAIR principles. Another key piece of CONP infrastructure is NeuroLibre, a preprint server capable of creating and hosting executable and fully reproducible scientific publications that embed text, figures, and code. As part of its holistic approach, the CONP has also constructed frameworks and guidance for ethics and data governance, provided support and developed resources to help train the next generation of neuroscientists, and has fostered and grown an engaged community through outreach and communications. In this manuscript, we provide a high-level overview of this multipronged platform and its vision of lowering the barriers to the practice of open neuroscience and yielding the associated benefits for both individual researchers and the wider community.},
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