Use BibTeX citations in documentation (#670)

* Use bibtex in CBMA docstrings. * Do kernel as well. * IBMA references. * Annotate module. * Decode module. * Transforms and examples. * Fix one entry. * Fix another entry. * Add dependency.
neurostuff · Apr 23, 2022 · b806510 · b806510
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diff --git a/docs/conf.py b/docs/conf.py
@@ -54,6 +54,7 @@
     "sphinx_copybutton",  # for copying code snippets
     "sphinx_gallery.gen_gallery",  # example gallery
     "sphinxarg.ext",  # argparse
+    "sphinxcontrib.bibtex",  # for foot-citations
     "recommonmark",  # markdown parser
 ]
 
@@ -203,6 +204,14 @@
 # Generate the plots for the gallery
 plot_gallery = True
 
+# -----------------------------------------------------------------------------
+# sphinxcontrib-bibtex
+# -----------------------------------------------------------------------------
+bibtex_bibfiles = ["./references.bib"]
+bibtex_style = "unsrt"
+bibtex_reference_style = "author_year"
+bibtex_footbibliography_header = ""
+
 
 def setup(app):
     """From https://github.com/rtfd/sphinx_rtd_theme/issues/117"""

diff --git a/docs/references.bib b/docs/references.bib
@@ -0,0 +1,353 @@
+@article{amft2015definition,
+  title={Definition and characterization of an extended social-affective default network},
+  author={Amft, Maren and Bzdok, Danilo and Laird, Angela R and Fox, Peter T and Schilbach, Leonhard and Eickhoff, Simon B},
+  journal={Brain Structure and Function},
+  volume={220},
+  number={2},
+  pages={1031--1049},
+  year={2015},
+  publisher={Springer},
+  url={https://doi.org/10.1007/s00429-013-0698-0},
+  doi={10.1007/s00429-013-0698-0}
+}
+
+@article{blei2003latent,
+  title={Latent dirichlet allocation},
+  author={Blei, David M and Ng, Andrew Y and Jordan, Michael I},
+  journal={Journal of machine Learning research},
+  volume={3},
+  number={Jan},
+  pages={993--1022},
+  year={2003},
+  url={https://dl.acm.org/doi/10.5555/944919.944937}
+}
+
+@article{brockwell2001comparison,
+  title={A comparison of statistical methods for meta-analysis},
+  author={Brockwell, Sarah E and Gordon, Ian R},
+  journal={Statistics in medicine},
+  volume={20},
+  number={6},
+  pages={825--840},
+  year={2001},
+  publisher={Wiley Online Library},
+  url={https://doi.org/10.1002/sim.650},
+  doi={10.1002/sim.650}
+}
+
+@article{bullmore1999global,
+  title={Global, voxel, and cluster tests, by theory and permutation, for a difference between two groups of structural MR images of the brain},
+  author={Bullmore, Edward T and Suckling, John and Overmeyer, Stephan and Rabe-Hesketh, Sophia and Taylor, Eric and Brammer, Michael J},
+  journal={IEEE transactions on medical imaging},
+  volume={18},
+  number={1},
+  pages={32--42},
+  year={1999},
+  publisher={IEEE},
+  url={https://doi.org/10.1109/42.750253},
+  doi={10.1109/42.750253}
+}
+
+@article{dersimonian1986meta,
+  title={Meta-analysis in clinical trials},
+  author={DerSimonian, Rebecca and Laird, Nan},
+  journal={Controlled clinical trials},
+  volume={7},
+  number={3},
+  pages={177--188},
+  year={1986},
+  publisher={Elsevier}
+}
+
+@article{eickhoff2012activation,
+  title={Activation likelihood estimation meta-analysis revisited},
+  author={Eickhoff, Simon B and Bzdok, Danilo and Laird, Angela R and Kurth, Florian and Fox, Peter T},
+  journal={Neuroimage},
+  volume={59},
+  number={3},
+  pages={2349--2361},
+  year={2012},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2011.09.017},
+  doi={10.1016/j.neuroimage.2011.09.017}
+}
+
+@article{eickhoff2016behavior,
+  title={Behavior, sensitivity, and power of activation likelihood estimation characterized by massive empirical simulation},
+  author={Eickhoff, Simon B and Nichols, Thomas E and Laird, Angela R and Hoffstaedter, Felix and Amunts, Katrin and Fox, Peter T and Bzdok, Danilo and Eickhoff, Claudia R},
+  journal={Neuroimage},
+  volume={137},
+  pages={70--85},
+  year={2016},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2016.04.072},
+  doi={10.1016/j.neuroimage.2016.04.072}
+}
+
+@article{enge2021meta,
+  title={A meta-analysis of fMRI studies of semantic cognition in children},
+  author={Enge, Alexander and Rahman, Rasha Abdel and Skeide, Michael A},
+  journal={NeuroImage},
+  volume={241},
+  pages={118436},
+  year={2021},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2021.118436},
+  doi={10.1016/j.neuroimage.2021.118436}
+}
+
+@article{fisher1946statistical,
+  title={Statistical methods for research workers.},
+  author={Fisher, Ronald Aylmer and others},
+  journal={Statistical methods for research workers.},
+  number={10th. ed.},
+  year={1946},
+  publisher={Oliver and Boyd}
+}
+
+@article{freedman1983nonstochastic,
+  title={A nonstochastic interpretation of reported significance levels},
+  author={Freedman, David and Lane, David},
+  journal={Journal of Business \& Economic Statistics},
+  volume={1},
+  number={4},
+  pages={292--298},
+  year={1983},
+  publisher={Taylor \& Francis}
+}
+
+@book{hedges2014statistical,
+  title={Statistical methods for meta-analysis},
+  author={Hedges, Larry V and Olkin, Ingram},
+  year={2014},
+  publisher={Academic press}
+}
+
+@article{hughett2008accurate,
+  title={Accurate computation of the F-to-z and t-to-z transforms for large arguments},
+  author={Hughett, Paul},
+  journal={Journal of Statistical Software},
+  volume={23},
+  pages={1--5},
+  year={2008},
+  url={https://doi.org/10.18637/jss.v023.c01},
+  doi={10.18637/jss.v023.c01}
+}
+
+@article{kosmidis2017improving,
+  title={Improving the accuracy of likelihood-based inference in meta-analysis and meta-regression},
+  author={Kosmidis, Ioannis and Guolo, Annamaria and Varin, Cristiano},
+  journal={Biometrika},
+  volume={104},
+  number={2},
+  pages={489--496},
+  year={2017},
+  publisher={Oxford University Press},
+  url={https://doi.org/10.1093/biomet/asx001},
+  doi={10.1093/biomet/asx001}
+}
+
+@article{laird2005ale,
+  title={ALE meta-analysis: Controlling the false discovery rate and performing statistical contrasts},
+  author={Laird, Angela R and Fox, P Mickle and Price, Cathy J and Glahn, David C and Uecker, Angela M and Lancaster, Jack L and Turkeltaub, Peter E and Kochunov, Peter and Fox, Peter T},
+  journal={Human brain mapping},
+  volume={25},
+  number={1},
+  pages={155--164},
+  year={2005},
+  publisher={Wiley Online Library},
+  url={https://doi.org/10.1002/hbm.20136},
+  doi={10.1002/hbm.20136}
+}
+
+@article{langner2014meta,
+  title={Meta-analytic connectivity modeling revisited: controlling for activation base rates},
+  author={Langner, Robert and Rottschy, Claudia and Laird, Angela R and Fox, Peter T and Eickhoff, Simon B},
+  journal={Neuroimage},
+  volume={99},
+  pages={559--570},
+  year={2014},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2014.06.007},
+  doi={10.1016/j.neuroimage.2014.06.007}
+}
+
+@article{newman2009distributed,
+  title={Distributed algorithms for topic models.},
+  author={Newman, David and Asuncion, Arthur and Smyth, Padhraic and Welling, Max},
+  journal={Journal of Machine Learning Research},
+  volume={10},
+  number={8},
+  year={2009},
+  url={http://jmlr.org/papers/v10/newman09a.html}
+}
+
+@article{nichols2005valid,
+  title={Valid conjunction inference with the minimum statistic},
+  author={Nichols, Thomas and Brett, Matthew and Andersson, Jesper and Wager, Tor and Poline, Jean-Baptiste},
+  journal={Neuroimage},
+  volume={25},
+  number={3},
+  pages={653--660},
+  year={2005},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2004.12.005},
+  doi={10.1016/j.neuroimage.2004.12.005}
+}
+
+@article{poldrack2011cognitive,
+  title={The cognitive atlas: toward a knowledge foundation for cognitive neuroscience},
+  author={Poldrack, Russell A and Kittur, Aniket and Kalar, Donald and Miller, Eric and Seppa, Christian and Gil, Yolanda and Parker, D Stott and Sabb, Fred W and Bilder, Robert M},
+  journal={Frontiers in neuroinformatics},
+  volume={5},
+  pages={17},
+  year={2011},
+  publisher={Frontiers},
+  url={https://doi.org/10.3389/fninf.2011.00017},
+  doi={10.3389/fninf.2011.00017}
+}
+
+@article{poldrack2012discovering,
+  title={Discovering relations between mind, brain, and mental disorders using topic mapping},
+  author={Poldrack, Russell A and Mumford, Jeanette A and Schonberg, Tom and Kalar, Donald and Barman, Bishal and Yarkoni, Tal},
+  year={2012},
+  publisher={Public Library of Science San Francisco, USA},
+  journal={PLOS Computational Biology},
+  url={https://doi.org/10.1371/journal.pcbi.1002707},
+  doi={10.1371/journal.pcbi.1002707}
+}
+
+@article{rubin2017decoding,
+  title={Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition},
+  author={Rubin, Timothy N and Koyejo, Oluwasanmi and Gorgolewski, Krzysztof J and Jones, Michael N and Poldrack, Russell A and Yarkoni, Tal},
+  journal={PLoS computational biology},
+  volume={13},
+  number={10},
+  pages={e1005649},
+  year={2017},
+  publisher={Public Library of Science San Francisco, CA USA},
+  url={https://doi.org/10.1371/journal.pcbi.1005649},
+  doi={10.1371/journal.pcbi.1005649}
+}
+
+@misc{sochat2015ttoz,
+  author = {Sochat, Vanessa},
+  title = {TtoZ Original Release},
+  month = oct,
+  year = 2015,
+  publisher = {Zenodo},
+  doi = {10.5281/zenodo.32508},
+  url = {https://doi.org/10.5281/zenodo.32508}
+}
+
+@article{stouffer1949american,
+  title={The american soldier: Adjustment during army life.(studies in social psychology in world war ii), vol. 1},
+  author={Stouffer, Samuel A and Suchman, Edward A and DeVinney, Leland C and Star, Shirley A and Williams Jr, Robin M},
+  journal={Studies in social psychology in World War II},
+  year={1949},
+  publisher={Princeton Univ. Press}
+}
+
+@article{turkeltaub2002meta,
+  title={Meta-analysis of the functional neuroanatomy of single-word reading: method and validation},
+  author={Turkeltaub, Peter E and Eden, Guinevere F and Jones, Karen M and Zeffiro, Thomas A},
+  journal={Neuroimage},
+  volume={16},
+  number={3},
+  pages={765--780},
+  year={2002},
+  publisher={Elsevier},
+  url={https://doi.org/10.1006/nimg.2002.1131},
+  doi={10.1006/nimg.2002.1131}
+}
+
+@article{turkeltaub2012minimizing,
+  title={Minimizing within-experiment and within-group effects in activation likelihood estimation meta-analyses},
+  author={Turkeltaub, Peter E and Eickhoff, Simon B and Laird, Angela R and Fox, Mick and Wiener, Martin and Fox, Peter},
+  journal={Human brain mapping},
+  volume={33},
+  number={1},
+  pages={1--13},
+  year={2012},
+  publisher={Wiley Online Library},
+  url={https://doi.org/10.1002/hbm.21186},
+  doi={10.1002/hbm.21186}
+}
+
+@article{wager2003valence,
+  title={Valence, gender, and lateralization of functional brain anatomy in emotion: a meta-analysis of findings from neuroimaging},
+  author={Wager, Tor D and Phan, K Luan and Liberzon, Israel and Taylor, Stephan F},
+  journal={Neuroimage},
+  volume={19},
+  number={3},
+  pages={513--531},
+  year={2003},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/S1053-8119(03)00078-8},
+  doi={10.1016/S1053-8119(03)00078-8}
+}
+
+@article{wager2004neuroimaging,
+  title={Neuroimaging studies of shifting attention: a meta-analysis},
+  author={Wager, Tor D and Jonides, John and Reading, Susan},
+  journal={Neuroimage},
+  volume={22},
+  number={4},
+  pages={1679--1693},
+  year={2004},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2004.03.052},
+  doi={10.1016/j.neuroimage.2004.03.052}
+}
+
+@article{wager2007meta,
+  title={Meta-analysis of functional neuroimaging data: current and future directions},
+  author={Wager, Tor D and Lindquist, Martin and Kaplan, Lauren},
+  journal={Social cognitive and affective neuroscience},
+  volume={2},
+  number={2},
+  pages={150--158},
+  year={2007},
+  publisher={Oxford University Press},
+  url={https://doi.org/10.1093/scan/nsm015},
+  doi={10.1093/scan/nsm015}
+}
+
+@article{yarkoni2011large,
+  title={Large-scale automated synthesis of human functional neuroimaging data},
+  author={Yarkoni, Tal and Poldrack, Russell A and Nichols, Thomas E and Van Essen, David C and Wager, Tor D},
+  journal={Nature methods},
+  volume={8},
+  number={8},
+  pages={665--670},
+  year={2011},
+  publisher={Nature Publishing Group},
+  url={https://doi.org/10.1038/nmeth.1635},
+  doi={10.1038/nmeth.1635}
+}
+
+@article{zaykin2011optimally,
+  title={Optimally weighted Z-test is a powerful method for combining probabilities in meta-analysis},
+  author={Zaykin, Dmitri V},
+  journal={Journal of evolutionary biology},
+  volume={24},
+  number={8},
+  pages={1836--1841},
+  year={2011},
+  publisher={Wiley Online Library},
+  url={https://doi.org/10.1111/j.1420-9101.2011.02297.x},
+  doi={10.1111/j.1420-9101.2011.02297.x}
+}
+
+@article{zhang2009cluster,
+  title={Cluster mass inference via random field theory},
+  author={Zhang, Hui and Nichols, Thomas E and Johnson, Timothy D},
+  journal={Neuroimage},
+  volume={44},
+  number={1},
+  pages={51--61},
+  year={2009},
+  publisher={Elsevier},
+  url={https://doi.org/10.1016/j.neuroimage.2008.08.017},
+  doi={10.1016/j.neuroimage.2008.08.017}
+}