Update figure-generating notebook (#1074)

* Update figure-generating notebook. * Update approach.rst * Improve figures. * Improve them again. * Try using footbibliography. * Fix things. * Add reference for benefits of FIT. * Update docs/approach.rst Co-authored-by: Dan Handwerker <[email protected]> * Re-run tedana + notebook. --------- Co-authored-by: Dan Handwerker <[email protected]>
ME-ICA · Sep 17, 2024 · d564ba9 · d564ba9
1 parent 61b989c
commit d564ba9
Show file tree

Hide file tree

Showing 23 changed files with 451 additions and 291 deletions.
diff --git a/docs/_static/a01_echo_timeseries.png b/docs/_static/a01_echo_timeseries.png
diff --git a/docs/_static/a02_echo_value_distributions.png b/docs/_static/a02_echo_value_distributions.png
diff --git a/docs/_static/a03_adaptive_mask.png b/docs/_static/a03_adaptive_mask.png
diff --git a/docs/_static/a03a_adaptive_mask_distributions.png b/docs/_static/a03a_adaptive_mask_distributions.png
diff --git a/docs/_static/a04_echo_log_value_distributions.png b/docs/_static/a04_echo_log_value_distributions.png
diff --git a/docs/_static/a05_loglinear_regression.png b/docs/_static/a05_loglinear_regression.png
diff --git a/docs/_static/a06_monoexponential_decay_model.png b/docs/_static/a06_monoexponential_decay_model.png
diff --git a/docs/_static/a07_monoexponential_decay_model_with_t2.png b/docs/_static/a07_monoexponential_decay_model_with_t2.png
diff --git a/docs/_static/a08_optimal_combination_echo_weights.png b/docs/_static/a08_optimal_combination_echo_weights.png
diff --git a/docs/_static/a09_optimal_combination_value_distributions.png b/docs/_static/a09_optimal_combination_value_distributions.png
diff --git a/docs/_static/a10_optimal_combination_timeseries.png b/docs/_static/a10_optimal_combination_timeseries.png
diff --git a/docs/_static/a11_pca_component_timeseries.png b/docs/_static/a11_pca_component_timeseries.png
diff --git a/docs/_static/a12_pca_reduced_data.png b/docs/_static/a12_pca_reduced_data.png
diff --git a/docs/_static/a13_ica_component_timeseries.png b/docs/_static/a13_ica_component_timeseries.png
diff --git a/docs/_static/a14_te_dependence_models_component_0.png b/docs/_static/a14_te_dependence_models_component_0.png
diff --git a/docs/_static/a14_te_dependence_models_component_1.png b/docs/_static/a14_te_dependence_models_component_1.png
diff --git a/docs/_static/a14_te_dependence_models_component_2.png b/docs/_static/a14_te_dependence_models_component_2.png
diff --git a/docs/_static/a15_denoised_data_timeseries.png b/docs/_static/a15_denoised_data_timeseries.png
diff --git a/docs/_static/a16_t1c_denoised_data_timeseries.png b/docs/_static/a16_t1c_denoised_data_timeseries.png
diff --git a/docs/approach.rst b/docs/approach.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -43,6 +43,7 @@
     "sphinx.ext.napoleon",
     "matplotlib.sphinxext.plot_directive",
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosectionlabel",
     "sphinx.ext.autosummary",
     "sphinx.ext.doctest",
     "sphinx.ext.ifconfig",
@@ -155,6 +156,9 @@ def setup(app):
 
 html_favicon = "_static/tedana_favicon.png"
 
+# Make sure the target is unique
+autosectionlabel_prefix_document = True
+
 # -----------------------------------------------------------------------------
 # sphinxcontrib-bibtex
 # -----------------------------------------------------------------------------

diff --git a/docs/notebooks/plot_approach_figures.ipynb b/docs/notebooks/plot_approach_figures.ipynb
diff --git a/tedana/resources/references.bib b/tedana/resources/references.bib
@@ -333,3 +333,24 @@ @article{tedana_decision_trees
   year    = {2024},
   doi     = {10.6084/m9.figshare.25251433.v2}
 }
+
+@article{power2018ridding,
+  title={Ridding fMRI data of motion-related influences: Removal of signals with distinct spatial and physical bases in multiecho data},
+  author={Power, Jonathan D and Plitt, Mark and Gotts, Stephen J and Kundu, Prantik and Voon, Valerie and Bandettini, Peter A and Martin, Alex},
+  journal={Proceedings of the National Academy of Sciences},
+  volume={115},
+  number={9},
+  pages={E2105--E2114},
+  year={2018},
+  publisher={National Acad Sciences}
+}
+
+@article{heunis2021effects,
+  title={The effects of multi-echo fMRI combination and rapid T2*-mapping on offline and real-time BOLD sensitivity},
+  author={Heunis, Stephan and Breeuwer, Marcel and Caballero-Gaudes, C{\'e}sar and Hellrung, Lydia and Huijbers, Willem and Jansen, Jacobus FA and Lamerichs, Rolf and Zinger, Svitlana and Aldenkamp, Albert P},
+  journal={Neuroimage},
+  volume={238},
+  pages={118244},
+  year={2021},
+  publisher={Elsevier}
+}