Update paper.md, add featured figure

paper.bib

@@ -40,4 +40,249 @@ @article{DeLeener201724
 doi = "https://doi.org/10.1016/j.neuroimage.2016.10.009",
 url = "http://www.sciencedirect.com/science/article/pii/S1053811916305560",
 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,
+  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,
+  language = "en"
+}
+
+@MISC{Ibrahim2001-xt,
+  title    = "Dielectric resonances and {B1} field inhomogeneity in {UHF}
+              {MRI}: computational analysis and experimental findings",
+  author   = "Ibrahim, Tamer S and Lee, Robert and Abduljalil, Amir M and
+              Baertlein, Brian A and Robitaille, Pierre-Marie L",
+  year     =  2001,
+  note     = "Accessed: 2020-8-10"
+}
+
+@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,
+  language = "en"
+}
+
+@MISC{Ibrahim2001-xt,
+  title    = "Dielectric resonances and {B1} field inhomogeneity in {UHF}
+              {MRI}: computational analysis and experimental findings",
+  author   = "Ibrahim, Tamer S and Lee, Robert and Abduljalil, Amir M and
+              Baertlein, Brian A and Robitaille, Pierre-Marie L",
+  year     =  2001,
+  note     = "Accessed: 2020-8-10"
+}
+
+@ARTICLE{Papp_undated-xl,
+  title  = "Universal pulses for the cervical spinal cord at 7T: a feasibility
+            study",
+  author = "Papp, Daniel and Boulant, Nicolas and Massire, Aurelien and
+            Mauconduit, Frank and Gras, Vincent 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,
+  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,
+  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,
+  language = "en"
 }

paper.md

@@ -1,48 +1,90 @@
 ---
-title: 'RF Shimming 7T'
+title: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"
+
 tags:
-  - shimming
+  - RF shimming
+  - spinal cord
+  - MRI
+  - high field
+  - 7T
 authors:
+   - name: Daniel Papp
+    orcid: 
+    affiliation: 1
+  - name: Kyle M. Gilbert
+    orcid: 
+    affiliation: "2, 3"
+  - name: Gaspard Cereza
+    orcid: 
+    affiliation: 1
+  - name: Alexandre D’Astous
+    orcid: 
+    affiliation: 1
+  - name: Mathieu Boudreau
+    orcid: 
+    affiliation: 1
+  - name: Marcus Couch
+    orcid: 
+    affiliation: 4
+  - name: Pedram Yazdanbakhsh
+    orcid: 
+    affiliation: 5
+  - name: Robert L. Barry
+    orcid: 
+    affiliation: 6
+  - name: Eva Alonso Ortiz
+    orcid: 
+    affiliation: 1
   - name: Julien Cohen-Adad
     orcid: 0000-0003-3662-9532
-    affiliation: "1, 2, 3, 4"
+    affiliation: "1, 7, 8"
 affiliations:
- - name: NeuroPoly Lab, Polytechnique Montréal, Montreal, Quebec, Canada
+ - name: NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada
    index: 1
- - name: Unité de Neuroimagerie Fonctionnelle (UNF), Centre de recherche de l’Institut Universitaire de Gériatrie de Montréal (CRIUGM), Montreal, Quebec, Canada
+ - name: Centre for Functional and Metabolic Mapping, The University of Western Ontario, London, ON, Canada
    index: 2
- - name: Mila - Quebec AI Institute, Montreal, QC, Canad
+ - name: Department of Medical Biophysics, The University of Western Ontario, London, ON, Canada
    index: 3
- - name: Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montreal, QC, Canada
+ - name: Siemens Healthcare Limited, Montreal, QC, Canada
    index: 4
-
-date: 17 January 2024
+ - name: McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
+   index: 5
+ - name: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
+   index: 6
+ - name: Mila - Quebec AI Institute, Montreal, QC, Canada
+   index: 7
+ - name: Functional Neuroimaging Unit, Centre de recherche de l'Institut universitaire de gériatrie de Montréal QC, Canada
+   index: 8
+
+date: 2 February 2024
 bibliography: paper.bib
 
 ---
 
 # Summary
 
-Text
+Data was collected from five participants between two 7T sites with a custom 8Tx/20Rx parallel transmission (pTx) coil. We explored two RF shimming approaches from an MRI vendor and four from an open-source toolbox, showcasing their ability to enhance transmit field and signal homogeneity along the cervical spinal cord.
+
+The results indicate significant improvements in B1+ efficiency and cerebrospinal fluid / spinal cord signal ratio across various RF shimming conditions compared to the vendor based methods.
+
+The study's findings highlight the potential of RF shimming to advance 7T MRI's clinical utility for central nervous system imaging by enabling more homogenous and efficient spinal cord imaging. Additionally, the research incorporates a reproducible Jupyter Notebook, enhancing the study's transparency and facilitating peer verification. By also making the data openly accessible on OpenNeuro, we ensure that the scientific community can further explore, validate, and build upon our findings, contributing to the collective advancement in high-resolution imaging techniques.
+
 
 # Statement of need
 
-Text
+Advancing the development of 7T MRI for spinal cord imaging is crucial for the enhanced diagnosis and monitoring of various neurodegenerative diseases [@Kearney2015-py] and traumas [@David2019-jy]. However, a significant challenge at this field strength is the transmit field inhomogeneity . Such inhomogeneity is particularly problematic for imaging the small, deep anatomical structures of[@Ibrahim2001-xt;@Collins2005-za;@Roschmann1987-om;@Yang2002-ui] the cervical spinal cord, as it can cause uneven signal intensity and elevate the local specific absorption ratio, compromising image quality. This multi-site study explores several radiofrequency (RF) shimming techniques in the cervical spinal cord at 7T.
 
 
 # Figures
 
-Figure
-
-# Acknowledgements
+![Overview of the RF shimming procedure.
+\label{fig:overview}](featured.png)
 
-Text
 
+# Acknowledgements
 
-1     |     INTRODUCTION
-========================
+Funded by the Canada Research Chair in Quantitative Magnetic Resonance Imaging [950-230815], the Canadian Institute of Health Research [CIHR FDN-143263], the Canada Foundation for Innovation [32454, 34824], the Fonds de Recherche du Québec - Santé [28826], the Natural Sciences and Engineering Research Council of Canada [RGPIN-2019-07244], the Canada First Research Excellence Fund (IVADO and TransMedTech), the Courtois NeuroMod project and the Quebec BioImaging Network [5886, 35450], and MITACS Accelerate Fellowship.
 
-Test citation [@DAstous2023]
 
 ## References