JOSS submision (#118)

* ADD basic info of the paper skip code spell on paper because it doesn't handle french * draft * fix joss workflow file name * FIX author syntax * FIX output path * FIX nilearn contributors * FIX typesetting * update RRID for projects that have them * Add Remi's details Co-authored-by: Remi Gau <[email protected]> * Add Quentin's details (#123) * Add N. Clarke orcid (#124) * ADD PB affiliations * make sure the paper changes don't trigger unrelated workflows * Mark the date for submission * FIX don't trigger test workflow on irrelevant PR * point to the latest doc in joss link * Formatting --------- Co-authored-by: Remi Gau <[email protected]> Co-authored-by: Quentin Dessain <[email protected]> Co-authored-by: Natasha Clarke <[email protected]>
bids-apps · Apr 12, 2024 · 9d6ca9f · 9d6ca9f
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diff --git a/.github/workflows/draft-paper.yml b/.github/workflows/draft-paper.yml
@@ -0,0 +1,27 @@
+on:
+  pull_request:
+  push:
+    branches: [main]
+    paths: ['paper/*']
+
+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: paper/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: paper/paper.pdf
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -10,6 +10,7 @@ on:
     branches:
     - main
     - maint/*
+    paths: ['giga_connectome/*', 'pyproject.toml', 'requirements.txt', 'Dockerfile']
 
 defaults:
   run:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -27,6 +27,7 @@ repos:
         additional_dependencies:
         - tomli
         args: ["--skip=*.svg"]
+        exclude: 'paper/.*'
 -   repo: https://github.com/PyCQA/flake8
     rev: 7.0.0
     hooks:

diff --git a/CITATION.cff b/CITATION.cff
@@ -20,10 +20,13 @@ authors:
   - family-names: Wang
     given-names: Hao-Ting
     email: [email protected]
+  - family-names: Gau
+    given-names: Rémi
   - family-names: Dessain
     given-names: Quentin
-  - family-names: Natasha
-    given-names: Clarke
-
+  - family-names: Clarke
+    given-names: Natasha
+  - family-names: Bellec
+    given-names: Pierre
 
 license: MIT
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -0,0 +1,281 @@
+@software{Nilearn,
+    author = {{Nilearn contributors}},
+    license = {BSD-4-Clause},
+    title = {{nilearn}},
+	year = {2024},
+    url = {https://github.com/nilearn/nilearn},
+    doi = {10.5281/zenodo.8397156}
+}
+
+@article{fmriprep,
+	title = {{fMRIPrep}: a robust preprocessing pipeline for functional {MRI}},
+	volume = {16},
+	issn = {1548-7091, 1548-7105},
+	doi = {10.1038/s41592-018-0235-4},
+	number = {1},
+	journal = {Nature Methods},
+	author = {Esteban, Oscar and Markiewicz, Christopher J. and Blair, Ross W. and Moodie, Craig A. and Isik, A. Ilkay and Erramuzpe, Asier and Kent, James D. and Goncalves, Mathias and DuPre, Elizabeth and Snyder, Madeleine and Oya, Hiroyuki and Ghosh, Satrajit S. and Wright, Jessey and Durnez, Joke and Poldrack, Russell A. and Gorgolewski, Krzysztof J.},
+	month = jan,
+	year = {2019},
+	pages = {111--116},
+}
+
+@article{bidsapp,
+	title = {{BIDS} apps: {Improving} ease of use, accessibility, and reproducibility of neuroimaging data analysis methods},
+	volume = {13},
+	issn = {1553-7358},
+	doi = {10.1371/journal.pcbi.1005209},
+	number = {3},
+	journal = {PLOS Computational Biology},
+	author = {Gorgolewski, Krzysztof J. and Alfaro-Almagro, Fidel and Auer, Tibor and Bellec, Pierre and Capotă, Mihai and Chakravarty, M. Mallar and Churchill, Nathan W. and Cohen, Alexander Li and Craddock, R. Cameron and Devenyi, Gabriel A. and Eklund, Anders and Esteban, Oscar and Flandin, Guillaume and Ghosh, Satrajit S. and Guntupalli, J. Swaroop and Jenkinson, Mark and Keshavan, Anisha and Kiar, Gregory and Liem, Franziskus and Raamana, Pradeep Reddy and Raffelt, David and Steele, Christopher J. and Quirion, Pierre-Olivier and Smith, Robert E. and Strother, Stephen C. and Varoquaux, Gaël and Wang, Yida and Yarkoni, Tal and Poldrack, Russell A.},
+	month = mar,
+	year = {2017},
+	pages = {e1005209},
+}
+
+@article{bids,
+	title = {The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments},
+	volume = {3},
+	issn = {2052-4463},
+	doi = {10.1038/sdata.2016.44},
+	number = {1},
+	journal = {Scientific Data},
+	author = {Gorgolewski, Krzysztof J. and Auer, Tibor and Calhoun, Vince D. and Craddock, R. Cameron and Das, Samir and Duff, Eugene P. and Flandin, Guillaume and Ghosh, Satrajit S. and Glatard, Tristan and Halchenko, Yaroslav O. and Handwerker, Daniel A. and Hanke, Michael and Keator, David and Li, Xiangrui and Michael, Zachary and Maumet, Camille and Nichols, B. Nolan and Nichols, Thomas E. and Pellman, John and Poline, Jean-Baptiste and Rokem, Ariel and Schaefer, Gunnar and Sochat, Vanessa and Triplett, William and Turner, Jessica A. and Varoquaux, Gaël and Poldrack, Russell A.},
+	month = jun,
+	year = {2016},
+	pages = {160044},
+}
+
+@article{wang_continuous_2024,
+	title = {Continuous evaluation of denoising strategies in resting-state {fMRI} connectivity using {fMRIPrep} and {Nilearn}},
+	volume = {20},
+	issn = {1553-7358},
+	doi = {10.1371/journal.pcbi.1011942},
+	number = {3},
+	urldate = {2024-03-28},
+	journal = {PLOS Computational Biology},
+	author = {Wang, Hao-Ting and Meisler, Steven L. and Sharmarke, Hanad and Clarke, Natasha and Gensollen, Nicolas and Markiewicz, Christopher J. and Paugam, François and Thirion, Bertrand and Bellec, Pierre},
+	month = mar,
+	year = {2024},
+	pages = {e1011942},
+}
+
+@article{templateflow,
+	title = {{TemplateFlow}: {FAIR}-sharing of multi-scale, multi-species brain models},
+	volume = {19},
+	issn = {1548-7105},
+	shorttitle = {{TemplateFlow}},
+	doi = {10.1038/s41592-022-01681-2},
+	language = {en},
+	number = {12},
+	journal = {Nature Methods},
+	author = {Ciric, Rastko and Thompson, William H. and Lorenz, Romy and Goncalves, Mathias and MacNicol, Eilidh E. and Markiewicz, Christopher J. and Halchenko, Yaroslav O. and Ghosh, Satrajit S. and Gorgolewski, Krzysztof J. and Poldrack, Russell A. and Esteban, Oscar},
+	month = dec,
+	year = {2022},
+	pages = {1568--1571},
+}
+
+@article{makris_decreased_2006,
+	title = {Decreased volume of left and total anterior insular lobule in schizophrenia},
+	volume = {83},
+	issn = {0920-9964},
+	doi = {10.1016/j.schres.2005.11.020},
+	number = {2-3},
+	journal = {Schizophrenia Research},
+	author = {Makris, Nikos and Goldstein, Jill M. and Kennedy, David and Hodge, Steven M. and Caviness, Verne S. and Faraone, Stephen V. and Tsuang, Ming T. and Seidman, Larry J.},
+	month = apr,
+	year = {2006},
+	pmid = {16448806},
+	pages = {155--171},
+}
+
+@article{goldstein_hypothalamic_2007,
+	title = {Hypothalamic abnormalities in schizophrenia: sex effects and genetic vulnerability},
+	volume = {61},
+	issn = {0006-3223},
+	shorttitle = {Hypothalamic abnormalities in schizophrenia},
+	doi = {10.1016/j.biopsych.2006.06.027},
+	language = {eng},
+	number = {8},
+	journal = {Biological Psychiatry},
+	author = {Goldstein, Jill M. and Seidman, Larry J. and Makris, Nikos and Ahern, Todd and O'Brien, Liam M. and Caviness, Verne S. and Kennedy, David N. and Faraone, Stephen V. and Tsuang, Ming T.},
+	month = apr,
+	year = {2007},
+	pmid = {17046727},
+	pages = {935--945},
+}
+
+@article{frazier_structural_2005,
+	title = {Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder},
+	volume = {162},
+	issn = {0002-953X},
+	doi = {10.1176/appi.ajp.162.7.1256},
+	language = {eng},
+	number = {7},
+	journal = {The American Journal of Psychiatry},
+	author = {Frazier, Jean A. and Chiu, Sufen and Breeze, Janis L. and Makris, Nikos and Lange, Nicholas and Kennedy, David N. and Herbert, Martha R. and Bent, Eileen K. and Koneru, Vamsi K. and Dieterich, Megan E. and Hodge, Steven M. and Rauch, Scott L. and Grant, P. Ellen and Cohen, Bruce M. and Seidman, Larry J. and Caviness, Verne S. and Biederman, Joseph},
+	month = jul,
+	year = {2005},
+	pmid = {15994707},
+	pages = {1256--1265},
+}
+
+@article{desikan_automated_2006,
+	title = {An automated labeling system for subdividing the human cerebral cortex on {MRI} scans into gyral based regions of interest},
+	volume = {31},
+	issn = {1053-8119},
+	doi = {10.1016/j.neuroimage.2006.01.021},
+	language = {eng},
+	number = {3},
+	journal = {NeuroImage},
+	author = {Desikan, Rahul S. and Ségonne, Florent and Fischl, Bruce and Quinn, Brian T. and Dickerson, Bradford C. and Blacker, Deborah and Buckner, Randy L. and Dale, Anders M. and Maguire, R. Paul and Hyman, Bradley T. and Albert, Marilyn S. and Killiany, Ronald J.},
+	month = jul,
+	year = {2006},
+	pmid = {16530430},
+	pages = {968--980},
+}
+
+@article{schaefer_local-global_2018,
+	title = {Local-{Global} {Parcellation} of the {Human} {Cerebral} {Cortex} from {Intrinsic} {Functional} {Connectivity} {MRI}},
+	volume = {28},
+	issn = {1460-2199},
+	doi = {10.1093/cercor/bhx179},
+	language = {eng},
+	number = {9},
+	journal = {Cerebral Cortex (New York, N.Y.: 1991)},
+	author = {Schaefer, Alexander and Kong, Ru and Gordon, Evan M. and Laumann, Timothy O. and Zuo, Xi-Nian and Holmes, Avram J. and Eickhoff, Simon B. and Yeo, B. T. Thomas},
+	month = sep,
+	year = {2018},
+	pmid = {28981612},
+	pmcid = {PMC6095216},
+	pages = {3095--3114},
+}
+
+@article{urchs_mist_2019,
+	title = {{MIST}: {A} multi-resolution parcellation of functional brain networks},
+	volume = {1},
+	issn = {2515-5059},
+	shorttitle = {{MIST}},
+	doi = {10.12688/mniopenres.12767.2},
+	language = {en},
+	urldate = {2024-03-28},
+	journal = {MNI Open Research},
+	author = {Urchs, Sebastian and Armoza, Jonathan and Moreau, Clara and Benhajali, Yassine and St-Aubin, Jolène and Orban, Pierre and Bellec, Pierre},
+	month = mar,
+	year = {2019},
+	pages = {3},
+}
+
+@article{dadi_fine-grain_2020,
+	title = {Fine-grain atlases of functional modes for {fMRI} analysis},
+	volume = {221},
+	issn = {1053-8119},
+	doi = {10.1016/j.neuroimage.2020.117126},
+	urldate = {2024-03-28},
+	journal = {NeuroImage},
+	author = {Dadi, Kamalaker and Varoquaux, Gaël and Machlouzarides-Shalit, Antonia and Gorgolewski, Krzysztof J. and Wassermann, Demian and Thirion, Bertrand and Mensch, Arthur},
+	month = nov,
+	year = {2020},
+	pages = {117126},
+}
+
+@article{clarke_2024,
+    title = {Investigating the convergence of resting-state functional connectivity profiles in {Alzheimer}'s disease with neuropsychiatric symptoms and schizophrenia},
+    author = {Clarke, Natasha and Moreau, Clara A. and Harvey, Annabelle and Wang, Hao-Ting and Orban, Pierre and Zahinoor, Ismail and Jacquemont, Sébastien and Bellec, Pierre},
+    year = {2024},
+    journal = {Brain Communications}
+}
+
+
+@article{HALFpipe,
+	title = {{ENIGMA} {HALFpipe}: {Interactive}, reproducible, and efficient analysis for resting-state and task-based {fMRI} data},
+	volume = {43},
+	issn = {1097-0193},
+	doi = {10.1002/hbm.25829},
+	language = {eng},
+	number = {9},
+	journal = {Human Brain Mapping},
+	author = {Waller, Lea and Erk, Susanne and Pozzi, Elena and Toenders, Yara J. and Haswell, Courtney C. and Büttner, Marc and Thompson, Paul M. and Schmaal, Lianne and Morey, Rajendra A. and Walter, Henrik and Veer, Ilya M.},
+	month = jun,
+	year = {2022},
+	pmid = {35305030},
+	pmcid = {PMC9120555},
+	pages = {2727--2742},
+}
+
+@misc{cpac,
+	title = {Moving {Beyond} {Processing} and {Analysis}-{Related} {Variation} in {Neuroscience}},
+	doi = {10.1101/2021.12.01.470790},
+	language = {en},
+	urldate = {2024-03-28},
+	publisher = {bioRxiv},
+	author = {Li, Xinhui and Esper, Nathalia Bianchini and Ai, Lei and Giavasis, Steve and Jin, Hecheng and Feczko, Eric and Xu, Ting and Clucas, Jon and Franco, Alexandre and Heinsfeld, Anibal Sólon and Adebimpe, Azeez and Vogelstein, Joshua T. and Yan, Chao-Gan and Esteban, Oscar and Poldrack, Russell A. and Craddock, Cameron and Fair, Damien and Satterthwaite, Theodore and Kiar, Gregory and Milham, Michael P.},
+	month = jan,
+	year = {2024},
+}
+
+@article{conn,
+	title = {Conn: a functional connectivity toolbox for correlated and anticorrelated brain networks},
+	volume = {2},
+	issn = {2158-0022},
+	doi = {10.1089/brain.2012.0073},
+	language = {eng},
+	number = {3},
+	journal = {Brain Connectivity},
+	author = {Whitfield-Gabrieli, Susan and Nieto-Castanon, Alfonso},
+	year = {2012},
+	pmid = {22642651},
+	pages = {125--141},
+}
+
+@misc{xcp-d,
+	title = {{XCP}-{D}: {A} {Robust} {Pipeline} for the post-processing of {fMRI} data},
+	shorttitle = {{XCP}-{D}},
+	doi = {10.1101/2023.11.20.567926},
+	language = {en},
+	urldate = {2024-03-28},
+	publisher = {bioRxiv},
+	author = {Mehta, Kahini and Salo, Taylor and Madison, Thomas and Adebimpe, Azeez and Bassett, Danielle S. and Bertolero, Max and Cieslak, Matthew and Covitz, Sydney and Houghton, Audrey and Keller, Arielle S. and Luo, Audrey and Miranda-Dominguez, Oscar and Nelson, Steve M. and Shafiei, Golia and Shanmugan, Sheila and Shinohara, Russell T. and Sydnor, Valerie J. and Feczko, Eric and Fair, Damien A. and Satterthwaite, Theodore D.},
+	month = nov,
+	year = {2023},
+}
+
+@article{ABIDE,
+	title = {The {Autism} {Brain} {Imaging} {Data} {Exchange}: {Towards} {Large}-{Scale} {Evaluation} of the {Intrinsic} {Brain} {Architecture} in {Autism}},
+	volume = {19},
+	issn = {1359-4184},
+	doi = {10.1038/mp.2013.78},
+	number = {6},
+	journal = {Molecular psychiatry},
+	author = {Di Martino, Adriana and Yan, Chao-Gan and Li, Qingyang and Denio, Erin and Castellanos, Francisco X. and Alaerts, Kaat and Anderson, Jeffrey S. and Assaf, Michal and Bookheimer, Susan Y. and Dapretto, Mirella and Deen, Ben and Delmonte, Sonja and Dinstein, Ilan and Ertl-Wagner, Birgit and Fair, Damien A. and Gallagher, Louise and Kennedy, Daniel P. and Keown, Christopher L. and Keysers, Christian and Lainhart, Janet E. and Lord, Catherine and Luna, Beatriz and Menon, Vinod and Minshew, Nancy and Monk, Christopher S. and Mueller, Sophia and Müller, Ralph-Axel and Nebel, Mary Beth and Nigg, Joel T. and O’Hearn, Kirsten and Pelphrey, Kevin A. and Peltier, Scott J. and Rudie, Jeffrey D. and Sunaert, Stefan and Thioux, Marc and Tyszka, J. Michael and Uddin, Lucina Q. and Verhoeven, Judith S. and Wenderoth, Nicole and Wiggins, Jillian L. and Mostofsky, Stewart H. and Milham, Michael P.},
+	month = jun,
+	year = {2014},
+	pmid = {23774715},
+	pmcid = {PMC4162310},
+	pages = {659--667},
+}
+
+@article{ukbiobank,
+	title = {{UK} {Biobank}: {An} {Open} {Access} {Resource} for {Identifying} the {Causes} of a {Wide} {Range} of {Complex} {Diseases} of {Middle} and {Old} {Age}},
+	volume = {12},
+	issn = {1549-1676},
+	doi = {10.1371/journal.pmed.1001779},
+	language = {en},
+	number = {3},
+	journal = {PLOS Medicine},
+	author = {Sudlow, Cathie and Gallacher, John and Allen, Naomi and Beral, Valerie and Burton, Paul and Danesh, John and Downey, Paul and Elliott, Paul and Green, Jane and Landray, Martin and Liu, Bette and Matthews, Paul and Ong, Giok and Pell, Jill and Silman, Alan and Young, Alan and Sprosen, Tim and Peakman, Tim and Collins, Rory},
+	month = mar,
+	year = {2015},
+	pages = {e1001779},
+}
+
+@article{adhd200,
+	title = {The adhd-200 consortium: a model to advance the translational potential of neuroimaging in clinical neuroscience},
+	volume = {6},
+	issn = {1662-5137},
+	doi = {10.3389/fnsys.2012.00062},
+	journal = {Frontiers in Systems Neuroscience},
+	author = {Milham, Michael P. Ph D. and Fair, Damien PA-C. and Mennes, Maarten Ph D. and Mostofsky, Stewart H. M. D.},
+	month = sep,
+	year = {2012}
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,6 +10,7 @@ on: @@
         branches:
         - main
         - maint/*
+        paths: ['giga_connectome/*', 'pyproject.toml', 'requirements.txt', 'Dockerfile']
     defaults:
       run:
@@ Expand Down @@