Merge pull request #9 from Inria-Empenn/hugoblox-import-publications

Hugo Blox Builder - Import latest publications

content/publication/maumet-best-nodate/cite.bib

@@ -0,0 +1,6 @@
+@article{maumet_best_nodate,
+ author = {Maumet, Camille and Ghosh, Satrajit and Halchenko, Yaroslav O and Jarecka, Dorota and Nichols, Nolan B and Poline, Jean-Baptiste and Hanke, Michael},
+ file = {Maumet et al. - The best of both worlds using semantic web with J.pdf:/home/alpron/Zotero/storage/MW5U3VID/Maumet et al. - The best of both worlds using semantic web with J.pdf:application/pdf},
+ language = {en},
+ title = {The best of both worlds: using semantic web with JSON-LD. An example with NIDM-Results & Datalad}
+}

content/publication/maumet-best-nodate/index.md

@@ -0,0 +1,16 @@
+---
+title: 'The best of both worlds: using semantic web with JSON-LD. An example with
+  NIDM-Results & Datalad'
+authors:
+- Camille Maumet
+- Satrajit Ghosh
+- Yaroslav O Halchenko
+- Dorota Jarecka
+- Nolan B Nichols
+- Jean-Baptiste Poline
+- Michael Hanke
+date: -01-01
+publishDate: '2024-07-24T11:50:09.793427Z'
+publication_types:
+- article-journal
+---

content/publication/maumet-towards-nodate-1/cite.bib

@@ -0,0 +1,7 @@
+@phdthesis{maumet_towards_nodate-1,
+ author = {Maumet, Camille},
+ file = {Maumet - Towards reproducible neuroimaging Solutions for s.pdf:/home/alpron/Zotero/storage/S7YM9AUP/Maumet - Towards reproducible neuroimaging Solutions for s.pdf:application/pdf},
+ keywords = {Important},
+ language = {en},
+ title = {Towards reproducible neuroimaging: Solutions for sharing and re-using brain imaging data}
+}

content/publication/maumet-towards-nodate-1/index.md

@@ -0,0 +1,12 @@
+---
+title: 'Towards reproducible neuroimaging: Solutions for sharing and re-using brain
+  imaging data'
+authors:
+- Camille Maumet
+date: -01-01
+publishDate: '2024-07-24T11:50:09.812264Z'
+publication_types:
+- thesis
+tags:
+- Important
+---

content/publication/maumet-towards-nodate/cite.bib

@@ -0,0 +1,6 @@
+@misc{maumet_towards_nodate,
+ author = {Maumet, Camille},
+ file = {Maumet - Towards reusable derived data in neuroimaging.pdf:/home/alpron/Zotero/storage/SPIMSHT9/Maumet - Towards reusable derived data in neuroimaging.pdf:application/pdf},
+ language = {en},
+ title = {Towards reusable derived data in neuroimaging}
+}

content/publication/maumet-towards-nodate/index.md

@@ -0,0 +1,9 @@
+---
+title: Towards reusable derived data in neuroimaging
+authors:
+- Camille Maumet
+date: -01-01
+publishDate: '2024-07-24T11:50:09.806228Z'
+publication_types:
+- manuscript
+---

content/publication/noauthor-bids-nodate/cite.bib

@@ -0,0 +1,10 @@
+@misc{noauthor_bids_nodate,
+ file = {Snapshot:/home/alpron/Zotero/storage/84FRG2PA/edit.html:text/html},
+ journal = {Google Docs},
+ keywords = {BIDS, provenance},
+ language = {fr},
+ shorttitle = {BIDS Extension Proposal (BEP028)},
+ title = {BIDS Extension Proposal (BEP028): Provenance},
+ url = {https://docs.google.com/document/d/1vw3VNDof5cecv2PkFp7Lw_pNUTUo8-m8V4SIdtGJVKs/edit?usp=sharing&usp=embed_facebook},
+ urldate = {2024-02-29}
+}

content/publication/noauthor-bids-nodate/index.md

@@ -0,0 +1,15 @@
+---
+title: 'BIDS Extension Proposal (BEP028): Provenance'
+date: -01-01
+publishDate: '2024-07-24T11:50:09.777118Z'
+publication_types:
+- manuscript
+publication: '*Google Docs*'
+tags:
+- BIDS
+- provenance
+links:
+- name: URL
+  url: 
+    https://docs.google.com/document/d/1vw3VNDof5cecv2PkFp7Lw_pNUTUo8-m8V4SIdtGJVKs/edit?usp=sharing&usp=embed_facebook
+---

content/publication/noauthor-computational-nodate/cite.bib

@@ -0,0 +1,7 @@
+@misc{noauthor_computational_nodate,
+ file = {Computational basis and ReproIn/DataLad\: ReproIn/DataLad\: A complete portable and reproducible fMRI study from scratch:/home/alpron/Zotero/storage/C7QV89WR/03-01-reproin.html:text/html},
+ keywords = {datalad},
+ title = {Computational basis and ReproIn/DataLad: A complete portable and reproducible fMRI study from scratch},
+ url = {http://www.repronim.org/ohbm2018-training/03-01-reproin/},
+ urldate = {2024-02-29}
+}

content/publication/noauthor-computational-nodate/index.md

@@ -0,0 +1,13 @@
+---
+title: 'Computational basis and ReproIn/DataLad: A complete portable and reproducible
+  fMRI study from scratch'
+date: -01-01
+publishDate: '2024-07-24T11:50:09.787184Z'
+publication_types:
+- manuscript
+tags:
+- datalad
+links:
+- name: URL
+  url: http://www.repronim.org/ohbm2018-training/03-01-reproin/
+---

content/publication/noauthor-datalad-nodate/cite.bib

@@ -0,0 +1,7 @@
+@misc{noauthor_datalad_nodate,
+ file = {DataLad extension module for neuroimaging studies — Datalad for Hirnis 0.0.8 documentation:/home/alpron/Zotero/storage/Z3HMSFLD/index.html:text/html},
+ keywords = {datalad},
+ title = {DataLad extension module for neuroimaging studies — Datalad for Hirnis 0.0.8 documentation},
+ url = {http://docs.datalad.org/projects/hirni/en/latest/index.html},
+ urldate = {2024-03-19}
+}

content/publication/noauthor-datalad-nodate/index.md

@@ -0,0 +1,13 @@
+---
+title: DataLad extension module for neuroimaging studies — Datalad for Hirnis 0.0.8
+  documentation
+date: -01-01
+publishDate: '2024-07-24T11:50:09.799622Z'
+publication_types:
+- manuscript
+tags:
+- datalad
+links:
+- name: URL
+  url: http://docs.datalad.org/projects/hirni/en/latest/index.html
+---

content/publication/renton-neurodesk-2024/cite.bib

@@ -0,0 +1,16 @@
+@article{renton_neurodesk_2024,
+ author = {Renton, Angela I. and Dao, Thuy T. and Johnstone, Tom and Civier, Oren and Sullivan, Ryan P. and White, David J. and Lyons, Paris and Slade, Benjamin M. and Abbott, David F. and Amos, Toluwani J. and Bollmann, Saskia and Botting, Andy and Campbell, Megan E. J. and Chang, Jeryn and Close, Thomas G. and Dörig, Monika and Eckstein, Korbinian and Egan, Gary F. and Evas, Stefanie and Flandin, Guillaume and Garner, Kelly G. and Garrido, Marta I. and Ghosh, Satrajit S. and Grignard, Martin and Halchenko, Yaroslav O. and Hannan, Anthony J. and Heinsfeld, Anibal S. and Huber, Laurentius and Hughes, Matthew E. and Kaczmarzyk, Jakub R. and Kasper, Lars and Kuhlmann, Levin and Lou, Kexin and Mantilla-Ramos, Yorguin-Jose and Mattingley, Jason B. and Meier, Michael L. and Morris, Jo and Narayanan, Akshaiy and Pestilli, Franco and Puce, Aina and Ribeiro, Fernanda L. and Rogasch, Nigel C. and Rorden, Chris and Schira, Mark M. and Shaw, Thomas B. and Sowman, Paul F. and Spitz, Gershon and Stewart, Ashley W. and Ye, Xincheng and Zhu, Judy D. and Narayanan, Aswin and Bollmann, Steffen},
+ doi = {10.1038/s41592-023-02145-x},
+ issn = {1548-7091, 1548-7105},
+ journal = {Nature Methods},
+ language = {en},
+ month = {May},
+ number = {5},
+ pages = {804--808},
+ shorttitle = {Neurodesk},
+ title = {Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging},
+ url = {https://www.nature.com/articles/s41592-023-02145-x},
+ urldate = {2024-07-23},
+ volume = {21},
+ year = {2024}
+}

content/publication/renton-neurodesk-2024/index.md

@@ -0,0 +1,66 @@
+---
+title: 'Neurodesk: an accessible, flexible and portable data analysis environment
+  for reproducible neuroimaging'
+authors:
+- Angela I. Renton
+- Thuy T. Dao
+- Tom Johnstone
+- Oren Civier
+- Ryan P. Sullivan
+- David J. White
+- Paris Lyons
+- Benjamin M. Slade
+- David F. Abbott
+- Toluwani J. Amos
+- Saskia Bollmann
+- Andy Botting
+- Megan E. J. Campbell
+- Jeryn Chang
+- Thomas G. Close
+- Monika Dörig
+- Korbinian Eckstein
+- Gary F. Egan
+- Stefanie Evas
+- Guillaume Flandin
+- Kelly G. Garner
+- Marta I. Garrido
+- Satrajit S. Ghosh
+- Martin Grignard
+- Yaroslav O. Halchenko
+- Anthony J. Hannan
+- Anibal S. Heinsfeld
+- Laurentius Huber
+- Matthew E. Hughes
+- Jakub R. Kaczmarzyk
+- Lars Kasper
+- Levin Kuhlmann
+- Kexin Lou
+- Yorguin-Jose Mantilla-Ramos
+- Jason B. Mattingley
+- Michael L. Meier
+- Jo Morris
+- Akshaiy Narayanan
+- Franco Pestilli
+- Aina Puce
+- Fernanda L. Ribeiro
+- Nigel C. Rogasch
+- Chris Rorden
+- Mark M. Schira
+- Thomas B. Shaw
+- Paul F. Sowman
+- Gershon Spitz
+- Ashley W. Stewart
+- Xincheng Ye
+- Judy D. Zhu
+- Aswin Narayanan
+- Steffen Bollmann
+date: '2024-05-01'
+publishDate: '2024-07-24T11:50:09.833267Z'
+publication_types:
+- article-journal
+publication: '*Nature Methods*'
+doi: 10.1038/s41592-023-02145-x
+links:
+- name: URL
+  url: https://www.nature.com/articles/s41592-023-02145-x
+---

content/publication/sanz-robinson-open-source-nodate/cite.bib

@@ -0,0 +1,6 @@
+@article{sanz-robinson_open-source_nodate,
+ author = {Sanz-Robinson, Jacob and Wang, Michelle and McPherson, Brent and Glatard, Tristan and Poline, Jean-Baptiste},
+ file = {Sanz-Robinson et al. - Open-source tools and platforms to investigate ana.pdf:/home/alpron/Zotero/storage/ZCERUVV7/Sanz-Robinson et al. - Open-source tools and platforms to investigate ana.pdf:application/pdf},
+ note = {Publisher: OSF},
+ title = {Open-source tools and platforms to investigate analytical variability in neuroimaging}
+}

content/publication/sanz-robinson-open-source-nodate/index.md

@@ -0,0 +1,13 @@
+---
+title: Open-source tools and platforms to investigate analytical variability in neuroimaging
+authors:
+- Jacob Sanz-Robinson
+- Michelle Wang
+- Brent McPherson
+- Tristan Glatard
+- Jean-Baptiste Poline
+date: -01-01
+publishDate: '2024-07-24T11:50:09.818267Z'
+publication_types:
+- article-journal
+---

content/publication/soskic-garden-nodate/cite.bib

@@ -0,0 +1,13 @@
+@article{soskic_garden_nodate,
+ abstract = {Abstract This study tackles the Garden of Forking Paths, as a challenge for replicability and reproducibility of ERP studies. Here, we applied a multiverse analysis to a sample ERP N400 dataset, donated by an independent research team. We analyzed this dataset using 14 pipelines selected to showcase the full range of methodological variability found in the N400 literature using systematic review approach. The selected pipelines were compared in depth by looking into statistical test outcomes, descriptive statistics, effect size, data quality, and statistical power. In this way we provide a worked example of how analytic flexibility can impact results in research fields with high dimensionality such as ERP, when analyzed using standard null-hypothesis significance testing. Out of the methodological decisions that were varied, high-pass filter cut-off, artifact removal method, baseline duration, reference, measurement latency and locations, and amplitude measure (peak vs. mean) were all shown to affect at least some of the study outcome measures. Low-pass filtering was the only step which did not notably influence any of these measures. This study shows that even some of the seemingly minor procedural deviations can influence the conclusions of an ERP study. We demonstrate the power of multiverse analysis in both identifying the most reliable effects in a given study, and for providing insights into consequences of methodological decisions.},
+ author = {Šoškić, Anđela and Styles, Suzy J. and Kappenman, Emily S. and Ković, Vanja},
+ doi = {https://doi.org/10.1111/psyp.14628},
+ journal = {Psychophysiology},
+ keywords = {to read},
+ note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/psyp.14628},
+ number = {n/a},
+ pages = {e14628},
+ title = {Garden of forking paths in ERP research – Effects of varying pre-processing and analysis steps in an N400 experiment},
+ url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/psyp.14628},
+ volume = {n/a}
+}

content/publication/soskic-garden-nodate/index.md

@@ -0,0 +1,38 @@
+---
+title: Garden of forking paths in ERP research – Effects of varying pre-processing
+  and analysis steps in an N400 experiment
+authors:
+- Anđela Šoškić
+- Suzy J. Styles
+- Emily S. Kappenman
+- Vanja Ković
+date: -01-01
+publishDate: '2024-07-24T11:50:09.825196Z'
+publication_types:
+- article-journal
+publication: '*Psychophysiology*'
+doi: https://doi.org/10.1111/psyp.14628
+abstract: Abstract This study tackles the Garden of Forking Paths, as a challenge
+  for replicability and reproducibility of ERP studies. Here, we applied a multiverse
+  analysis to a sample ERP N400 dataset, donated by an independent research team.
+  We analyzed this dataset using 14 pipelines selected to showcase the full range
+  of methodological variability found in the N400 literature using systematic review
+  approach. The selected pipelines were compared in depth by looking into statistical
+  test outcomes, descriptive statistics, effect size, data quality, and statistical
+  power. In this way we provide a worked example of how analytic flexibility can impact
+  results in research fields with high dimensionality such as ERP, when analyzed using
+  standard null-hypothesis significance testing. Out of the methodological decisions
+  that were varied, high-pass filter cut-off, artifact removal method, baseline duration,
+  reference, measurement latency and locations, and amplitude measure (peak vs. mean)
+  were all shown to affect at least some of the study outcome measures. Low-pass filtering
+  was the only step which did not notably influence any of these measures. This study
+  shows that even some of the seemingly minor procedural deviations can influence
+  the conclusions of an ERP study. We demonstrate the power of multiverse analysis
+  in both identifying the most reliable effects in a given study, and for providing
+  insights into consequences of methodological decisions.
+tags:
+- to read
+links:
+- name: URL
+  url: https://onlinelibrary.wiley.com/doi/abs/10.1111/psyp.14628
+---