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@article{DAstous2023,
author = {D'Astous, Alexandre and Cereza, Gaspard and Papp, Daniel and Gilbert, Kyle M. and Stockmann, Jason P. and Alonso-Ortiz, Eva and Cohen-Adad, Julien},
title = {Shimming toolbox: An open-source software toolbox for B0 and B1 shimming in MRI},
journal = {Magnetic Resonance in Medicine},
volume = {89},
number = {4},
pages = {1401-1417},
keywords = {B0, B1, inhomogeneities, MRI, open-source software, parallel transmit, Python, shimming},
doi = {10.1002/mrm.29528},
abstract = {Purpose Introduce Shimming Toolbox ( https://shimming-toolbox.org), an open-source software package for prototyping new methods and performing static, dynamic, and real-time B0 shimming as well as B1 shimming experiments. Methods Shimming Toolbox features various field mapping techniques, manual and automatic masking for the brain and spinal cord, B0 and B1 shimming capabilities accessible through a user-friendly graphical user interface. Validation of Shimming Toolbox was demonstrated in three scenarios: (i) B0 dynamic shimming in the brain at 7T using custom AC/DC coils, (ii) B0 real-time shimming in the spinal cord at 3T, and (iii) B1 static shimming in the spinal cord at 7T. Results The B0 dynamic shimming of the brain at 7T took about 10 min to perform. It showed a 47\% reduction in the standard deviation of the B0 field, associated with noticeable improvements in geometric distortions in EPI images. Real-time dynamic xyz-shimming in the spinal cord took about 5 min and showed a 30\% reduction in the standard deviation of the signal distribution. B1 static shimming experiments in the spinal cord took about 10 min to perform and showed a 40\% reduction in the coefficient of variation of the B1 field. Conclusion Shimming Toolbox provides an open-source platform where researchers can collaborate, prototype and conveniently test B0 and B1 shimming experiments. Future versions will include additional field map preprocessing techniques, optimization algorithms, and compatibility across multiple MRI manufacturers.},
year = {2023}
}
@article{DeLeener201724,
title = "SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord \{MRI\} data ",
journal = "NeuroImage ",
volume = "145, Part A",
number = "",
pages = "24 - 43",
year = "2017",
note = "",
issn = "1053-8119",
doi = "10.1016/j.neuroimage.2016.10.009",
author = "De Leener, Benjamin and Lévy, Simon and Dupont, Sara M. and Fonov, Vladimir S. and Stikov, Nikola and Collins, D. Louis and Callot, Virginie and Cohen-Adad, Julien",
}
@ARTICLE{Kearney2015-py,
title = "Spinal cord {MRI} in multiple sclerosis--diagnostic, prognostic
and clinical value",
author = "Kearney, Hugh and Miller, David H and Ciccarelli, Olga",
abstract = "Multiple sclerosis (MS) is an inflammatory disorder of the CNS
that affects both the brain and the spinal cord. MRI studies in
MS focus more often on the brain than on the spinal cord, owing
to the technical challenges in imaging this smaller, mobile
structure. However, spinal cord abnormalities at disease onset
have important implications for diagnosis and prognosis.
Furthermore, later in the disease course, in progressive MS,
myelopathy becomes the primary characteristic of the clinical
presentation, and extensive spinal cord pathology--including
atrophy, diffuse abnormalities and numerous focal lesions--is
common. Recent spinal cord imaging studies have employed
increasingly sophisticated techniques to improve detection and
quantification of spinal cord lesions, and to elucidate their
relationship with physical disability. Quantitative MRI measures
of cord size and tissue integrity could be more sensitive to the
axonal loss and other pathological processes in the spinal cord
than is conventional MRI, putting quantitative MRI in a key role
to elucidate the association between disability and spinal cord
abnormalities seen in people with MS. In this Review, we
summarize the most recent MS spinal cord imaging studies and
discuss the new insights they have provided into the mechanisms
of neurological impairment. Finally, we suggest directions for
further and future research.",
journal = "Nat. Rev. Neurol.",
volume = 11,
number = 6,
pages = "327--338",
month = jun,
year = 2015,
doi = "10.1038/nrneurol.2015.80",
language = "en"
}
@ARTICLE{David2019-jy,
title = "Traumatic and nontraumatic spinal cord injury: pathological
insights from neuroimaging",
author = "David, Gergely and Mohammadi, Siawoosh and Martin, Allan R and
Cohen-Adad, Julien and Weiskopf, Nikolaus and Thompson, Alan and
Freund, Patrick",
abstract = "Pathophysiological changes in the spinal cord white and grey
matter resulting from injury can be observed with MRI techniques.
These techniques provide sensitive markers of macrostructural and
microstructural tissue integrity, which correlate with
histological findings. Spinal cord MRI findings in traumatic
spinal cord injury (tSCI) and nontraumatic spinal cord injury -
the most common form of which is degenerative cervical myelopathy
(DCM) - have provided important insights into the
pathophysiological processes taking place not just at the focal
injury site but also rostral and caudal to the spinal injury.
Although tSCI and DCM have different aetiologies, they show
similar degrees of spinal cord pathology remote from the injury
site, suggesting the involvement of similar secondary
degenerative mechanisms. Advanced quantitative MRI protocols that
are sensitive to spinal cord pathology have the potential to
improve diagnosis and, more importantly, predict outcomes in
patients with tSCI or nontraumatic spinal cord injury. This
Review describes the insights into tSCI and DCM that have been
revealed by neuroimaging and outlines current activities and
future directions for the field.",
journal = "Nat. Rev. Neurol.",
volume = 15,
number = 12,
pages = "718--731",
month = dec,
year = 2019,
doi = "10.1038/s41582-019-0270-5",
language = "en"
}
@article{Ibrahim2001-xt,
title = {Dielectric resonances and B1 field inhomogeneity in UHFMRI: computational analysis and experimental findings},
journal = {Magnetic Resonance Imaging},
volume = {19},
number = {2},
pages = {219-226},
year = {2001},
issn = {0730-725X},
doi = {10.1016/S0730-725X(01)00300-9},
author = "Ibrahim, Tamer S and Lee, Robert and Abduljalil, Amir M and
Baertlein, Brian A and Robitaille, Pierre-Marie L",
}
@ARTICLE{Collins2005-za,
title = "Central brightening due to constructive interference with,
without, and despite dielectric resonance",
author = "Collins, Christopher M and Liu, Wanzhan and Schreiber, Weston and
Yang, Qing X and Smith, Michael B",
abstract = "PURPOSE: To aid in discussion about the mechanism for central
brightening in high field magnetic resonance imaging (MRI),
especially regarding the appropriateness of using the term
dielectric resonance to describe the central brightening seen in
images of the human head. MATERIALS AND METHODS: We present both
numerical calculations and experimental images at 3 T of a
35-cm-diameter spherical phantom of varying salinity both with
one surface coil and with two surface coils on opposite sides,
and further numerical calculations at frequencies corresponding
to dielectric resonances for the sphere. RESULTS: With two
strategically placed surface coils it is possible to create
central brightening even when one coil alone excites an image
intensity pattern either bright on one side only or bright on
both sides with central darkening. This central brightening can
be created with strategic coil placement even when the resonant
pattern would favor central darkening. Results in a conductive
sample show that central brightening can similarly be achieved in
weakly conductive dielectric materials where any true resonances
would be heavily damped, such as in human tissues. CONCLUSION:
Constructive interference and wavelength effects are likely
bigger contributors to central brightening in MR images of weakly
conductive biological samples than is true dielectric resonance.",
journal = "J. Magn. Reson. Imaging",
volume = 21,
number = 2,
pages = "192--196",
month = feb,
year = 2005,
doi = "10.1002/jmri.20245",
language = "en"
}
@ARTICLE{Roschmann1987-om,
title = "Radiofrequency penetration and absorption in the human body:
limitations to high-field whole-body nuclear magnetic resonance
imaging",
author = "R{\"o}schmann, P",
abstract = "This study presents experimental results about the effective
depth of penetration and about the radiofrequency (rf) power
absorption in humans as a function of frequency. The frequency
range investigated covers 10 up to 220 MHz. For the main part,
the results were derived from bench measurements of the quality
factor Q, and of the resonance frequency shift due to the loading
of the coil. Different types of head-, body-, and surface coils
were investigated loaded with volunteers or metallic phantoms.
For spin-echo imaging at 2 T (85 MHz), the local specific
absorption rate (SAR) was found to be approximately equal to 0.05
W/kg using a pi pulse of 1-ms duration and pulse repetition time
TR = 1 s. Measurements of the quality factor Q as a function of
frequency show that the SAR depends upon the frequency f
according to approximately f2.15. The effective depth of rf
penetration as derived drops from 17 cm at 85 MHz to 7 cm at 220
MHz. Head imaging with B1 penetrating from practically all sides
into the object should be possible up to 220 MHz (5 T) with SAR
values staying within the local limit of 2 W/kg as set by the
FDA. Whole-body imaging of large subjects as well as surface coil
imaging is depth limited above 100-MHz frequency. Perturbation
methods are applied in order to separate the total rf power
deposition in the patient into dielectric and magnetic
contributions. The observed effects due to interactions of rf
magnetic fields with biological tissue contradict predictions
based on homogeneous tissue models. A refined tissue model with
regions of high electrical conductivity, subdivided by
quasi-insulating adipose layers, provides a rationale for a
better understanding of the underlying processes. At frequencies
below 100 MHz, the rf power deposition in patients is apparently
more evenly distributed over the exposed body volume than
currently assumed.",
journal = "Med. Phys.",
volume = 14,
number = 6,
pages = "922--931",
month = nov,
year = 1987,
doi = "10.1118/1.595995",
language = "en"
}
@ARTICLE{Yang2002-ui,
title = "Analysis of wave behavior in lossy dielectric samples at high
field",
author = "Yang, Qing X and Wang, Jinghua and Zhang, Xiaoliang and Collins,
Christopher M and Smith, Michael B and Liu, Haiying and Zhu,
Xiao-Hong and Vaughan, J Thomas and Ugurbil, Kamil and Chen, Wei",
abstract = "Radiofrequency (RF) field wave behavior and associated nonuniform
image intensity at high magnetic field strengths are examined
experimentally and numerically. The RF field produced by a
10-cm-diameter surface coil at 300 MHz is evaluated in a
16-cm-diameter spherical phantom with variable salinity, and in
the human head. Temporal progression of the RF field indicates
that the standing wave and associated dielectric resonance
occurring in a pure water phantom near 300 MHz is greatly
dampened in the human head due to the strong decay of the
electromagnetic wave. The characteristic image intensity
distribution in the human head is the result of spatial phase
distribution and amplitude modulation by the interference of the
RF traveling waves determined by a given sample-coil
configuration. The numerical calculation method is validated with
experimental results. The general behavior of the RF field with
respect to the average brain electrical properties in a frequency
range of 42-350 MHz is also analyzed.",
journal = "Magn. Reson. Med.",
volume = 47,
number = 5,
pages = "982--989",
month = may,
year = 2002,
doi = "10.1002/mrm.10137",
language = "en"
}
@ARTICLE{DELEENER2018170,
title = {PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space},
journal = {NeuroImage},
volume = {165},
pages = {170-179},
year = {2018},
issn = {1053-8119},
doi = {10.1016/j.neuroimage.2017.10.041},
author = {Benjamin {De Leener} and Vladimir S. Fonov and D. Louis Collins and Virginie Callot and Nikola Stikov and Julien Cohen-Adad},
keywords = {Spinal cord, MRI, Template, Atlas, ICBM},
abstract = {Template-based analysis of multi-parametric MRI data of the spinal cord sets the foundation for standardization and reproducibility, thereby helping the discovery of new biomarkers of spinal-related diseases. While MRI templates of the spinal cord have been recently introduced, none of them cover the entire spinal cord. In this study, we introduced an unbiased multimodal MRI template of the spinal cord and the brainstem, called PAM50, which is anatomically compatible with the ICBM152 brain template and uses the same coordinate system. The PAM50 template is based on 50 healthy subjects, covers the full spinal cord (C1 to L2 vertebral levels) and the brainstem, is available for T1-, T2-and T2*-weighted MRI contrasts and includes a probabilistic atlas of the gray matter and white matter tracts. Template creation accuracy was assessed by computing the mean and maximum distance error between each individual spinal cord centerline and the PAM50 centerline, after registration to the template. Results showed high accuracy for both T1- (mean = 0.37 ± 0.06 mm; max = 1.39 ± 0.58 mm) and T2-weighted (mean = 0.11 ± 0.03 mm; max = 0.71 ± 0.27 mm) contrasts. Additionally, the preservation of the spinal cord topology during the template creation process was verified by comparing the cross-sectional area (CSA) profile, averaged over all subjects, and the CSA profile of the PAM50 template. The fusion of the PAM50 and ICBM152 templates will facilitate group and multi-center studies of combined brain and spinal cord MRI, and enable the use of existing atlases of the brainstem compatible with the ICBM space.}
}