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@comment{% Generated by Paperpile. Check out https://paperpile.com for more information.
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@article{Avants2009-cw,
author = {Avants, Brian B and Tustison, Nick and Song, Gang},
journal = {Insight J.},
number = {365},
pages = {1--35},
title = {Advanced normalization tools ({ANTS})},
doi = {10.54294/uvnhin},
volume = {2},
year = {2009}
}
@article{Bane2018-wt,
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
(P = 0.004), and lower than that of the common IR-SE protocol
(coefficient of variation 1.5T: VFA/IR-SE = 11.13\%/8.21\%, P =
0.028; 3 T: VFA/IR-SE = 22.87\%/5.46\%, P = 0.001). Among the
site-specific protocols, Look-Locker inversion recovery and VFA
(2-3 flip angles) protocols showed the best accuracy and
repeatability (errors < 15\%). CONCLUSIONS: The VFA protocols
with 2 to 3 flip angles optimized for different applications
achieved acceptable balance of extensive spatial coverage,
accuracy, and repeatability in T1 quantification (errors < 15\%).
Further optimization in terms of flip-angle choice for each
tissue application, and the use of B1 correction, are needed to
improve the robustness of VFA protocols for T1 mapping. Magn
Reson Med 79:2564-2575, 2018. \copyright{} 2017 International
Society for Magnetic Resonance in Medicine.},
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},
doi = {10.1002/mrm.26903},
journal = {Magn. Reson. Med.},
keywords = {DCE-MRI; T1 mapping; multicenter; phantom},
language = {en},
month = {May},
number = {5},
pages = {2564--2575},
title = {Accuracy, repeatability, and interplatform reproducibility of
{T1} quantification methods used for {DCE-MRI}: Results from a
multicenter phantom study},
volume = {79},
year = {2018}
}
@article{barral,
abstract = {Abstract In this article, a robust methodology for in vivo T1 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 T1 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 T1 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. T1 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. Magn Reson Med, 2010. © 2010 Wiley-Liss, Inc.},
author = {Barral, Joëlle K. and Gudmundson, Erik and Stikov, Nikola and Etezadi-Amoli, Maryam and Stoica, Petre and Nishimura, Dwight G.},
doi = {10.1002/mrm.22497},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.22497},
journal = {Magnetic Resonance in Medicine},
keywords = {T1 mapping, relaxometry, nonlinear least squares, brain imaging, skin imaging},
number = {4},
pages = {1057-1067},
title = {A robust methodology for in vivo T1 mapping},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/mrm.22497},
volume = {64},
year = {2010}
}
@article{Barral2010-qm,
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.},
author = {Barral, Jo{\"e}lle K and Gudmundson, Erik and Stikov, Nikola and
Etezadi-Amoli, Maryam and Stoica, Petre and Nishimura, Dwight G},
doi = {10.1002/mrm.22497},
journal = {Magn. Reson. Med.},
language = {en},
month = {October},
number = {4},
pages = {1057--1067},
title = {A robust methodology for in vivo {T1} mapping},
volume = {64},
year = {2010}
}
@article{Beg2021-ps,
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.},
author = {{Beg} and {Taka} and {Kluyver} and {Konovalov} and {Ragan-Kelley}
and {Thiery} and {Fangohr}},
doi = {10.1109/MCSE.2021.3052101},
journal = {https://www.computer.org › csdl › magazine ›
2021/02https://www.computer.org › csdl › magazine › 2021/02},
month = {March},
pages = {36--46},
title = {Using Jupyter for Reproducible Scientific Workflows},
volume = {23},
year = {2021}
}
@article{Boettiger2015-vd,
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.},
address = {New York, NY, USA},
author = {Boettiger, Carl},
doi = {10.1145/2723872.2723882},
journal = {Oper. Syst. Rev.},
month = {January},
number = {1},
pages = {71--79},
publisher = {Association for Computing Machinery},
title = {An introduction to Docker for reproducible research},
volume = {49},
year = {2015}
}
@article{Bottomley1984-qx,
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.},
author = {Bottomley, P A and Foster, T H and Argersinger, R E and Pfeifer,
L M},
doi = {10.1118/1.595535},
journal = {Med. Phys.},
language = {en},
number = {4},
pages = {425--448},
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},
volume = {11},
year = {1984}
}
@incollection{Boudreau2020-jf,
author = {Boudreau, Mathieu and Keenan, Kathryn E and Stikov, Nikola},
booktitle = {Quantitative Magnetic Resonance Imaging},
month = {November},
issn = {9780128170571},
pages = {19--45},
title = {Quantitative {T1} and T1r Mapping},
doi = {10.1016/b978-0-12-817057-1.00004-4},
year = {2020}
}
@article{Cabana2015-zg,
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.},
language = {en},
month = {September},
number = {5},
pages = {263--277},
publisher = {Wiley},
title = {Quantitative magnetization transfer imaging\textit{made}easy
with {\textit{qMTLab}}: Software for data simulation, analysis,
and visualization},
doi = {10.1002/cmr.a.21357},
volume = {44A},
year = {2015}
}
@article{Captur2016-xn,
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.},
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},
doi = {10.1186/s12968-016-0280-z},
journal = {J. Cardiovasc. Magn. Reson.},
keywords = {Phantom; Standardization; T1 mapping},
language = {en},
month = {September},
number = {1},
pages = {58},
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},
volume = {18},
year = {2016}
}
@misc{Cheng2006-qe,
author = {Cheng, Hai-Ling Margaret and Wright, Graham A},
doi = {10.1002/mrm.20791},
journal = {Magnetic Resonance in Medicine},
number = {3},
pages = {566--574},
title = {Rapid high-resolutionT1 mapping by variable flip angles: Accurate
and precise measurements in the presence of radiofrequency field
inhomogeneity},
volume = {55},
year = {2006}
}
@article{Damadian1971-sc,
abstract = {Spin echo nuclear magnetic resonance measurements may be used as
a method for discriminating between malignant tumors and normal
tissue. Measurements of spin-lattice (T(1)) and spin-spin (T(2))
magnetic relaxation times were made in six normal tissues in the
rat (muscle, kidney, stomach, intestine, brain, and liver) and in
two malignant solid tumors, Walker sarcoma and Novikoff hepatoma.
Relaxation times for the two malignant tumors were distinctly
outside the range of values for the normal tissues studied, an
indication that the malignant tissues were characterized by an
increase in the motional freedom of tissue water molecules. The
possibility of using magnetic relaxation methods for rapid
discrimination between benign and malignant surgical specimens
has also been considered. Spin-lattice relaxation times for two
benign fibroadenomas were distinct from those for both malignant
tissues and were the same as those of muscle.},
author = {Damadian, R},
doi = {10.1126/science.171.3976.1151},
journal = {Science},
language = {en},
month = {March},
number = {3976},
pages = {1151--1153},
title = {Tumor detection by nuclear magnetic resonance},
volume = {171},
year = {1971}
}
@misc{Deoni2003-qc,
author = {Deoni, Sean C L and Rutt, Brian K and Peters, Terry M},
doi = {10.1002/mrm.10407},
journal = {Magnetic Resonance in Medicine},
number = {3},
pages = {515--526},
title = {Rapid combinedT1 andT2 mapping using gradient recalled acquisition
in the steady state},
volume = {49},
year = {2003}
}
@article{Dieringer2014-qz,
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.},
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},
doi = {10.1371/journal.pone.0091318},
journal = {PLoS One},
language = {en},
month = {March},
number = {3},
pages = {e91318},
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},
volume = {9},
year = {2014}
}
@article{Drain1949-yk,
abstract = {This direct method of measuring nuclear spin-lattice relaxation
times is based on Bloch's nuclear induction experiment in which
the material investigated is subjected to a magnetic field that
is varied several times per second through the value for nuclear
resonance. Under certain conditions a simple calculation may be
made of the relation between the magnitude of the nuclear
induction effect, the relaxation time, and the time intervals
between successive passages through resonance. Experimental
observation of this relation then determines the relaxation time
directly.},
author = {Drain, L E},
doi = {10.1088/0370-1298/62/5/306},
journal = {Proc. Phys. Soc. A},
language = {en},
month = {May},
number = {5},
pages = {301},
publisher = {IOP Publishing},
title = {A Direct Method of Measuring Nuclear {Spin-Lattice} Relaxation
Times},
volume = {62},
year = {1949}
}
@article{Ernst1966-pp,
abstract = {The application of a new Fourier transform technique to magnetic
resonance spectroscopy is explored. The method consists of
applying a sequence of short rf pulses to the sample to be
investigated and Fourier?transforming the response of the
system. The main advantages of this technique compared with the
usual spectral sweep method are the much shorter time required
to record a spectrum and the higher inherent sensitivity. It is
shown theoretically and experimentally that it is possible to
enhance the sensitivity of high resolution proton magnetic
resonance spectroscopy in a restricted time up to a factor of
ten or more. The time necessary to achieve the same sensitivity
is a factor of 100 shorter than with conventional methods. The
enhancement of the sensitivity is essentially given by the
square root of the ratio of line width to total width of the
spectrum. The method is of particular advantage for complicated
high resolution spectra with much fine structure.},
author = {Ernst, R R and Anderson, W A},
doi = {10.1063/1.1719961},
journal = {Rev. Sci. Instrum.},
month = {January},
number = {1},
pages = {93--102},
publisher = {American Institute of Physics},
title = {Application of Fourier Transform Spectroscopy to Magnetic
Resonance},
volume = {37},
year = {1966}
}
@article{Fram1987-jj,
abstract = {We present a method for rapid measurement of T1 relaxation times
using gradient refocused images at limited flip angles and short
repetition times. This ``variable nutation'' techniques was
investigated using a T1 phantom. There was a high correlation
between measurements obtained with the variable nutation and
partial saturation techniques. The ability of this method to
create calculated T1 images is also demonstrated. We conclude
that the variable nutation method may allow measurement of T1
relaxation times with a significant reduction in acquisition time
compared to partial saturation techniques.},
author = {Fram, E K and Herfkens, R J and Johnson, G A and Glover, G H and
Karis, J P and Shimakawa, A and Perkins, T G and Pelc, N J},
doi = {10.1016/0730-725X(87)90021-X},
journal = {Magn. Reson. Imaging},
language = {en},
number = {3},
pages = {201--208},
title = {Rapid calculation of {T1} using variable flip angle gradient
refocused imaging},
volume = {5},
year = {1987}
}
@article{Fryback1991-sy,
abstract = {The authors discuss the assessment of the contribution of
diagnostic imaging to the patient management process. A
hierarchical model of efficacy is presented as an organizing
structure for appraisal of the literature on efficacy of imaging.
Demonstration of efficacy at each lower level in this hierarchy
is logically necessary, but not sufficient, to assure efficacy at
higher levels. Level 1 concerns technical quality of the images;
Level 2 addresses diagnostic accuracy, sensitivity, and
specificity associated with interpretation of the images. Next,
Level 3 focuses on whether the information produces change in the
referring physician's diagnostic thinking. Such a change is a
logical prerequisite for Level 4 efficacy, which concerns effect
on the patient management plan. Level 5 efficacy studies measure
(or compute) effect of the information on patient outcomes.
Finally, at Level 6, analyses examine societal costs and benefits
of a diagnostic imaging technology. The pioneering contributions
of Dr. Lee B. Lusted in the study of diagnostic imaging efficacy
are highlighted.},
author = {Fryback, D G and Thornbury, J R},
doi = {10.1177/0272989X9101100203},
journal = {Med. Decis. Making},
language = {en},
number = {2},
pages = {88--94},
title = {The efficacy of diagnostic imaging},
volume = {11},
year = {1991}
}
@misc{Hahn1949-wf,
author = {Hahn, Erwin L},
doi = {10.1103/PhysRev.76.145},
journal = {Physical Review},
number = {1},
pages = {145--146},
title = {An Accurate Nuclear Magnetic Resonance Method for Measuring
{Spin-Lattice} Relaxation Times},
volume = {76},
year = {1949}
}
@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},
journal = {J. Open Source Softw.},
month = {September},
number = {53},
pages = {2343},
publisher = {The Open Journal},
title = {{qMRLab}: Quantitative {MRI} analysis, under one umbrella},
volume = {5},
year = {2020}
}
@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{Keenan2018-px,
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.},
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},
doi = {10.1002/mrm.26982},
journal = {Magn. Reson. Med.},
keywords = {phantom; quality assurance; quantitative; system consistency},
language = {en},
month = {January},
number = {1},
pages = {48--61},
title = {Quantitative magnetic resonance imaging phantoms: A review and
the need for a system phantom},
volume = {79},
year = {2018}
}
@article{Keenan2019-ni,
abstract = {5 Technical Efficacy: Stage 5 J. Magn. Reson. Imaging 2019.},
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},
doi = {10.1002/jmri.26598},
journal = {J. Magn. Reson. Imaging},
keywords = {phantom; quantitative MRI; reference objects; standards;
validation},
language = {en},
month = {June},
number = {7},
pages = {e26--e39},
title = {Recommendations towards standards for quantitative {MRI} ({qMRI})
and outstanding needs},
volume = {49},
year = {2019}
}
@article{Keenan2021-ly,
abstract = {Recent innovations in quantitative magnetic resonance imaging
(MRI) measurement methods have led to improvements in accuracy,
repeatability, and acquisition speed, and have prompted renewed
interest to reevaluate the medical value of quantitative T1. The
purpose of this study was to determine the bias and
reproducibility of T1 measurements in a variety of MRI systems
with an eye toward assessing the feasibility of applying
diagnostic threshold T1 measurement across multiple clinical
sites. We used the International Society of Magnetic Resonance in
Medicine/National Institute of Standards and Technology
(ISMRM/NIST) system phantom to assess variations of T1
measurements, using a slow, reference standard inversion recovery
sequence and a rapid, commonly-available variable flip angle
sequence, across MRI systems at 1.5 tesla (T) (two vendors, with
number of MRI systems n = 9) and 3 T (three vendors, n = 18). We
compared the T1 measurements from inversion recovery and variable
flip angle scans to ISMRM/NIST phantom reference values using
Analysis of Variance (ANOVA) to test for statistical differences
between T1 measurements grouped according to MRI scanner
manufacturers and/or static field strengths. The inversion
recovery method had minor over- and under-estimations compared to
the NMR-measured T1 values at both 1.5 T and 3 T. Variable flip
angle measurements had substantially greater deviations from the
NMR-measured T1 values than the inversion recovery measurements.
At 3 T, the measured variable flip angle T1 for one vendor is
significantly different than the other two vendors for most of
the samples throughout the clinically relevant range of T1. There
was no consistent pattern of discrepancy between vendors. We
suggest establishing rigorous quality control procedures for
validating quantitative MRI methods to promote confidence and
stability in associated measurement techniques and to enable
translation of diagnostic threshold from the research center to
the entire clinical community.},
author = {Keenan, Kathryn E and Gimbutas, Zydrunas and Dienstfrey, Andrew
and Stupic, Karl F and Boss, Michael A and Russek, Stephen E and
Chenevert, Thomas L and Prasad, P V and Guo, Junyu and Reddick,
Wilburn E and Cecil, Kim M and Shukla-Dave, Amita and Aramburu
Nunez, David and Shridhar Konar, Amaresh and Liu, Michael Z and
Jambawalikar, Sachin R and Schwartz, Lawrence H and Zheng, Jie
and Hu, Peng and Jackson, Edward F},
doi = {10.1371/journal.pone.0252966},
journal = {PLoS One},
language = {en},
month = {June},
number = {6},
pages = {e0252966},
title = {Multi-site, multi-platform comparison of {MRI} {T1} measurement
using the system phantom},
volume = {16},
year = {2021}
}
@incollection{Kluyver2016-nl,
address = {Amsterdam, NY},
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},
booktitle = {Positioning and Power in Academic Publishing: Players, Agents
and Agendas},
pages = {87--90},
publisher = {IOS Press},
doi = {10.3233/978-1-61499-649-1-87},
title = {Jupyter Notebooks -- a publishing format for reproducible
computational workflows},
year = {2016}
}
@article{Lazari2021-oy,
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.},
author = {Lazari, Alberto and Lipp, Ilona},
doi = {10.1016/j.neuroimage.2021.117744},
journal = {Neuroimage},
keywords = {Diffusion; Histology; MRI; Magnetization transfer;
Microstructural imaging; Myelin; Relaxometry; Validation},
language = {en},
month = {April},
pages = {117744},
title = {Can {MRI} measure myelin? Systematic review, qualitative
assessment, and meta-analysis of studies validating
microstructural imaging with myelin histology},
volume = {230},
year = {2021}
}
@article{Look1970-no,
abstract = {By producing a train of absorption or dispersion signals
(continuous‐wave magnetic resonance) or free induction decays
(pulsed magnetic resonance) it is possible to save time in
spin‐lattice relaxation measurements due to the fact that it is
not necessary to wait for equilibrium magnetization before
initiating the train. The relaxation time may be calculated from
the train according to a simple rapidly converging iteration.},
author = {Look, D C and Locker, D R},
doi = {10.1063/1.1684482},
journal = {Rev. Sci. Instrum.},
month = {February},
number = {2},
pages = {250--251},
publisher = {AIP Publishing},
title = {Time saving in measurement of {NMR} and {EPR} relaxation times},
volume = {41},
year = {1970}
}
@article{Mancini2020-sv,
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.},
author = {Mancini, Matteo and Karakuzu, Agah and Cohen-Adad, Julien and
Cercignani, Mara and Nichols, Thomas E and Stikov, Nikola},
doi = {10.55458/neurolibre.00004},
journal = {Elife},
keywords = {MRI; brain; central nervous system; histology; human;
meta-analysis; mouse; myelin; neuroscience; rat},
language = {en},
month = {October},
title = {An interactive meta-analysis of {MRI} biomarkers of myelin},
volume = {9},
year = {2020}
}
@misc{Marques2010-po,
author = {Marques, Jos{\'e} P and Kober, Tobias and Krueger, Gunnar and van
der Zwaag, Wietske and Van de Moortele, Pierre-Fran{\c c}ois and
Gruetter, Rolf},
doi = {10.1016/j.neuroimage.2009.10.002},
journal = {NeuroImage},
number = {2},
pages = {1271--1281},
title = {{MP2RAGE}, a self bias-field corrected sequence for improved
segmentation and T1-mapping at high field},
volume = {49},
year = {2010}
}
@article{Marques2013-yg,
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.},
author = {Marques, Jos{\'e} P and Gruetter, Rolf},
doi = {10.1371/journal.pone.0069294},
journal = {PLoS One},
language = {en},
month = {July},
number = {7},
pages = {e69294},
title = {New developments and applications of the {MP2RAGE}
sequence--focusing the contrast and high spatial resolution {R1}
mapping},
volume = {8},
year = {2013}
}
@misc{McCarthy2019-qd,
author = {McCarthy, Paul},
title = {FSLeyes},
month = may,
year = 2022,
publisher = {Zenodo},
version = {1.4.0},
doi = {10.5281/zenodo.6511596},
url = {https://doi.org/10.5281/zenodo.6511596}
}
@misc{Merkel2014-cu,
author = {Merkel, Dirk},
howpublished = {\url{https://www.seltzer.com/margo/teaching/CS508.19/papers/merkel14.pdf}},
note = {Accessed: 2023-2-14},
title = {Docker: Lightweight Linux containers for consistent
development and deployment},
year = {2014}
}
@article{Messroghli2004-iv,
abstract = {A novel pulse sequence scheme is presented that allows the
measurement and mapping of myocardial T1 in vivo on a 1.5 Tesla
MR system within a single breath-hold. Two major modifications
of conventional Look-Locker (LL) imaging are introduced: 1)
selective data acquisition, and 2) merging of data from multiple
LL experiments into one data set. Each modified LL inversion
recovery (MOLLI) study consisted of three successive LL
inversion recovery (IR) experiments with different inversion
times. We acquired images in late diastole using a single-shot
steady-state free-precession (SSFP) technique, combined with
sensitivity encoding to achieve a data acquisition window of <
200 ms duration. We calculated T1 using signal intensities from
regions of interest and pixel by pixel. T1 accuracy at different
heart rates derived from simulated ECG signals was tested in
phantoms. T1 estimates showed small systematic error for T1
values from 191 to 1196 ms. In vivo T1 mapping was performed in
two healthy volunteers and in one patient with acute myocardial
infarction before and after administration of Gd-DTPA. T1 values
for myocardium and noncardiac structures were in good agreement
with values available from the literature. The region of
infarction was clearly visualized. MOLLI provides
high-resolution T1 maps of human myocardium in native and
post-contrast situations within a single breath-hold.},
author = {Messroghli, Daniel R and Radjenovic, Aleksandra and Kozerke,
Sebastian and Higgins, David M and Sivananthan, Mohan U and
Ridgway, John P},
journal = {Magn. Reson. Med.},
language = {en},
month = {July},
doi = {10.1002/mrm.20110},
number = {1},
pages = {141--146},
publisher = {Wiley},
title = {Modified {Look-Locker} inversion recovery ({MOLLI}) for
high-resolution {T1} mapping of the heart},
volume = {52},
year = {2004}
}
@article{Piechnik2010-be,
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.},
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},
doi = {10.1186/1532-429X-12-69},
journal = {J. Cardiovasc. Magn. Reson.},
language = {en},
month = {November},
number = {1},
pages = {69},
title = {Shortened Modified {Look-Locker} Inversion recovery ({ShMOLLI})
for clinical myocardial T1-mapping at 1.5 and 3 {T} within a 9
heartbeat breathhold},
volume = {12},
year = {2010}
}