Upate figure legends

content/index.ipynb

@@ -1130,11 +1130,6 @@
     "print(f\"Paired t-tests:\\n{comparison_results}\")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1398,6 +1393,13 @@
     "display(HTML('figure1.html'))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<b>Figure 3.</b>B1+ efficiency (A) and CSF/Cord signal ratio from the GRE scan (B) across subjects and across different RF shimming conditions. Data werewas measured in the spinal cord from C3 to T2 vertebral levels. To match the x-ticks across subjects, the C2-C3 and the T2-T3 intervertebral discs of each subject were aligned with that of the PAM50 template  {cite:p}`DELEENER2018170`, and the curves were linearly scaled."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1548,6 +1550,13 @@
     "plt.show()\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<b>Figure 2.</b>B1+ efficiency for one participant (sub-05) across all seven RF shimming conditions. The top left panel shows the tfl_b1map magnitude image with an overlay of the mask that was used to perform RF shimming. Text inserts show the mean (in nT/V) and CoV (in %) of B1+ efficiency along the spinal cord between C3 and T2. "
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

paper.bib

@@ -233,4 +233,18 @@ @ARTICLE{Yang2002-ui
   month    =  may,
   year     =  2002,
   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 = {https://doi.org/10.1016/j.neuroimage.2017.10.041},
+url = {https://www.sciencedirect.com/science/article/pii/S1053811917308686},
+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.}
 }