add joss paper

.github/workflows/draft-pdf.yml

@@ -0,0 +1,28 @@
+name: joss-paper
+
+on:
+    push:
+        branches:
+            - joss
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss/paper.pdf

joss/paper.bib

@@ -0,0 +1,136 @@
+@article{sinha2023solving,
+  title={Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA},
+  author={Sinha, Harsh and Raamana, Pradeep Reddy},
+  journal={bioRxiv},
+  pages={2023--07},
+  year={2023},
+  publisher={Cold Spring Harbor Laboratory}
+}
+
+@software{brett_2023_7795644,
+  author       = {Brett, Matthew and
+                  Markiewicz, Christopher J. and
+                  Hanke, Michael and
+                  Côté, Marc-Alexandre and
+                  Cipollini, Ben and
+                  McCarthy, Paul and
+                  Jarecka, Dorota and
+                  Cheng, Christopher P. and
+                  Halchenko, Yaroslav O. and
+                  Cottaar, Michiel and
+                  Larson, Eric and
+                  Ghosh, Satrajit and
+                  Wassermann, Demian and
+                  Gerhard, Stephan and
+                  Lee, Gregory R. and
+                  Baratz, Zvi and
+                  Wang, Hao-Ting and
+                  Kastman, Erik and
+                  Kaczmarzyk, Jakub and
+                  Guidotti, Roberto and
+                  Daniel, Jonathan and
+                  Duek, Or and
+                  Rokem, Ariel and
+                  Madison, Cindee and
+                  Papadopoulos Orfanos, Dimitri and
+                  Sólon, Anibal and
+                  Moloney, Brendan and
+                  Morency, Félix C. and
+                  Goncalves, Mathias and
+                  Markello, Ross and
+                  Riddell, Cameron and
+                  Burns, Christopher and
+                  Millman, Jarrod and
+                  Gramfort, Alexandre and
+                  Leppäkangas, Jaakko and
+                  van den Bosch, Jasper J.F. and
+                  Vincent, Robert D. and
+                  Braun, Henry and
+                  Subramaniam, Krish and
+                  Van, Andrew and
+                  Gorgolewski, Krzysztof J. and
+                  Raamana, Pradeep Reddy and
+                  Klug, Julian and
+                  Nichols, B. Nolan and
+                  Baker, Eric M. and
+                  Hayashi, Soichi and
+                  Pinsard, Basile and
+                  Haselgrove, Christian and
+                  Hymers, Mark and
+                  Esteban, Oscar and
+                  Koudoro, Serge and
+                  Pérez-García, Fernando and
+                  Dockès, Jérôme and
+                  Oosterhof, Nikolaas N. and
+                  Amirbekian, Bago and
+                  Christian, Horea and
+                  Nimmo-Smith, Ian and
+                  Nguyen, Ly and
+                  Reddigari, Samir and
+                  St-Jean, Samuel and
+                  Panfilov, Egor and
+                  Garyfallidis, Eleftherios and
+                  Varoquaux, Gael and
+                  Legarreta, Jon Haitz and
+                  Hahn, Kevin S. and
+                  Waller, Lea and
+                  Hinds, Oliver P. and
+                  Fauber, Bennet and
+                  Perez, Fabian and
+                  Roberts, Jacob and
+                  Poline, Jean-Baptiste and
+                  Stutters, Jon and
+                  Jordan, Kesshi and
+                  Cieslak, Matthew and
+                  Moreno, Miguel Estevan and
+                  Hrnčiar, Tomáš and
+                  Haenel, Valentin and
+                  Schwartz, Yannick and
+                  Darwin, Benjamin C and
+                  Thirion, Bertrand and
+                  Gauthier, Carl and
+                  Solovey, Igor and
+                  Gonzalez, Ivan and
+                  Palasubramaniam, Jath and
+                  Lecher, Justin and
+                  Leinweber, Katrin and
+                  Raktivan, Konstantinos and
+                  Calábková, Markéta and
+                  Fischer, Peter and
+                  Gervais, Philippe and
+                  Gadde, Syam and
+                  Ballinger, Thomas and
+                  Roos, Thomas and
+                  Reddam, Venkateswara Reddy and
+                  freec84},
+  title        = {nipy/nibabel: 5.1.0},
+  month        = apr,
+  year         = 2023,
+  publisher    = {Zenodo},
+  version      = {5.1.0},
+  doi          = {10.5281/zenodo.7795644},
+  url          = {https://doi.org/10.5281/zenodo.7795644}
+}
+
+@article{Yarkoni2019, doi = {10.21105/joss.01294}, url = {https://doi.org/10.21105/joss.01294}, year = {2019}, publisher = {The Open Journal}, volume = {4}, number = {40}, pages = {1294}, author = {Tal Yarkoni and Christopher J. Markiewicz and Alejandro de la Vega and Krzysztof J. Gorgolewski and Taylor Salo and Yaroslav O. Halchenko and Quinten McNamara and Krista DeStasio and Jean-Baptiste Poline and Dmitry Petrov and Valérie Hayot-Sasson and Dylan M. Nielson and Johan Carlin and Gregory Kiar and Kirstie Whitaker and Elizabeth DuPre and Adina Wagner and Lee S. Tirrell and Mainak Jas and Michael Hanke and Russell A. Poldrack and Oscar Esteban and Stefan Appelhoff and Chris Holdgraf and Isla Staden and Bertrand Thirion and Dave F. Kleinschmidt and John A. Lee and Matteo Visconti Oleggio di Castello and Michael P. Notter and Ross Blair}, title = {PyBIDS: Python tools for BIDS datasets}, journal = {Journal of Open Source Software} }
+
+@ARTICLE{Wang,
+
+AUTHOR={Wang, Sijia and Peterson, Daniel J. and Gatenby, J. C. and Li, Wenbin and Grabowski, Thomas J. and Madhyastha, Tara M.},   
+
+TITLE={Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion MRI},      
+
+JOURNAL={Frontiers in Neuroinformatics},      
+
+VOLUME={11},           
+
+YEAR={2017},      
+
+URL={https://www.frontiersin.org/articles/10.3389/fninf.2017.00017},       
+
+DOI={10.3389/fninf.2017.00017},      
+
+ISSN={1662-5196},   
+
+ABSTRACT={Correction of echo planar imaging (EPI)-induced distortions (called “unwarping”) improves anatomical fidelity for diffusion magnetic resonance imaging (MRI) and functional imaging investigations. Commonly used unwarping methods require the acquisition of supplementary images during the scanning session. Alternatively, distortions can be corrected by nonlinear registration to a non-EPI acquired structural image. In this study, we compared reliability using two methods of unwarping: (1) nonlinear registration to a structural image using symmetric normalization (SyN) implemented in Advanced Normalization Tools (ANTs); and (2) unwarping using an acquired field map. We performed this comparison in two different test-retest data sets acquired at differing sites (N = 39 and N = 32). In both data sets, nonlinear registration provided higher test-retest reliability of the output fractional anisotropy (FA) maps than field map-based unwarping, even when accounting for the effect of interpolation on the smoothness of the images. In general, field map-based unwarping was preferable if and only if the field maps were acquired optimally.}
+}