Update paper.md for pdf

paper.bib

@@ -21,7 +21,7 @@ @article{DAstous2023
 number = {4},
 pages = {1401-1417},
 keywords = {B0, B1, inhomogeneities, MRI, open-source software, parallel transmit, Python, shimming},
-doi = {https://doi.org/10.1002/mrm.29528},
+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}
 }
@@ -35,7 +35,7 @@ @article{DeLeener201724
 year = "2017",
 note = "",
 issn = "1053-8119",
-doi = "https://doi.org/10.1016/j.neuroimage.2016.10.009",
+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",
 }
 
@@ -72,7 +72,7 @@ @ARTICLE{Kearney2015-py
   pages    = "327--338",
   month    =  jun,
   year     =  2015,
-  doi      =  "https://doi.org/10.1038/nrneurol.2015.80",
+  doi      =  "10.1038/nrneurol.2015.80",
   language = "en"
 }
 
@@ -108,7 +108,7 @@ @ARTICLE{David2019-jy
   pages    = "718--731",
   month    =  dec,
   year     =  2019,
-  doi      =  "https://doi.org/10.1038/s41582-019-0270-5",
+  doi      =  "10.1038/s41582-019-0270-5",
   language = "en"
 }
 
@@ -120,7 +120,7 @@ @article{Ibrahim2001-xt
 pages = {219-226},
 year = {2001},
 issn = {0730-725X},
-doi = {https://doi.org/10.1016/S0730-725X(01)00300-9},
+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",
 }
@@ -158,7 +158,7 @@ @ARTICLE{Collins2005-za
   pages    = "192--196",
   month    =  feb,
   year     =  2005,
-  doi      =  "https://doi.org/10.1002/jmri.20245",
+  doi      =  "10.1002/jmri.20245",
   language = "en"
 }
 
@@ -204,7 +204,7 @@ @ARTICLE{Roschmann1987-om
   pages    = "922--931",
   month    =  nov,
   year     =  1987,
-  doi      = "https://doi.org/10.1118/1.595995",
+  doi      = "10.1118/1.595995",
   language = "en"
 }
 
@@ -237,7 +237,7 @@ @ARTICLE{Yang2002-ui
   pages    = "982--989",
   month    =  may,
   year     =  2002,
-  doi      = "https://doi.org/10.1002/mrm.10137",
+  doi      = "10.1002/mrm.10137",
   language = "en"
 }
 
@@ -248,7 +248,7 @@ @ARTICLE{DELEENER2018170
 pages = {170-179},
 year = {2018},
 issn = {1053-8119},
-doi = {https://doi.org/10.1016/j.neuroimage.2017.10.041},
+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.}

paper.md

@@ -54,7 +54,7 @@ affiliations:
    index: 6
  - name: Harvard Medical School, Boston, MA, USA
    index: 7
- - name: Harvard-Massachusetts Institute of Technology Health Sciences & Technology, Cambridge, MA, USA
+ - name: Harvard-Massachusetts Institute of Technology Health Sciences and Technology, Cambridge, MA, USA
    index: 8
  - name: Mila - Quebec AI Institute, Montreal, QC, Canada
    index: 9