🎨 SSOT monkey preconfig refs

Author: shnizzedy

docs/_sources/references/preconfigs.bib

@@ -9,4 +9,56 @@ @article{Hoff21
   langid = {english}
 }
 
+@article{Rami20,
+  title = {Maternal {{Interleukin-6 Is Associated With Macaque Offspring Amygdala Development}} and {{Behavior}}},
+  author = {Ramirez, Julian S B and Graham, Alice M and Thompson, Jacqueline R and Zhu, Jennifer Y and Sturgeon, Darrick and Bagley, Jennifer L and Thomas, Elina and Papadakis, Samantha and Bah, Muhammed and Perrone, Anders and Earl, Eric and {Miranda-Dominguez}, Oscar and Feczko, Eric and Fombonne, Eric J and Amaral, David G and Nigg, Joel T and Sullivan, Elinor L and Fair, Damien A},
+  year = {2020},
+  month = mar,
+  journal = {Cerebral Cortex},
+  volume = {30},
+  number = {3},
+  pages = {1573--1585},
+  issn = {1047-3211},
+  doi = {10.1093/cercor/bhz188}
+}
+
+@misc{Stur20,
+  title = {{{DCAN-Labs/nhp-abcd-bids-pipeline}} {{Version}} 0.1.0},
+  author = {Sturgeon, Darrick and Earl, Eric and Snider, Kathy and Perrone, Anders and Ramirez, Julian and Mitchell, A. J. and Fair, Damien},
+  year = {2020},
+  month = jun,
+  doi = {10.5281/zenodo.3888969#.Xw31IpNKjyU},
+  howpublished = {Zenodo},
+  langid = {english}
+}
 
+@article{Wang21a,
+  title = {U-Net Model for Brain Extraction: {{Trained}} on Humans for Transfer to Non-Human Primates},
+  shorttitle = {U-Net Model for Brain Extraction},
+  author = {Wang, Xindi and Li, Xin-Hui and Cho, Jae Wook and Russ, Brian E. and Rajamani, Nanditha and Omelchenko, Alisa and Ai, Lei and Korchmaros, Annachiara and Sawiak, Stephen and Benn, R. Austin and {Garcia-Saldivar}, Pamela and Wang, Zheng and Kalin, Ned H. and Schroeder, Charles E. and Craddock, R. Cameron and Fox, Andrew S. and Evans, Alan C. and Messinger, Adam and Milham, Michael P. and Xu, Ting},
+  year = {2021},
+  month = jul,
+  journal = {NeuroImage},
+  volume = {235},
+  pages = {118001},
+  issn = {1095-9572},
+  doi = {10.1016/j.neuroimage.2021.118001},
+  langid = {english},
+  pmcid = {PMC8529630},
+  pmid = {33789137}
+}
+
+@article{Xu19,
+  title = {Interindividual Variability of Functional Connectivity in Awake and Anesthetized Rhesus Macaque Monkeys},
+  author = {Xu, Ting and Sturgeon, Darrick and Ramirez, Julian S. B. and {Froudist-Walsh}, Se{\'a}n and Margulies, Daniel S. and Schroeder, Charles E. and Fair, Damien A. and Milham, Michael P.},
+  year = {2019},
+  month = jun,
+  journal = {Biological Psychiatry: Cognitive Neuroscience and Neuroimaging},
+  series = {The {{Bridging}} of {{Scales}}: {{Techniques}} for {{Translational Neuroscience}}},
+  volume = {4},
+  number = {6},
+  pages = {543--553},
+  issn = {2451-9022},
+  doi = {10.1016/j.bpsc.2019.02.005},
+  langid = {english}
+}

docs/_sources/user/pipelines/preconfig.rst

@@ -91,14 +91,11 @@ Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/r
 
 RBC-options pipeline was built and integrated in C-PAC based on the Reproducible Brain Charts initiative, which aims to aggregate and harmonize phenotypic and neuroimage data to delineate node mechanisms regarding developmental basis of psychopathology in youth and yield reproducible growth charts of brain development :cite:`cite-rbc-Hoff21`.
 
-.. rubric:: References
-
 .. bibliography:: /references/preconfigs.bib
    :style: cpac_docs_style
    :cited:
    :keyprefix: cite-rbc-
 
-
 benchmark-ANTS: C-PAC Benchmark with ANTs Registration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -119,10 +116,16 @@ Monkey: Default with Monkey Preprocessing
 
 Pipeline Configuration YAML: `https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_monkey.yml <https://github.com/FCP-INDI/C-PAC/blob/main/CPAC/resources/configs/pipeline_config_monkey.yml>`_
 
-This pipeline is based on the work of Xu et al. (2019) and `nhp-ABCD-BIDS-pipeline. <https://zenodo.org/record/3888969#.Xw31IpNKjyU>`_
+This pipeline is based on the work of Xu et al. :cite:`cite-monkey-Xu19` and nhp-ABCD-BIDS-pipeline. :cite:`cite-monkey-Stur20`
 
-* `Nanditha Rajamani, et al. "U-Net Model for Brain Extraction: Training in Humans and Transferring to Non-human Primates." OHBM (2019) <https://ww5.aievolution.com/hbm1901/index.cfm?do=abs.viewAbs&abs=4924>`_
-* `Julian S B Ramirez, Alice M Graham, Jacqueline R Thompson, Jennifer Y Zhu, Darrick Sturgeon, Jennifer L Bagley, Elina Thomas, Samantha Papadakis, Muhammed Bah, Anders Perrone, Eric Earl, Oscar Miranda-Dominguez, Eric Feczko, Eric J Fombonne, David G Amaral, Joel T Nigg, Elinor L Sullivan, Damien A Fair, Maternal Interleukin-6 Is Associated With Macaque Offspring Amygdala Development and Behavior, Cerebral Cortex, Volume 30, Issue 3, March 2020, Pages 1573–1585 <https://doi.org/10.1093/cercor/bhz188>`_
+.. bibliography:: /references/preconfigs.bib
+   :style: cpac_docs_style
+   :cited:
+   :keyprefix: cite-monkey-
+
+.. bibliography:: /references/preconfigs.bib
+   Wang21a
+   Rami20
 
 Based on the preprocessing decisions of the default pipeline, this preconfiguration allows you to preprocess all of your macaque data, includes: