Add ASLPrep DOIs to README and boilerplate (#225)

* Add Nature Methods DOI to README.

* Add ASLPrep DOIs to boilerplate.

README.rst

@@ -22,9 +22,13 @@
    :target: https://codecov.io/gh/PennLINC/aslprep
    :alt: Codecov
 
+.. image:: https://img.shields.io/badge/Nature%20Methods-10.1038%2Fs41592--022--01458--7-purple
+   :target: https://doi.org/10.1038/s41592-022-01458-7
+   :alt: Publication DOI
+
 .. image:: https://zenodo.org/badge/256420694.svg
    :target: https://zenodo.org/badge/latestdoi/256420694
-   :alt: DOI
+   :alt: Zenodo DOI
 
 .. image:: https://img.shields.io/github/license/pennlinc/aslprep
    :target: https://opensource.org/licenses/BSD-3-Clause

aslprep/data/boilerplate.bib

@@ -1,4 +1,25 @@
 
+@article{aslprep_nature_methods,
+	title={ASLPrep: a platform for processing of arterial spin labeled MRI and quantification of regional brain perfusion},
+	author={Adebimpe, Azeez and Bertolero, Maxwell and Dolui, Sudipto and Cieslak, Matthew and Murtha, Kristin and Baller, Erica B and Boeve, Bradley and Boxer, Adam and Butler, Ellyn R and Cook, Phil and others},
+	journal={Nature methods},
+	volume={19},
+	number={6},
+	pages={683--686},
+	year={2022},
+	publisher={Nature Publishing Group US New York}
+}
+
+@article{aslprep_zenodo,
+	title={ASLPrep <version>},
+	author={Azeez Adebimpe and Maxwell Bertolero and Kristin Murtha and Andrew Ross and Matt Flounders and Ellyn Butler and Matt Cieslak and Sydney Covitz and Tinashe Michael Tapera},
+	publisher={Zenodo},
+	year={2023},
+	doi={10.5281/zenodo.3759082},
+	url={https://doi.org/10.5281/zenodo.3759082},
+	journal={Software}
+}
+
 @article{bbr,
 	title = {Accurate and robust brain image alignment using boundary-based registration},
 	volume = {48},

aslprep/workflows/base.py

@@ -209,23 +209,24 @@ def init_single_subject_wf(subject_id):
     workflow.__desc__ = f"""
 ### Arterial Spin-Labeled MRI Preprocessing and Cerebral Blood Flow Computation
 
-Arterial spin-labeled MRI images were preprocessed using *ASLPrep* {config.environment.version},
+Arterial spin-labeled MRI images were preprocessed using *ASLPrep* {config.environment.version}
+[@aslprep_nature_methods;@aslprep_zenodo],
 which is based on *Nipype* {config.environment.nipype_version} [@nipype].
 
 """
     workflow.__postdesc__ = f""" \
 Many internal operations of *ASLPrep* use
 *Nilearn* {NILEARN_VERSION} [@nilearn], *NumPy* [@numpy], and *SciPy* [@scipy].
-For more details of the pipeline, see [the  *ASLPrep*  documentation.]\
-(https://aslprep.readthedocs.io/en/latest/workflows.html).
+For more details of the pipeline, see
+[the  *ASLPrep*  documentation.](https://aslprep.readthedocs.io/en/latest/workflows.html).
 
 
 ### Copyright Waiver
 
 The above methods description  was automatically generated by *ASLPrep*
 with the express intention that users should copy and paste this text into
-their manuscripts unchanged. It is released under the unchanged [CC0]\
-(https://creativecommons.org/publicdomain/zero/1.0/) license.
+their manuscripts unchanged. It is released under the unchanged
+[CC0](https://creativecommons.org/publicdomain/zero/1.0/) license.
 
 ### References
 

docs/workflows.rst

@@ -4,9 +4,10 @@
 ASL processing pipeline details
 ###############################
 
-*ASLPrep* adapts its pipeline depending on what data and metadata are
-available and are used as inputs. It requires the input data to be
-BIDS-valid and include necessary ASL parameters.
+*ASLPrep* :footcite:p:`aslprep_nature_methods,aslprep_zenodo`
+adapts its pipeline depending on what data and metadata are
+available and are used as inputs.
+It requires the input data to be BIDS-valid and include necessary ASL parameters.
 
 .. workflow::
     :graph2use: orig