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% Generated by Paperpile. Check out https://paperpile.com for more information.
% BibTeX export options can be customized via Settings -> BibTeX.
@ARTICLE{Dieringer2014-qz,
title = "Rapid parametric mapping of the longitudinal relaxation time {T1}
using two-dimensional variable flip angle magnetic resonance
imaging at 1.5 Tesla, 3 Tesla, and 7 Tesla",
author = "Dieringer, Matthias A and Deimling, Michael and Santoro, Davide
and Wuerfel, Jens and Madai, Vince I and Sobesky, Jan and von
Knobelsdorff-Brenkenhoff, Florian and Schulz-Menger, Jeanette and
Niendorf, Thoralf",
abstract = "INTRODUCTION: Visual but subjective reading of longitudinal
relaxation time (T1) weighted magnetic resonance images is
commonly used for the detection of brain pathologies. For this
non-quantitative measure, diagnostic quality depends on hardware
configuration, imaging parameters, radio frequency transmission
field (B1+) uniformity, as well as observer experience.
Parametric quantification of the tissue T1 relaxation parameter
offsets the propensity for these effects, but is typically time
consuming. For this reason, this study examines the feasibility
of rapid 2D T1 quantification using a variable flip angles (VFA)
approach at magnetic field strengths of 1.5 Tesla, 3 Tesla, and 7
Tesla. These efforts include validation in phantom experiments
and application for brain T1 mapping. METHODS: T1 quantification
included simulations of the Bloch equations to correct for slice
profile imperfections, and a correction for B1+. Fast gradient
echo acquisitions were conducted using three adjusted flip angles
for the proposed T1 quantification approach that was benchmarked
against slice profile uncorrected 2D VFA and an
inversion-recovery spin-echo based reference method. Brain T1
mapping was performed in six healthy subjects, one multiple
sclerosis patient, and one stroke patient. RESULTS: Phantom
experiments showed a mean T1 estimation error of (-63$\pm$1.5)\%
for slice profile uncorrected 2D VFA and (0.2$\pm$1.4)\% for the
proposed approach compared to the reference method. Scan time for
single slice T1 mapping including B1+ mapping could be reduced to
5 seconds using an in-plane resolution of (2$\times$2) mm2, which
equals a scan time reduction of more than 99\% compared to the
reference method. CONCLUSION: Our results demonstrate that rapid
2D T1 quantification using a variable flip angle approach is
feasible at 1.5T/3T/7T. It represents a valuable alternative for
rapid T1 mapping due to the gain in speed versus conventional
approaches. This progress may serve to enhance the capabilities
of parametric MR based lesion detection and brain tissue
characterization.",
journal = "PLoS One",
volume = 9,
number = 3,
pages = "e91318",
month = mar,
year = 2014,
language = "en",
doi = {10.1371/journal.pone.0091318}
}
@ARTICLE{Stanisz2005-qg,
title = "T1, {T2} relaxation and magnetization transfer in tissue at {3T}",
author = "Stanisz, Greg J and Odrobina, Ewa E and Pun, Joseph and
Escaravage, Michael and Graham, Simon J and Bronskill, Michael J
and Henkelman, R Mark",
abstract = "T1, T2, and magnetization transfer (MT) measurements were
performed in vitro at 3 T and 37 degrees C on a variety of
tissues: mouse liver, muscle, and heart; rat spinal cord and
kidney; bovine optic nerve, cartilage, and white and gray matter;
and human blood. The MR parameters were compared to those at 1.5
T. As expected, the T2 relaxation time constants and quantitative
MT parameters (MT exchange rate, R, macromolecular pool fraction,
M0B, and macromolecular T2 relaxation time, T2B) at 3 T were
similar to those at 1.5 T. The T1 relaxation time values,
however, for all measured tissues increased significantly with
field strength. Consequently, the phenomenological MT parameter,
magnetization transfer ratio, MTR, was lower by approximately 2
to 10\%. Collectively, these results provide a useful reference
for optimization of pulse sequence parameters for MRI at 3 T.",
journal = "Magn. Reson. Med.",
doi = {10.1002/mrm.20605},
volume = 54,
number = 3,
pages = "507--512",
month = sep,
year = 2005,
language = "en"
}
@INCOLLECTION{Kluyver2016-nl,
title = "Jupyter Notebooks -- a publishing format for reproducible
computational workflows",
booktitle = "Positioning and Power in Academic Publishing: Players, Agents
and Agendas",
author = "Kluyver, Thomas and Ragan-Kelley, Benjamin and Granger, Brian
and Bussonnier, Matthias and Frederic, Jonathan and Kelley, Kyle
and Hamrick, Jessica and Grout, Jason and Corlay, Sylvain and
Ivanov, Paul and Abdalla, Safia and Willing, Carol",
publisher = "IOS Press",
doi = {10.3233/978-1-61499-649-1-87},
pages = "87--90",
year = 2016,
address = "Amsterdam, NY"
}
@ARTICLE{Barral2010-qm,
title = "A robust methodology for in vivo {T1} mapping",
author = "Barral, Jo{\"e}lle K and Gudmundson, Erik and Stikov, Nikola and
Etezadi-Amoli, Maryam and Stoica, Petre and Nishimura, Dwight G",
abstract = "In this article, a robust methodology for in vivo T(1) mapping is
presented. The approach combines a gold standard scanning
procedure with a novel fitting procedure. Fitting complex data to
a five-parameter model ensures accuracy and precision of the T(1)
estimation. A reduced-dimension nonlinear least squares method is
proposed. This method turns the complicated multi-parameter
minimization into a straightforward one-dimensional search. As
the range of possible T(1) values is known, a global grid search
can be used, ensuring that a global optimal solution is found.
When only magnitude data are available, the algorithm is adapted
to concurrently restore polarity. The performance of the new
algorithm is demonstrated in simulations and phantom experiments.
The new algorithm is as accurate and precise as the
conventionally used Levenberg-Marquardt algorithm but much
faster. This gain in speed makes the use of the five-parameter
model viable. In addition, the new algorithm does not require
initialization of the search parameters. Finally, the methodology
is applied in vivo to conventional brain imaging and to skin
imaging. T(1) values are estimated for white matter and gray
matter at 1.5 T and for dermis, hypodermis, and muscle at 1.5 T,
3 T, and 7 T.",
journal = "Magn. Reson. Med.",
volume = 64,
number = 4,
pages = "1057--1067",
month = oct,
doi = {10.1002/mrm.22497},
year = 2010,
language = "en"
}
@ARTICLE{Bottomley1984-qx,
title = "A review of normal tissue hydrogen {NMR} relaxation times and
relaxation mechanisms from 1-100 {MHz}: dependence on tissue
type, {NMR} frequency, temperature, species, excision, and age",
author = "Bottomley, P A and Foster, T H and Argersinger, R E and Pfeifer,
L M",
abstract = "The longitudinal (T1) and transverse (T2) hydrogen (1H) nuclear
magnetic resonance (NMR) relaxation times of normal human and
animal tissue in the frequency range 1-100 MHz are compiled and
reviewed as a function of tissue type, NMR frequency,
temperature, species, in vivo versus in vitro status, time after
excision, and age. The dominant observed factors affecting T1 are
tissue type and NMR frequency (V). All tissue frequency
dispersions can be fitted to the simple expression T1 = AVB in
the range 1-100 MHz, with A and B tissue-dependent constants.
This equation provides as good or better fit to the data as
previous more complex formulas. T2 is found to be multicomponent,
essentially independent of NMR frequency, and dependent mainly on
tissue type. Mean and raw values of T1 and T2 for each tissue are
tabulated and/or plotted versus frequency and the fitting
parameters A, B and the standard deviations determined to
establish the normal range of relaxation times applicable to NMR
imaging. The mechanisms for tissue NMR relaxation are reviewed
with reference to the fast exchange two state (FETS) model of
water in biological systems, and an overview of the dynamic state
of water and macromolecular hydrogen compatible with the
frequency, temperature, and multicomponent data is postulated.
This suggests that 1H tissue T1 is determined predominantly by
intermolecular (possibly rotational) interactions between
macromolecules and a single bound hydration layer, and the T2 is
governed mainly by exchange diffusion of water between the bound
layer and a free water phase. Deficiencies in measurement
techniques are identified as major sources of data
irreproducibility.",
journal = "Med. Phys.",
doi = {10.1118/1.595535},
volume = 11,
number = 4,
pages = "425--448",
year = 1984,
language = "en"
}
@article{Karakuzu2022-xq,
abstract = {NeuroLibre is a preprint server for neuroscience Jupyter Books,
blending code, visualization and narrative text into one
document. NeuroLibre archives the environment, code and data and
also implements a technical review to ensure readers can
reproduce the work. NeuroLibre offers an online platform where
readers can reproduce or modify each preprint from a web browser,
without any installation required. We hope that NeuroLibre will
contribute to usher the research community in a new area of open
and reproducible neuroscience. The preprint server is built with
open source components, and can be freely adapted to meet the
needs of other communities in the future as well.},
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},
journal = {OSF preprints},
keywords = {Communication; Open Science; Publishing; Reproducibility},
language = {en},
month = {April},
publisher = {Open Science Framework},
title = {{NeuroLibre} : A preprint server for full-fledged reproducible
neuroscience},
doi = {10.31219/osf.io/h89js},
year = {2022}
}
@ARTICLE{Cabana2015-zg,
title = "Quantitative magnetization transfer imaging\textit{made}easy
with {\textit{qMTLab}}: Software for data simulation, analysis,
and visualization",
author = "Cabana, Jean-Fran{\c c}ois and Gu, Ye and Boudreau, Mathieu and
Levesque, Ives R and Atchia, Yaaseen and Sled, John G and
Narayanan, Sridar and Arnold, Douglas L and Pike, G Bruce and
Cohen-Adad, Julien and Duval, Tanguy and Vuong, Manh-Tung and
Stikov, Nikola",
journal = "Concepts Magn. Reson. Part A Bridg. Educ. Res.",
publisher = "Wiley",
volume = "44A",
number = 5,
doi = {10.1002/cmr.a.21357},
pages = "263--277",
month = sep,
year = 2015,
keywords = "Software",
language = "en"
}
@ARTICLE{Karakuzu2022-af,
title = "Vendor-neutral sequences and fully transparent workflows improve
inter-vendor reproducibility of quantitative {MRI}",
author = "Karakuzu, Agah and Biswas, Labonny and Cohen-Adad, Julien and
Stikov, Nikola",
abstract = "PURPOSE: We developed an end-to-end workflow that starts with a
vendor-neutral acquisition and tested the hypothesis that
vendor-neutral sequences decrease inter-vendor variability of T1,
magnetization transfer ratio (MTR), and magnetization transfer
saturation-index (MTsat) measurements. METHODS: We developed and
deployed a vendor-neutral 3D spoiled gradient-echo (SPGR)
sequence on three clinical scanners by two MRI vendors. We then
acquired T1 maps on the ISMRM-NIST system phantom, as well as T1,
MTR, and MTsat maps in three healthy participants. We performed
hierarchical shift function analysis in vivo to characterize the
differences between scanners when the vendor-neutral sequence is
used instead of commercial vendor implementations. Inter-vendor
deviations were compared for statistical significance to test the
hypothesis. RESULTS: In the phantom, the vendor-neutral sequence
reduced inter-vendor differences from 8\% to 19.4\% to 0.2\% to
5\% with an overall accuracy improvement, reducing ground truth
T1 deviations from 7\% to 11\% to 0.2\% to 4\%. In vivo, we found
that the variability between vendors is significantly reduced (p
= 0.015) for all maps (T1, MTR, and MTsat) using the
vendor-neutral sequence. CONCLUSION: We conclude that
vendor-neutral workflows are feasible and compatible with
clinical MRI scanners. The significant reduction of inter-vendor
variability using vendor-neutral sequences has important
implications for qMRI research and for the reliability of
multicenter clinical trials.",
journal = "Magn. Reson. Med.",
volume = 88,
number = 3,
pages = "1212--1228",
doi = {10.1002/mrm.29292},
month = sep,
year = 2022,
keywords = "magnetization transfer; multicenter; open source; qMRI;
relaxometry; reproducibility; vendor neutral;Quantitative MRI",
language = "en"
}
@ARTICLE{Keenan2018-px,
title = "Quantitative magnetic resonance imaging phantoms: A review and
the need for a system phantom",
author = "Keenan, Kathryn E and Ainslie, Maureen and Barker, Alex J and
Boss, Michael A and Cecil, Kim M and Charles, Cecil and
Chenevert, Thomas L and Clarke, Larry and Evelhoch, Jeffrey L and
Finn, Paul and Gembris, Daniel and Gunter, Jeffrey L and Hill,
Derek L G and Jack, Jr, Clifford R and Jackson, Edward F and Liu,
Guoying and Russek, Stephen E and Sharma, Samir D and Steckner,
Michael and Stupic, Karl F and Trzasko, Joshua D and Yuan, Chun
and Zheng, Jie",
abstract = "The MRI community is using quantitative mapping techniques to
complement qualitative imaging. For quantitative imaging to reach
its full potential, it is necessary to analyze measurements
across systems and longitudinally. Clinical use of quantitative
imaging can be facilitated through adoption and use of a standard
system phantom, a calibration/standard reference object, to
assess the performance of an MRI machine. The International
Society of Magnetic Resonance in Medicine AdHoc Committee on
Standards for Quantitative Magnetic Resonance was established in
February 2007 to facilitate the expansion of MRI as a mainstream
modality for multi-institutional measurements, including, among
other things, multicenter trials. The goal of the Standards for
Quantitative Magnetic Resonance committee was to provide a
framework to ensure that quantitative measures derived from MR
data are comparable over time, between subjects, between sites,
and between vendors. This paper, written by members of the
Standards for Quantitative Magnetic Resonance committee, reviews
standardization attempts and then details the need, requirements,
and implementation plan for a standard system phantom for
quantitative MRI. In addition, application-specific phantoms and
implementation of quantitative MRI are reviewed. Magn Reson Med
79:48-61, 2018. \copyright{} 2017 International Society for
Magnetic Resonance in Medicine.",
journal = "Magn. Reson. Med.",
volume = 79,
number = 1,
pages = "48--61",
month = jan,
year = 2018,
keywords = "phantom; quality assurance; quantitative; system consistency",
language = "en",
doi = {10.1002/mrm.26982},
}
@ARTICLE{Avants2009-cw,
title = "Advanced normalization tools ({ANTS})",
author = "Avants, Brian B and Tustison, Nick and Song, Gang",
journal = "Insight J.",
volume = 2,
number = 365,
doi = {10.54294/uvnhin},
pages = "1--35",
year = 2009
}
@ARTICLE{Piechnik2010-be,
title = "Shortened Modified {Look-Locker} Inversion recovery ({ShMOLLI})
for clinical myocardial T1-mapping at 1.5 and 3 {T} within a 9
heartbeat breathhold",
author = "Piechnik, Stefan K and Ferreira, Vanessa M and Dall'Armellina,
Erica and Cochlin, Lowri E and Greiser, Andreas and Neubauer,
Stefan and Robson, Matthew D",
abstract = "BACKGROUND: T1 mapping allows direct in-vivo quantitation of
microscopic changes in the myocardium, providing new diagnostic
insights into cardiac disease. Existing methods require long
breath holds that are demanding for many cardiac patients. In
this work we propose and validate a novel, clinically applicable,
pulse sequence for myocardial T1-mapping that is compatible with
typical limits for end-expiration breath-holding in patients.
MATERIALS AND METHODS: The Shortened MOdified Look-Locker
Inversion recovery (ShMOLLI) method uses sequential inversion
recovery measurements within a single short breath-hold. Full
recovery of the longitudinal magnetisation between sequential
inversion pulses is not achieved, but conditional interpretation
of samples for reconstruction of T1-maps is used to yield
accurate measurements, and this algorithm is implemented directly
on the scanner. We performed computer simulations for 100 ms<T1 <
2.7 s and heart rates 40-100 bpm followed by phantom validation
at 1.5T and 3T. In-vivo myocardial T1-mapping using this method
and the previous gold-standard (MOLLI) was performed in 10
healthy volunteers at 1.5T and 3T, 4 volunteers with contrast
injection at 1.5T, and 4 patients with recent myocardial
infarction (MI) at 3T. RESULTS: We found good agreement between
the average ShMOLLI and MOLLI estimates for T1 < 1200 ms. In
contrast to the original method, ShMOLLI showed no dependence on
heart rates for long T1 values, with estimates characterized by a
constant 4\% underestimation for T1 = 800-2700 ms. In-vivo,
ShMOLLI measurements required 9.0 $\pm$ 1.1 s (MOLLI = 17.6 $\pm$
2.9 s). Average healthy myocardial T1 s by ShMOLLI at 1.5T were
966 $\pm$ 48 ms (mean $\pm$ SD) and 1166 $\pm$ 60 ms at 3T. In MI
patients, the T1 in unaffected myocardium (1216 $\pm$ 42 ms) was
similar to controls at 3T. Ischemically injured myocardium showed
increased T1 = 1432 $\pm$ 33 ms (p < 0.001). The difference
between MI and remote myocardium was estimated 15\% larger by
ShMOLLI than MOLLI (p < 0.04) which suffers from heart rate
dependencies for long T1. The in-vivo variability within ShMOLLI
T1-maps was only 14\% (1.5T) or 18\% (3T) higher than the MOLLI
maps, but the MOLLI acquisitions were twice longer than ShMOLLI
acquisitions. CONCLUSION: ShMOLLI is an efficient method that
generates immediate, high-resolution myocardial T1-maps in a
short breath-hold with high precision. This technique provides a
valuable clinically applicable tool for myocardial tissue
characterisation.",
journal = "J. Cardiovasc. Magn. Reson.",
volume = 12,
number = 1,
pages = "69",
month = nov,
year = 2010,
doi = {10.1186/1532-429X-12-69},
language = "en"
}
@ARTICLE{Lazari2021-oy,
title = "Can {MRI} measure myelin? Systematic review, qualitative
assessment, and meta-analysis of studies validating
microstructural imaging with myelin histology",
author = "Lazari, Alberto and Lipp, Ilona",
abstract = "Recent years have seen an increased understanding of the
importance of myelination in healthy brain function and
neuropsychiatric diseases. Non-invasive microstructural magnetic
resonance imaging (MRI) holds the potential to expand and
translate these insights to basic and clinical human research,
but the sensitivity and specificity of different MR markers to
myelination is a subject of debate. To consolidate current
knowledge on the topic, we perform a systematic review and
meta-analysis of studies that validate microstructural imaging by
combining it with myelin histology. We find meta-analytic
evidence for correlations between various myelin histology
metrics and markers from different MRI modalities, including
fractional anisotropy, radial diffusivity, macromolecular pool,
magnetization transfer ratio, susceptibility and longitudinal
relaxation rate, but not mean diffusivity. Meta-analytic
correlation effect sizes range widely, between R2 = 0.26 and R2 =
0.82. However, formal comparisons between MRI-based myelin
markers are limited by methodological variability, inconsistent
reporting and potential for publication bias, thus preventing the
establishment of a single most sensitive strategy to measure
myelin with MRI. To facilitate further progress, we provide a
detailed characterisation of the evaluated studies as an online
resource. We also share a set of 12 recommendations for future
studies validating putative MR-based myelin markers and deploying
them in vivo in humans.",
journal = "Neuroimage",
volume = 230,
pages = "117744",
month = apr,
year = 2021,
doi = {10.1016/j.neuroimage.2021.117744},
keywords = "Diffusion; Histology; MRI; Magnetization transfer;
Microstructural imaging; Myelin; Relaxometry; Validation",
language = "en"
}
@ARTICLE{Mancini2020-sv,
title = "An interactive meta-analysis of {MRI} biomarkers of myelin",
author = "Mancini, Matteo and Karakuzu, Agah and Cohen-Adad, Julien and
Cercignani, Mara and Nichols, Thomas E and Stikov, Nikola",
abstract = "Several MRI measures have been proposed as in vivo biomarkers of
myelin, each with applications ranging from plasticity to
pathology. Despite the availability of these myelin-sensitive
modalities, specificity and sensitivity have been a matter of
discussion. Debate about which MRI measure is the most suitable
for quantifying myelin is still ongoing. In this study, we
performed a systematic review of published quantitative
validation studies to clarify how different these measures are
when compared to the underlying histology. We analyzed the
results from 43 studies applying meta-analysis tools, controlling
for study sample size and using interactive visualization
(https://neurolibre.github.io/myelin-meta-analysis). We report
the overall estimates and the prediction intervals for the
coefficient of determination and find that MT and
relaxometry-based measures exhibit the highest correlations with
myelin content. We also show which measures are, and which
measures are not statistically different regarding their
relationship with histology.",
journal = "Elife",
volume = 9,
month = oct,
doi = {10.55458/neurolibre.00004},
year = 2020,
keywords = "MRI; brain; central nervous system; histology; human;
meta-analysis; mouse; myelin; neuroscience; rat;Myelin",
language = "en"
}
@ARTICLE{Pykett1978-mk,
title = "A line scan image study of a tumorous rat leg by {NMR}",
author = "Pykett, I L and Mansfield, P",
journal = "Phys. Med. Biol.",
volume = 23,
number = 5,
pages = "961--967",
month = sep,
year = 1978,
doi = {10.1097/00004728-197904000-00056},
language = "en"
}
@ARTICLE{Bojorquez2017-xh,
title = "What are normal relaxation times of tissues at 3 T?",
author = "Bojorquez, Jorge Zavala and Bricq, St{\'e}phanie and Acquitter,
Clement and Brunotte, Fran{\c c}ois and Walker, Paul M and
Lalande, Alain",
abstract = "The T1 and T2 relaxation times are the basic parameters behind
magnetic resonance imaging. The accurate knowledge of the T1 and
T2 values of tissues allows to perform quantitative imaging and
to develop and optimize magnetic resonance sequences. A vast
extent of methods and sequences has been developed to calculate
the T1 and T2 relaxation times of different tissues in diverse
centers. Surprisingly, a wide range of values has been reported
for similar tissues (e.g. T1 of white matter from 699 to 1735ms
and T2 of fat from 41 to 371ms), and the true values that
represent each specific tissue are still unclear, which have
deterred their common use in clinical diagnostic imaging. This
article presents a comprehensive review of the reported
relaxation times in the literature in vivo at 3T for a large span
of tissues. It gives a detailed analysis of the different methods
and sequences used to calculate the relaxation times, and it
explains the reasons of the spread of reported relaxation times
values in the literature.",
journal = "Magn. Reson. Imaging",
volume = 35,
pages = "69--80",
month = jan,
year = 2017,
doi = {10.1016/j.mri.2016.08.021},
keywords = "3 tesla; Relaxation times; T(1); T(2)",
language = "en"
}
@BOOK{Seiberlich2020-xe,
title = "Quantitative Magnetic Resonance Imaging",
author = "Seiberlich, Nicole and Gulani, Vikas and Campbell, Adrienne and
Sourbron, Steven and Doneva, Mariya Ivanova and Calamante,
Fernando and Hu, Houchun Harry",
abstract = "Quantitative Magnetic Resonance Imaging is a `go-to' reference
for methods and applications of quantitative magnetic resonance
imaging, with specific sections on Relaxometry, Perfusion, and
Diffusion. Each section will start with an explanation of the
basic techniques for mapping the tissue property in question,
including a description of the challenges that arise when using
these basic approaches. For properties which can be measured in
multiple ways, each of these basic methods will be described in
separate chapters. Following the basics, a chapter in each
section presents more advanced and recently proposed techniques
for quantitative tissue property mapping, with a concluding
chapter on clinical applications. The reader will learn: The
basic physics behind tissue property mapping How to implement
basic pulse sequences for the quantitative measurement of tissue
properties The strengths and limitations to the basic and more
rapid methods for mapping the magnetic relaxation properties T1,
T2, and T2* The pros and cons for different approaches to
mapping perfusion The methods of Diffusion-weighted imaging and
how this approach can be used to generate diffusion tensor maps
and more complex representations of diffusion How flow,
magneto-electric tissue property, fat fraction, exchange,
elastography, and temperature mapping are performed How fast
imaging approaches including parallel imaging, compressed
sensing, and Magnetic Resonance Fingerprinting can be used to
accelerate or improve tissue property mapping schemes How tissue
property mapping is used clinically in different organs
Structured to cater for MRI researchers and graduate students
with a wide variety of backgrounds Explains basic methods for
quantitatively measuring tissue properties with MRI - including
T1, T2, perfusion, diffusion, fat and iron fraction,
elastography, flow, susceptibility - enabling the implementation
of pulse sequences to perform measurements Shows the limitations
of the techniques and explains the challenges to the clinical
adoption of these traditional methods, presenting the latest
research in rapid quantitative imaging which has the possibility
to tackle these challenges Each section contains a chapter
explaining the basics of novel ideas for quantitative mapping,
such as compressed sensing and Magnetic Resonance
Fingerprinting-based approaches",
publisher = "Academic Press",
month = nov,
year = 2020,
keywords = "Books;Quantitative MRI",
language = "en"
}
@ARTICLE{Lee2019-ei,
title = "Establishing intra- and inter-vendor reproducibility of {T1}
relaxation time measurements with {3T} {MRI}",
author = "Lee, Yoojin and Callaghan, Martina F and Acosta-Cabronero, Julio
and Lutti, Antoine and Nagy, Zoltan",
abstract = "PURPOSE: Parametric imaging methods (e.g., T1 relaxation time
mapping) have been shown to be more reproducible across time and
vendors than weighted (e.g., T1 -weighted) images. The purpose
of this work was to more extensively evaluate the validity of
this assertion. METHODS: Seven volunteers underwent
twice-repeated acquisitions of variable flip-angle T1 mapping,
including B1 + calibration, on a 3T Philips Achieva and 3T
Siemens Trio scanner. Intra-scanner and inter-vendor T1
variability were calculated. To determine T1 reproducibility
levels in longitudinal settings, or after changing hardware or
software, four additional data sets were acquired from two of
the participants; one participant was scanned on a different 3T
Siemens Trio scanner and another on the same 3T Philips Achieva
scanner but after a software upgrade. RESULTS: Intra-scanner
variability of voxel-wise T1 values was consistent between the
two vendors, averaging 0.7/0.7/1.3/1.4\% in white
matter/cortical gray matter/subcortical gray matter/cerebellum,
respectively. We observed, however, a systematic bias between
the two vendors of https://doi.org/10.0/7.8/8.6/10.0\%,
respectively. The T1 bias across two scanners of the same model
was greater than intra-scanner variability, although still only
at 1.4/1.0/1.9/2.3\%, respectively. A greater bias was
identified for data sets acquired before/after software upgrade
in white matter/cortical gray matter (3.6/2.7\%) whereas
variability in subcortical gray matter/cerebellum was comparable
(1.7/1.9\%). CONCLUSION: We established intra- and inter-vendor
reproducibility levels for a widely used T1 mapping protocol. We
anticipate that these results will guide the design of
multi-center studies, particularly those encompassing multiple
vendors. Furthermore, this baseline level of reproducibility
should be established or surpassed during the piloting phase of
such studies.",
journal = "Magn. Reson. Med.",
publisher = "Wiley",
volume = 81,
number = 1,
pages = "454--465",
month = jan,
year = 2019,
keywords = "3T; T1 relaxation; bias; multi-vendor; parametric imaging;
reproducibility",
copyright = "http://onlinelibrary.wiley.com/termsAndConditions\#vor",
language = "en"
}
@MISC{Hahn1949-wf,
title = "An Accurate Nuclear Magnetic Resonance Method for Measuring
{Spin-Lattice} Relaxation Times",
author = "Hahn, Erwin L",
journal = "Physical Review",
volume = 76,
doi = {10.1103/PhysRev.76.145},
number = 1,
pages = "145--146",
year = 1949
}
@ARTICLE{Boettiger2015-vd,
title = "An introduction to Docker for reproducible research",
author = "Boettiger, Carl",
abstract = "As computational work becomes more and more integral to many
aspects of scientific research, computational reproducibility
has become an issue of increasing importance to computer systems
researchers and domain scientists alike. Though computational
reproducibility seems more straight forward than replicating
physical experiments, the complex and rapidly changing nature of
computer environments makes being able to reproduce and extend
such work a serious challenge. In this paper, I explore common
reasons that code developed for one research project cannot be
successfully executed or extended by subsequent researchers. I
review current approaches to these issues, including virtual
machines and workflow systems, and their limitations. I then
examine how the popular emerging technology Docker combines
several areas from systems research - such as operating system
virtualization, cross-platform portability, modular re-usable
elements, versioning, and a 'DevOps' philosophy, to address
these challenges. I illustrate this with several examples of
Docker use with a focus on the R statistical environment.",
journal = "Oper. Syst. Rev.",
publisher = "Association for Computing Machinery",
volume = 49,
number = 1,
pages = "71--79",
month = jan,
year = 2015,
doi = {10.1145/2723872.2723882},
address = "New York, NY, USA"
}
@ARTICLE{Sled2001-fz,
title = "Quantitative imaging of magnetization transfer exchange and
relaxation properties in vivo using {MRI}",
author = "Sled, J G and Pike, G B",
abstract = "We describe a novel imaging technique that yields all of the
observable properties of the binary spin-bath model for
magnetization transfer (MT) and demonstrate this method for in
vivo studies of the human head. Based on a new model of the
steady-state behavior of the magnetization during a pulsed
MT-weighted imaging sequence, this approach yields parametric
images of the fractional size of the restricted pool, the
magnetization exchange rate, the T(2) of the restricted pool, as
well as the relaxation times in the free pool. Validated
experimentally on agar gels and samples of uncooked beef, we
demonstrate the method's application on two normal subjects and a
patient with multiple sclerosis.",
journal = "Magn. Reson. Med.",
volume = 46,
number = 5,
doi = {10.1002/mrm.1278},
pages = "923--931",
month = nov,
year = 2001,
language = "en"
}
@MISC{Deoni2003-qc,
title = "Rapid combinedT1 andT2 mapping using gradient recalled acquisition
in the steady state",
author = "Deoni, Sean C L and Rutt, Brian K and Peters, Terry M",
journal = "Magnetic Resonance in Medicine",
volume = 49,
doi = {10.1002/mrm.10407},
number = 3,
pages = "515--526",
year = 2003
}
@MISC{Merkel2014-cu,
title = "Docker: Lightweight Linux containers for consistent
development and deployment",
author = "Merkel, Dirk",
year = 2014,
howpublished = "\url{https://www.seltzer.com/margo/teaching/CS508.19/papers/merkel14.pdf}",
note = "Accessed: 2023-2-14"
}
@ARTICLE{Karakuzu2020-ul,
title = "{qMRLab}: Quantitative {MRI} analysis, under one umbrella",
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",
journal = "J. Open Source Softw.",
publisher = "The Open Journal",
volume = 5,
doi = {10.21105/joss.02343},
number = 53,
pages = "2343",
month = sep,
year = 2020,
keywords = "Software",
copyright = "http://creativecommons.org/licenses/by/4.0/"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Beg2021-ps,
title = "Using Jupyter for Reproducible Scientific Workflows",
author = "{Beg} and {Taka} and {Kluyver} and {Konovalov} and {Ragan-Kelley}
and {Thiery} and {Fangohr}",
abstract = "Literate computing has emerged as an important tool for
computational studies and open science, with growing folklore of
best practices. In this work, we report two case studies---one in
computational magnetism and another in computational
mathematics---where domain-specific software was exposed to the
Jupyter environment. This enables high level control of
simulations and computation, interactive exploration of
computational results, batch processing on HPC resources, and
reproducible workflow documentation in Jupyter notebooks. In the
first study, Ubermag drives existing computational micromagnetics
software through a domain-specific language embedded in Python.
In the second study, a dedicated Jupyter kernel interfaces with
the GAP system for computational discrete algebra and its
dedicated programming language. In light of these case studies,
we discuss the benefits of this approach, including progress
toward more reproducible and reusable research results and
outputs, notably through the use of infrastructure such as
JupyterHub and Binder.",
journal = "https://www.computer.org › csdl › magazine ›
2021/02https://www.computer.org › csdl › magazine › 2021/02",
volume = 23,
pages = "36--46",
month = mar,
year = 2021,
doi = {10.1109/MCSE.2021.3052101},
}
@INPROCEEDINGS{Project_Jupyter2018-ll,
title = "Binder 2.0 - Reproducible, interactive, sharable environments
for science at scale",
booktitle = "Proceedings of the Python in Science Conference",
author = "{Project Jupyter} and Bussonnier, Matthias and Forde, Jessica
and Freeman, Jeremy and Granger, Brian and Head, Tim and
Holdgraf, Chris and Kelley, Kyle and Nalvarte, Gladys and
Osheroff, Andrew and Pacer, M and Panda, Yuvi and Perez,
Fernando and Ragan-Kelley, Benjamin and Willing, Carol",
abstract = "Several of the design decisions and goals that went into the
development of the current generation of Binder are detailed.
Binder is an open source web service that lets users create
sharable, interactive, reproducible environments in the cloud.
It is powered by other core projects in the open source
ecosystem, including JupyterHub and Kubernetes for managing
cloud resources. Binder works with pre-existing workflows in
the analytics community, aiming to create interactive versions
of repositories that exist on sites like GitHub with minimal
extra effort needed. This paper details several of the design
decisions and goals that went into the development of the
current generation of Binder.",
publisher = "SciPy",
year = 2018,
language = "en",
conference = "Python in Science Conference",
location = "Austin, Texas",
doi = { 10.25080/Majora-4af1f417-011 }
}
@ARTICLE{Marques2013-yg,
title = "New developments and applications of the {MP2RAGE}
sequence--focusing the contrast and high spatial resolution {R1}
mapping",
author = "Marques, Jos{\'e} P and Gruetter, Rolf",
abstract = "MR structural T1-weighted imaging using high field systems (>3T)
is severely hampered by the existing large transmit field
inhomogeneities. New sequences have been developed to better cope
with such nuisances. In this work we show the potential of a
recently proposed sequence, the MP2RAGE, to obtain improved grey
white matter contrast with respect to conventional T1-w
protocols, allowing for a better visualization of thalamic nuclei
and different white matter bundles in the brain stem.
Furthermore, the possibility to obtain high spatial resolution
(0.65 mm isotropic) R1 maps fully independent of the transmit
field inhomogeneities in clinical acceptable time is
demonstrated. In this high resolution R1 maps it was possible to
clearly observe varying properties of cortical grey matter
throughout the cortex and observe different hippocampus fields
with variations of intensity that correlate with known myelin
concentration variations.",
journal = "PLoS One",
volume = 8,
number = 7,
pages = "e69294",
month = jul,
doi = {10.1371/journal.pone.0069294},
year = 2013,
language = "en"
}
@ARTICLE{Redpath1994-sb,
title = "Technical note: use of a double inversion recovery pulse sequence
to image selectively grey or white brain matter",
author = "Redpath, T W and Smith, F W",
abstract = "The design of a double inversion recovery (DIR) sequence, to
image selectively grey or white brain matter, is described.
Suitable choice of inversion times allows either cerebrospinal
fluid (CSF) and white matter to be suppressed, to image the
cortex alone, or CSF and grey matter to be suppressed, to image
the white matter. The DIR sequence was found to give clear
delineation of the cerebral cortex.",
journal = "Br. J. Radiol.",
volume = 67,
doi = {10.1259/0007-1285-67-804-1258},
number = 804,
pages = "1258--1263",
month = dec,
year = 1994,
language = "en"
}
@ARTICLE{Keenan2019-ni,
title = "Recommendations towards standards for quantitative {MRI} ({qMRI})
and outstanding needs",
author = "Keenan, Kathryn E and Biller, Joshua R and Delfino, Jana G and
Boss, Michael A and Does, Mark D and Evelhoch, Jeffrey L and
Griswold, Mark A and Gunter, Jeffrey L and Hinks, R Scott and
Hoffman, Stuart W and Kim, Geena and Lattanzi, Riccardo and Li,
Xiaojuan and Marinelli, Luca and Metzger, Gregory J and
Mukherjee, Pratik and Nordstrom, Robert J and Peskin, Adele P and
Perez, Elena and Russek, Stephen E and Sahiner, Berkman and
Serkova, Natalie and Shukla-Dave, Amita and Steckner, Michael and
Stupic, Karl F and Wilmes, Lisa J and Wu, Holden H and Zhang,
Huiming and Jackson, Edward F and Sullivan, Daniel C",
abstract = "5 Technical Efficacy: Stage 5 J. Magn. Reson. Imaging 2019.",
journal = "J. Magn. Reson. Imaging",
volume = 49,
number = 7,
pages = "e26--e39",
month = jun,
year = 2019,
doi = {10.1002/jmri.26598},
keywords = "phantom; quantitative MRI; reference objects; standards;
validation",
language = "en"
}
@ARTICLE{Stupic2021-hu,
title = "A standard system phantom for magnetic resonance imaging",
author = "Stupic, Karl F and Ainslie, Maureen and Boss, Michael A and
Charles, Cecil and Dienstfrey, Andrew M and Evelhoch, Jeffrey L
and Finn, Paul and Gimbutas, Zydrunas and Gunter, Jeffrey L and
Hill, Derek L G and Jack, Clifford R and Jackson, Edward F and
Karaulanov, Todor and Keenan, Kathryn E and Liu, Guoying and
Martin, Michele N and Prasad, Pottumarthi V and Rentz, Nikki S
and Yuan, Chun and Russek, Stephen E",
abstract = "PURPOSE: A standard MRI system phantom has been designed and
fabricated to assess scanner performance, stability,
comparability and assess the accuracy of quantitative relaxation
time imaging. The phantom is unique in having traceability to the
International System of Units, a high level of precision, and
monitoring by a national metrology institute. Here, we describe
the phantom design, construction, imaging protocols, and
measurement of geometric distortion, resolution, slice profile,
signal-to-noise ratio (SNR), proton-spin relaxation times, image
uniformity and proton density. METHODS: The system phantom,
designed by the International Society of Magnetic Resonance in
Medicine ad hoc committee on Standards for Quantitative MR, is a
200 mm spherical structure that contains a 57-element fiducial
array; two relaxation time arrays; a proton density/SNR array;
resolution and slice-profile insets. Standard imaging protocols
are presented, which provide rapid assessment of geometric
distortion, image uniformity, T1 and T2 mapping, image
resolution, slice profile, and SNR. RESULTS: Fiducial array
analysis gives assessment of intrinsic geometric distortions,
which can vary considerably between scanners and correction
techniques. This analysis also measures scanner/coil image
uniformity, spatial calibration accuracy, and local volume
distortion. An advanced resolution analysis gives both scanner
and protocol contributions. SNR analysis gives both temporal and
spatial contributions. CONCLUSIONS: A standard system phantom is
useful for characterization of scanner performance, monitoring a
scanner over time, and to compare different scanners. This type
of calibration structure is useful for quality assurance,
benchmarking quantitative MRI protocols, and to transition MRI
from a qualitative imaging technique to a precise metrology with
documented accuracy and uncertainty.",
journal = "Magn. Reson. Med.",
volume = 86,
number = 3,
pages = "1194--1211",
doi = {10.1002/mrm.28779},
month = sep,
year = 2021,
keywords = "MRI standards; phantom; quality assurance; quantitative MRI",
language = "en"
}
% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Captur2016-xn,
title = "A medical device-grade {T1} and {ECV} phantom for global {T1}
mapping quality assurance-the {T1} Mapping and {ECV}
Standardization in cardiovascular magnetic resonance ({T1MES})
program",
author = "Captur, Gabriella and Gatehouse, Peter and Keenan, Kathryn E and
Heslinga, Friso G and Bruehl, Ruediger and Prothmann, Marcel and
Graves, Martin J and Eames, Richard J and Torlasco, Camilla and
Benedetti, Giulia and Donovan, Jacqueline and Ittermann, Bernd
and Boubertakh, Redha and Bathgate, Andrew and Royet, Celine and
Pang, Wenjie and Nezafat, Reza and Salerno, Michael and Kellman,
Peter and Moon, James C",
abstract = "BACKGROUND: T1 mapping and extracellular volume (ECV) have the
potential to guide patient care and serve as surrogate end-points
in clinical trials, but measurements differ between
cardiovascular magnetic resonance (CMR) scanners and pulse
sequences. To help deliver T1 mapping to global clinical care, we
developed a phantom-based quality assurance (QA) system for
verification of measurement stability over time at individual
sites, with further aims of generalization of results across
sites, vendor systems, software versions and imaging sequences.
We thus created T1MES: The T1 Mapping and ECV Standardization
Program. METHODS: A design collaboration consisting of a
specialist MRI small-medium enterprise, clinicians, physicists
and national metrology institutes was formed. A phantom was
designed covering clinically relevant ranges of T1 and T2 in
blood and myocardium, pre and post-contrast, for 1.5 T and 3 T.
Reproducible mass manufacture was established. The device
received regulatory clearance by the Food and Drug Administration
(FDA) and Conformit{\'e} Europ{\'e}ene (CE) marking. RESULTS: The
T1MES phantom is an agarose gel-based phantom using nickel
chloride as the paramagnetic relaxation modifier. It was
reproducibly specified and mass-produced with a rigorously
repeatable process. Each phantom contains nine differently-doped
agarose gel tubes embedded in a gel/beads matrix. Phantoms were
free of air bubbles and susceptibility artifacts at both field
strengths and T1 maps were free from off-resonance artifacts. The
incorporation of high-density polyethylene beads in the main gel
fill was effective at flattening the B 1 field. T1 and T2 values
measured in T1MES showed coefficients of variation of 1 \% or
less between repeat scans indicating good short-term
reproducibility. Temperature dependency experiments confirmed
that over the range 15-30 °C the short-T1 tubes were more stable
with temperature than the long-T1 tubes. A batch of 69 phantoms
was mass-produced with random sampling of ten of these showing
coefficients of variations for T1 of 0.64 $\pm$ 0.45 \% and 0.49
$\pm$ 0.34 \% at 1.5 T and 3 T respectively. CONCLUSION: The
T1MES program has developed a T1 mapping phantom to CE/FDA
manufacturing standards. An initial 69 phantoms with a
multi-vendor user manual are now being scanned fortnightly in
centers worldwide. Future results will explore T1 mapping
sequences, platform performance, stability and the potential for
standardization.",
journal = "J. Cardiovasc. Magn. Reson.",
volume = 18,
number = 1,
pages = "58",
month = sep,
doi = {10.1186/s12968-016-0280-z},
year = 2016,
keywords = "Phantom; Standardization; T1 mapping",
language = "en"
}
@ARTICLE{Bane2018-wt,
title = "Accuracy, repeatability, and interplatform reproducibility of
{T1} quantification methods used for {DCE-MRI}: Results from a
multicenter phantom study",
author = "Bane, Octavia and Hectors, Stefanie J and Wagner, Mathilde and
Arlinghaus, Lori L and Aryal, Madhava P and Cao, Yue and
Chenevert, Thomas L and Fennessy, Fiona and Huang, Wei and
Hylton, Nola M and Kalpathy-Cramer, Jayashree and Keenan, Kathryn
E and Malyarenko, Dariya I and Mulkern, Robert V and Newitt,
David C and Russek, Stephen E and Stupic, Karl F and Tudorica,
Alina and Wilmes, Lisa J and Yankeelov, Thomas E and Yen, Yi-Fei
and Boss, Michael A and Taouli, Bachir",
abstract = "PURPOSE: To determine the in vitro accuracy, test-retest
repeatability, and interplatform reproducibility of T1
quantification protocols used for dynamic contrast-enhanced MRI
at 1.5 and 3 T. METHODS: A T1 phantom with 14 samples was imaged
at eight centers with a common inversion-recovery spin-echo
(IR-SE) protocol and a variable flip angle (VFA) protocol using
seven flip angles, as well as site-specific protocols (VFA with
different flip angles, variable repetition time, proton density,
and Look-Locker inversion recovery). Factors influencing the
accuracy (deviation from reference NMR T1 measurements) and
repeatability were assessed using general linear mixed models.
Interplatform reproducibility was assessed using coefficients of
variation. RESULTS: For the common IR-SE protocol, accuracy
(median error across platforms = 1.4-5.5\%) was influenced
predominantly by T1 sample (P < 10-6 ), whereas test-retest
repeatability (median error = 0.2-8.3\%) was influenced by the
scanner (P < 10-6 ). For the common VFA protocol, accuracy
(median error = 5.7-32.2\%) was influenced by field strength (P =
0.006), whereas repeatability (median error = 0.7-25.8\%) was
influenced by the scanner (P < 0.0001). Interplatform
reproducibility with the common VFA was lower at 3 T than 1.5 T