Add citation for Imaging Neuroscience article

CITATION.cff

@@ -0,0 +1,192 @@
+cff-version: 1.2.0
+message: If you use this code, please cite it as below.
+
+title: Methods for decoding cortical gradients of functional connectivity
+
+abstract: |
+  Macroscale gradients have emerged as a central principle for understanding functional brain 
+  organization. Previous studies have demonstrated that a principal gradient of connectivity in 
+  the human brain exists, with unimodal primary sensorimotor regions situated at one end and 
+  transmodal regions associated with the default mode network and representative of abstract 
+  functioning at the other. The functional significance and interpretation of macroscale gradients 
+  remains a central topic of discussion in the neuroimaging community, with some studies 
+  demonstrating that gradients may be described using meta-analytic functional decoding techniques. 
+  However, additional methodological development is necessary to fully leverage available 
+  meta-analytic methods and resources and quantitatively evaluate their relative performance. 
+  Here, we conducted a comprehensive series of analyses to investigate and improve the framework 
+  of data-driven, meta-analytic methods, thereby establishing a principled approach for gradient 
+  segmentation and functional decoding. We found that a two-segment solution determined by a 
+  k-means segmentation approach and an LDA-based meta-analysis combined with the NeuroQuery 
+  database was the optimal combination of methods for decoding functional connectivity gradients. 
+  Finally, we proposed a method for decoding additional components of the gradient decomposition. 
+  The current work aims to provide recommendations on best practices and flexible methods for 
+  gradient-based functional decoding of fMRI data.
+
+repository-code: https://github.com/JulioAPeraza/gradec
+
+identifiers:
+  - type: doi
+    value: https://doi.org/10.1162/imag_a_00081
+    description: Methods for decoding cortical gradients of functional connectivity
+
+contact:
+  - given-names: Julio A
+    family-names: Peraza
+    email: [email protected]
+    affiliation: Department of Physics, Florida International University, Miami, FL, USA
+
+license: Apache License 2.0
+
+authors:
+  - given-names: Julio A
+    family-names: Peraza
+    orcid: 0000-0003-3816-5903
+    affiliation: Department of Physics, Florida International University, Miami, FL, USA
+  - given-names: Taylor
+    family-names: Salo
+    orcid: 0000-0001-9813-3167
+    affiliation: Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
+  - given-names: Michael C
+    family-names: Michael
+    orcid: 0000-0002-1860-4449
+    affiliation: LTI Engineering and Software, Quebec City, QC, Canada
+  - given-names: Katherine L
+    family-names: Bottenhorn
+    orcid: 0000-0002-7796-8795
+    affiliation: Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
+  - given-names: Jean-Baptiste
+    family-names: Poline
+    orcid: 0000-0002-9794-749X
+    affiliation: Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
+  - given-names: Jérôme
+    family-names: Dockès
+    orcid: 0000-0002-5304-2496
+    affiliation: Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
+  - given-names: James D
+    family-names: Kent
+    orcid: 0000-0002-4892-2659
+    affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
+  - given-names: Jessica E
+    family-names: Bartley
+    orcid: 0000-0001-7269-9701
+    affiliation: Department of Physics, Florida International University, Miami, FL, USA
+  - given-names: Jessica S
+    family-names: Flannery
+    orcid: 0000-0003-3274-1578
+    affiliation: Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA
+  - given-names: Lauren D
+    family-names: Hill-Bowen
+    orcid: 0000-0002-9817-7757
+    affiliation: Department of Psychology, Florida International University, Miami, FL, USA
+  - given-names: Rosario
+    family-names: Pintos Lobo
+    orcid: 0000-0002-7679-1385
+    affiliation: Department of Psychology, Florida International University, Miami, FL, USA
+  - given-names: Ranjita
+    family-names: Poudel
+    orcid: 0000-0003-4343-1153
+    affiliation: Department of Health Outcomes and Behavior, Moffitt Cancer Center, Tampa, FL, USA
+  - given-names: Kimberly L
+    family-names: Ray
+    orcid: 0000-0003-1302-2834
+    affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
+  - given-names: Jennifer L
+    family-names: Robinson
+    orcid: 0000-0001-7389-3047
+    affiliation: Department of Psychology, Auburn University, Auburn, AL, USA
+  - given-names: Robert W
+    family-names: Laird
+    affiliation: Department of Physics, Florida International University, Miami, FL, USA
+  - given-names: Matthew T
+    family-names: Sutherland
+    orcid: 0000-0002-6091-4037
+    affiliation: Department of Psychology, Florida International University, Miami, FL, USA
+  - given-names: Alejandro
+    family-names: de la Vega
+    orcid: 0000-0001-9062-3778
+    affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
+  - given-names: Angela R
+    family-names: Laird
+    orcid: 0000-0003-3379-8744
+    affiliation: Department of Physics, Florida International University, Miami, FL, USA
+
+preferred-citation:
+  authors:
+    - given-names: Julio A
+      family-names: Peraza
+      orcid: 0000-0003-3816-5903
+      affiliation: Department of Physics, Florida International University, Miami, FL, USA
+    - given-names: Taylor
+      family-names: Salo
+      orcid: 0000-0001-9813-3167
+      affiliation: Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
+    - given-names: Michael C
+      family-names: Michael
+      orcid: 0000-0002-1860-4449
+      affiliation: LTI Engineering and Software, Quebec City, QC, Canada
+    - given-names: Katherine L
+      family-names: Bottenhorn
+      orcid: 0000-0002-7796-8795
+      affiliation: Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
+    - given-names: Jean-Baptiste
+      family-names: Poline
+      orcid: 0000-0002-9794-749X
+      affiliation: Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
+    - given-names: Jérôme
+      family-names: Dockès
+      orcid: 0000-0002-5304-2496
+      affiliation: Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
+    - given-names: James D
+      family-names: Kent
+      orcid: 0000-0002-4892-2659
+      affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
+    - given-names: Jessica E
+      family-names: Bartley
+      orcid: 0000-0001-7269-9701
+      affiliation: Department of Physics, Florida International University, Miami, FL, USA
+    - given-names: Jessica S
+      family-names: Flannery
+      orcid: 0000-0003-3274-1578
+      affiliation: Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA
+    - given-names: Lauren D
+      family-names: Hill-Bowen
+      orcid: 0000-0002-9817-7757
+      affiliation: Department of Psychology, Florida International University, Miami, FL, USA
+    - given-names: Rosario
+      family-names: Pintos Lobo
+      orcid: 0000-0002-7679-1385
+      affiliation: Department of Psychology, Florida International University, Miami, FL, USA
+    - given-names: Ranjita
+      family-names: Poudel
+      orcid: 0000-0003-4343-1153
+      affiliation: Department of Health Outcomes and Behavior, Moffitt Cancer Center, Tampa, FL, USA
+    - given-names: Kimberly L
+      family-names: Ray
+      orcid: 0000-0003-1302-2834
+      affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
+    - given-names: Jennifer L
+      family-names: Robinson
+      orcid: 0000-0001-7389-3047
+      affiliation: Department of Psychology, Auburn University, Auburn, AL, USA
+    - given-names: Robert W
+      family-names: Laird
+      affiliation: Department of Physics, Florida International University, Miami, FL, USA
+    - given-names: Matthew T
+      family-names: Sutherland
+      orcid: 0000-0002-6091-4037
+      affiliation: Department of Psychology, Florida International University, Miami, FL, USA
+    - given-names: Alejandro
+      family-names: de la Vega
+      orcid: 0000-0001-9062-3778
+      affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
+    - given-names: Angela R
+      family-names: Laird
+      orcid: 0000-0003-3379-8744
+      affiliation: Department of Physics, Florida International University, Miami, FL, USA
+
+  title: "Methods for decoding cortical gradients of functional connectivity"
+  doi: 10.1162/imag_a_00081
+  date-released: 2024-02-02
+  url: "https://doi.org/10.1162/imag_a_00081"
+  journal: Imaging Neuroscience
+  type: article

README.md

@@ -1,5 +1,6 @@
 # Gradec
-A Python library for meta-analytic functional decoding of cortical gradient of functional 
+
+A Python library for meta-analytic functional decoding of cortical gradient of functional
 connectivity.
 
 [![Latest Version](https://img.shields.io/pypi/v/gradec.svg)](https://pypi.python.org/pypi/gradec/)
@@ -19,18 +20,20 @@ Please see our [installation instructions](https://gradec.readthedocs.io/en/stab
 for information on how to install gradec.
 
 ### Installation with pip
+
 ```
 pip install gradec
 ```
 
 ### Local installation (development version)
+
 ```
 pip install git+https://github.com/JulioAPeraza/gradec.git
 ```
 
 ## Citing gradec
 
-If you use gradec in your research, we recommend citing the Zenodo DOI associated with the gradec version you used.
+If you use gradec in your research, we recommend citing the Zenodo DOI associated with the gradec version you used, as well as the Imaging Neuroscience journal article: https://doi.org/10.1162/imag_a_00081.
 You can find the Zenodo DOI associated with each gradec release at https://zenodo.org/record/8161766.
 
 ## Contributing

docs/index.rst

@@ -11,6 +11,46 @@ To install Gradec check out our `installation guide`_.
 
 .. _installation guide: installation.html
 
+Citing Gradec
+-------------
+
+If you use gradec in your research, we recommend citing the Zenodo DOI associated with the gradec 
+version you used, as well as the Imaging Neuroscience journal 
+article: https://doi.org/10.1162/imag_a_00081.
+You can find the Zenodo DOI associated with each gradec release 
+at https://zenodo.org/record/8161766.
+
+.. code-block:: bibtex
+    :caption: BibTeX entries for Gradec version 0.0.1rc3.
+
+    # This is the Imaging Neuroscience paper.
+    @article{10.1162/imag_a_00081,
+        author = {Peraza, Julio A. and Salo, Taylor and Riedel, Michael C. and Bottenhorn, Katherine L. and Poline, Jean-Baptiste and Dockès, Jérôme and Kent, James D. and Bartley, Jessica E. and Flannery, Jessica S. and Hill-Bowen, Lauren D. and Lobo, Rosario Pintos and Poudel, Ranjita and Ray, Kimberly L. and Robinson, Jennifer L. and Laird, Robert W. and Sutherland, Matthew T. and de la Vega, Alejandro and Laird, Angela R.},
+        title = "{Methods for decoding cortical gradients of functional connectivity}",
+        journal = {Imaging Neuroscience},
+        volume = {2},
+        pages = {1-32},
+        year = {2024},
+        month = {02},
+        abstract = "{Macroscale gradients have emerged as a central principle for understanding functional brain organization. Previous studies have demonstrated that a principal gradient of connectivity in the human brain exists, with unimodal primary sensorimotor regions situated at one end and transmodal regions associated with the default mode network and representative of abstract functioning at the other. The functional significance and interpretation of macroscale gradients remains a central topic of discussion in the neuroimaging community, with some studies demonstrating that gradients may be described using meta-analytic functional decoding techniques. However, additional methodological development is necessary to fully leverage available meta-analytic methods and resources and quantitatively evaluate their relative performance. Here, we conducted a comprehensive series of analyses to investigate and improve the framework of data-driven, meta-analytic methods, thereby establishing a principled approach for gradient segmentation and functional decoding. We found that a two-segment solution determined by a k-means segmentation approach and an LDA-based meta-analysis combined with the NeuroQuery database was the optimal combination of methods for decoding functional connectivity gradients. Finally, we proposed a method for decoding additional components of the gradient decomposition. The current work aims to provide recommendations on best practices and flexible methods for gradient-based functional decoding of fMRI data.}",
+        issn = {2837-6056},
+        doi = {10.1162/imag_a_00081},
+        url = {https://doi.org/10.1162/imag\_a\_00081},
+        eprint = {https://direct.mit.edu/imag/article-pdf/doi/10.1162/imag\_a\_00081/2326234/imag\_a\_00081.pdf},
+    }
+
+    # This is the Zenodo citation for version 0.0.1rc3.
+    @software{peraza_2023_8161766,
+       author = {Peraza, Julio A. and Kent, James D. and Salo, Taylor and De La Vega, Alejandro and Laird, Angela R.},
+       title = {JulioAPeraza/gradec: 0.0.1rc3},
+       month = jul,
+       year = 2023,
+       publisher = {Zenodo},
+       version = {0.0.1rc3},
+       doi = {10.5281/zenodo.8161766},
+       url = {https://doi.org/10.5281/zenodo.8161766}
+    }
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents: