From a8daefb4eace4b109a387042c4f61b27653c27a0 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 21 Mar 2024 19:35:02 -0400 Subject: [PATCH 1/4] add references in citation file --- CITATION.cff | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 23f53ad4bd..22990c0443 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -28,6 +28,46 @@ identifiers: - description: PDFs of the BIDS specification for versions 1.0.0 to 1.8.0 type: doi value: 10.5281/zenodo.3686061 + # papers to inject in the how to cite section + # ### Original publication + - description: Original publication + type: doi + value: 10.1038/sdata.2016.44 + # ### Datatype specific publications + - description: EEG + type: doi + value: 10.1038/s41597-019-0104-8 + - description: iEEG + type: doi + value: 10.1038/s41597-019-0105-7 + - description: MEG + type: doi + value: 10.1038/sdata.2018.110 + - description: PET + type: doi + value: 10.1038/s41597-022-01164-1 + - description: PET guidelines + type: doi + value: 10.1177/0271678X20905433 + - description: Genetics + type: doi + value: 10.1093/gigascience/giaa104 + - description: Microscopy + type: doi + value: 10.3389/fnins.2022.871228 + - description: qMRI + type: doi + value: 10.1038/s41597-022-01571-4 + - description: ASL + type: doi + value: 10.1038/s41597-022-01615-9 + - description: NIRS + type: doi + value: 10.31219/osf.io/7nmcp + - description: Motion + type: doi + value: 10.31234/osf.io/w6z79 + keywords: - brain imaging data structure From 868c89862bd580c451fd8a41f181f1ca208b88b5 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 21 Mar 2024 19:41:44 -0400 Subject: [PATCH 2/4] add delimiters --- src/introduction.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/introduction.md b/src/introduction.md index e56f6ddef7..ac4bba7142 100644 --- a/src/introduction.md +++ b/src/introduction.md @@ -65,6 +65,8 @@ For example: > Brain Imaging Data Structure (Gorgolewski, K., Auer, T., Calhoun, V. et al., 2016) > with the extension for EEG data (Pernet, C.R., Appelhoff, S., Gorgolewski, K.J. et al., 2019). + + ### Original publication - Gorgolewski, K.J., Auer, T., Calhoun, V.D., Craddock, R.C., Das, S., Duff, @@ -184,6 +186,8 @@ For example: PsyArXiv. [doi:10.31234/osf.io/w6z79](https://doi.org/10.31234/osf.io/w6z79) + + ### Research Resource Identifier (RRID) BIDS has also a From 77d5254148169c22e5e836f03cb05b2871627e8f Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 22 Mar 2024 09:24:36 -0400 Subject: [PATCH 3/4] try using mkdocs-bibtex --- .codespellrc | 2 +- mkdocs.yml | 5 + requirements.txt | 1 + src/apa-6th-edition.csl | 1580 +++++++++++++++++++++++++++++++++++++++ src/introduction.md | 4 + src/references.bib | 240 ++++++ 6 files changed, 1831 insertions(+), 1 deletion(-) create mode 100644 src/apa-6th-edition.csl create mode 100644 src/references.bib diff --git a/.codespellrc b/.codespellrc index 22cd48ca96..3eab212235 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,5 +1,5 @@ [codespell] -skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build +skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build,src/apa-6th-edition.csl,src/references.bib ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel builtin = clear,rare,en-GB_to_en-US # this overloads default dictionaries and I have not yet figured out diff --git a/mkdocs.yml b/mkdocs.yml index 051aa2aaa6..f0114623b3 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -103,6 +103,7 @@ markdown_extensions: - pymdownx.superfences - admonition - pymdownx.details + - footnotes plugins: - search - branchcustomization: @@ -112,6 +113,10 @@ plugins: - css/watermark.css - macros: module_name: tools/mkdocs_macros_bids/main + - bibtex: + bib_file: "src/references.bib" + cite_inline: True + csl_file: src/apa-6th-edition.csl - redirects: redirect_maps: "01-introduction.md": "introduction.md" diff --git a/requirements.txt b/requirements.txt index 25f0520a6a..cd74f0c5ec 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,5 +4,6 @@ pymdown-extensions>=7.0.0 mkdocs-branchcustomization-plugin~=0.1.3 mkdocs-macros-plugin mkdocs-redirects +mkdocs-bibtex numpy tools/schemacode/[render] diff --git a/src/apa-6th-edition.csl b/src/apa-6th-edition.csl new file mode 100644 index 0000000000..201c16c1ce --- /dev/null +++ b/src/apa-6th-edition.csl @@ -0,0 +1,1580 @@ + + diff --git a/src/introduction.md b/src/introduction.md index ac4bba7142..bdd205194a 100644 --- a/src/introduction.md +++ b/src/introduction.md @@ -67,6 +67,8 @@ For example: + + ### Original publication - Gorgolewski, K.J., Auer, T., Calhoun, V.D., Craddock, R.C., Das, S., Duff, @@ -79,6 +81,8 @@ For example: Scientific Data, 3 (160044). [doi:10.1038/sdata.2016.44](https://doi.org/10.1038/sdata.2016.44) +[@gorgolewski_brain_2016] + ### Datatype specific publications #### EEG diff --git a/src/references.bib b/src/references.bib new file mode 100644 index 0000000000..ceecca2cc7 --- /dev/null +++ b/src/references.bib @@ -0,0 +1,240 @@ + +@article{gorgolewski_brain_2016, + title = {The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments}, + volume = {3}, + issn = {2052-4463}, + url = {https://www.nature.com/articles/sdata201644}, + doi = {10.1038/sdata.2016.44}, + abstract = {Abstract + The development of magnetic resonance imaging (MRI) techniques has defined modern neuroimaging. Since its inception, tens of thousands of studies using techniques such as functional MRI and diffusion weighted imaging have allowed for the non-invasive study of the brain. Despite the fact that MRI is routinely used to obtain data for neuroscience research, there has been no widely adopted standard for organizing and describing the data collected in an imaging experiment. This renders sharing and reusing data (within or between labs) difficult if not impossible and unnecessarily complicates the application of automatic pipelines and quality assurance protocols. To solve this problem, we have developed the Brain Imaging Data Structure (BIDS), a standard for organizing and describing MRI datasets. The BIDS standard uses file formats compatible with existing software, unifies the majority of practices already common in the field, and captures the metadata necessary for most common data processing operations.}, + language = {en}, + number = {1}, + urldate = {2023-07-03}, + 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{gorgolewski_bids_2017, + title = {{BIDS} apps: {Improving} ease of use, accessibility, and reproducibility of neuroimaging data analysis methods}, + volume = {13}, + issn = {1553-7358}, + shorttitle = {{BIDS} apps}, + url = {https://dx.plos.org/10.1371/journal.pcbi.1005209}, + doi = {10.1371/journal.pcbi.1005209}, + language = {en}, + number = {3}, + urldate = {2023-07-03}, + 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.}, + editor = {Schneidman, Dina}, + month = mar, + year = {2017}, + pages = {e1005209}, +} + +@article{pernet_eeg-bids_2019, + title = {{EEG}-{BIDS}, an extension to the brain imaging data structure for electroencephalography}, + volume = {6}, + issn = {2052-4463}, + url = {https://www.nature.com/articles/s41597-019-0104-8}, + doi = {10.1038/s41597-019-0104-8}, + language = {en}, + number = {1}, + urldate = {2023-07-03}, + journal = {Scientific Data}, + author = {Pernet, Cyril R. and Appelhoff, Stefan and Gorgolewski, Krzysztof J. and Flandin, Guillaume and Phillips, Christophe and Delorme, Arnaud and Oostenveld, Robert}, + month = jun, + year = {2019}, + pages = {103}, +} + +@article{holdgraf_ieeg-bids_2019, + title = {{iEEG}-{BIDS}, extending the {Brain} {Imaging} {Data} {Structure} specification to human intracranial electrophysiology}, + volume = {6}, + issn = {2052-4463}, + url = {https://www.nature.com/articles/s41597-019-0105-7}, + doi = {10.1038/s41597-019-0105-7}, + language = {en}, + number = {1}, + urldate = {2023-07-03}, + journal = {Scientific Data}, + author = {Holdgraf, Christopher and Appelhoff, Stefan and Bickel, Stephan and Bouchard, Kristofer and D’Ambrosio, Sasha and David, Olivier and Devinsky, Orrin and Dichter, Benjamin and Flinker, Adeen and Foster, Brett L. and Gorgolewski, Krzysztof J. and Groen, Iris and Groppe, David and Gunduz, Aysegul and Hamilton, Liberty and Honey, Christopher J. and Jas, Mainak and Knight, Robert and Lachaux, Jean-Philippe and Lau, Jonathan C. and Lee-Messer, Christopher and Lundstrom, Brian N. and Miller, Kai J. and Ojemann, Jeffrey G. and Oostenveld, Robert and Petridou, Natalia and Piantoni, Gio and Pigorini, Andrea and Pouratian, Nader and Ramsey, Nick F. and Stolk, Arjen and Swann, Nicole C. and Tadel, François and Voytek, Bradley and Wandell, Brian A. and Winawer, Jonathan and Whitaker, Kirstie and Zehl, Lyuba and Hermes, Dora}, + month = jun, + year = {2019}, + pages = {102}, +} + +@article{niso_meg-bids_2018, + title = {{MEG}-{BIDS}, the brain imaging data structure extended to magnetoencephalography}, + volume = {5}, + issn = {2052-4463}, + url = {https://www.nature.com/articles/sdata2018110}, + doi = {10.1038/sdata.2018.110}, + abstract = {Abstract + We present a significant extension of the Brain Imaging Data Structure (BIDS) to support the specific aspects of magnetoencephalography (MEG) data. MEG measures brain activity with millisecond temporal resolution and unique source imaging capabilities. So far, BIDS was a solution to organise magnetic resonance imaging (MRI) data. The nature and acquisition parameters of MRI and MEG data are strongly dissimilar. Although there is no standard data format for MEG, we propose MEG-BIDS as a principled solution to store, organise, process and share the multidimensional data volumes produced by the modality. The standard also includes well-defined metadata, to facilitate future data harmonisation and sharing efforts. This responds to unmet needs from the multimodal neuroimaging community and paves the way to further integration of other techniques in electrophysiology. MEG-BIDS builds on MRI-BIDS, extending BIDS to a multimodal data structure. We feature several data-analytics software that have adopted MEG-BIDS, and a diverse sample of open MEG-BIDS data resources available to everyone.}, + language = {en}, + number = {1}, + urldate = {2023-07-03}, + journal = {Scientific Data}, + author = {Niso, Guiomar and Gorgolewski, Krzysztof J. and Bock, Elizabeth and Brooks, Teon L. and Flandin, Guillaume and Gramfort, Alexandre and Henson, Richard N. and Jas, Mainak and Litvak, Vladimir and T. Moreau, Jeremy and Oostenveld, Robert and Schoffelen, Jan-Mathijs and Tadel, Francois and Wexler, Joseph and Baillet, Sylvain}, + month = jun, + year = {2018}, + pages = {180110}, +} + +@article{norgaard_pet-bids_2022, + title = {{PET}-{BIDS}, an extension to the brain imaging data structure for positron emission tomography}, + volume = {9}, + issn = {2052-4463}, + url = {https://www.nature.com/articles/s41597-022-01164-1}, + doi = {10.1038/s41597-022-01164-1}, + language = {en}, + number = {1}, + urldate = {2023-07-03}, + journal = {Scientific Data}, + author = {Norgaard, Martin and Matheson, Granville J. and Hansen, Hanne D. and Thomas, Adam and Searle, Graham and Rizzo, Gaia and Veronese, Mattia and Giacomel, Alessio and Yaqub, Maqsood and Tonietto, Matteo and Funck, Thomas and Gillman, Ashley and Boniface, Hugo and Routier, Alexandre and Dalenberg, Jelle R. and Betthauser, Tobey and Feingold, Franklin and Markiewicz, Christopher J. and Gorgolewski, Krzysztof J. and Blair, Ross W. and Appelhoff, Stefan and Gau, Remi and Salo, Taylor and Niso, Guiomar and Pernet, Cyril and Phillips, Christophe and Oostenveld, Robert and Gallezot, Jean-Dominique and Carson, Richard E. and Knudsen, Gitte M. and Innis, Robert B. and Ganz, Melanie}, + month = mar, + year = {2022}, + pages = {65}, +} + +@article{bourget_microscopy-bids_2022, + title = {Microscopy-{BIDS}: {An} {Extension} to the {Brain} {Imaging} {Data} {Structure} for {Microscopy} {Data}}, + volume = {16}, + issn = {1662-453X}, + shorttitle = {Microscopy-{BIDS}}, + url = {https://www.frontiersin.org/articles/10.3389/fnins.2022.871228/full}, + doi = {10.3389/fnins.2022.871228}, + abstract = {The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. First developed for magnetic resonance imaging (MRI) datasets, the community-led specification evolved rapidly to include other modalities such as magnetoencephalography, positron emission tomography, and quantitative MRI (qMRI). In this work, we present an extension to BIDS for microscopy imaging data, along with example datasets. Microscopy-BIDS supports common imaging methods, including 2D/3D, + ex + / + in vivo + , micro-CT, and optical and electron microscopy. Microscopy-BIDS also includes comprehensible metadata definitions for hardware, image acquisition, and sample properties. This extension will facilitate future harmonization efforts in the context of multi-modal, multi-scale imaging such as the characterization of tissue microstructure with qMRI.}, + urldate = {2023-07-03}, + journal = {Frontiers in Neuroscience}, + author = {Bourget, Marie-Hélène and Kamentsky, Lee and Ghosh, Satrajit S. and Mazzamuto, Giacomo and Lazari, Alberto and Markiewicz, Christopher J. and Oostenveld, Robert and Niso, Guiomar and Halchenko, Yaroslav O. and Lipp, Ilona and Takerkart, Sylvain and Toussaint, Paule-Joanne and Khan, Ali R. and Nilsonne, Gustav and Castelli, Filippo Maria and {The BIDS Maintainers} and Cohen-Adad, Julien}, + month = apr, + year = {2022}, + pages = {871228}, +} + +@article{moreau_genetics-bids_2020, + title = {The genetics-{BIDS} extension: {Easing} the search for genetic data associated with human brain imaging}, + volume = {9}, + issn = {2047-217X}, + shorttitle = {The genetics-{BIDS} extension}, + url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaa104/5928221}, + doi = {10.1093/gigascience/giaa104}, + abstract = {Abstract + Metadata are what makes databases searchable. Without them, researchers would have difficulty finding data with features they are interested in. Brain imaging genetics is at the intersection of two disciplines, each with dedicated dictionaries and ontologies facilitating data search and analysis. Here, we present the genetics Brain Imaging Data Structure extension, consisting of metadata files for human brain imaging data to which they are linked, and describe succinctly the genomic and transcriptomic data associated with them, which may be in different databases. This extension will facilitate identifying micro-scale molecular features that are linked to macro-scale imaging repositories, facilitating data aggregation across studies.}, + language = {en}, + number = {10}, + urldate = {2023-07-03}, + journal = {GigaScience}, + author = {Moreau, Clara A and Jean-Louis, Martineau and Blair, Ross and Markiewicz, Christopher J and Turner, Jessica A and Calhoun, Vince D and Nichols, Thomas E and Pernet, Cyril R}, + month = oct, + year = {2020}, + pages = {giaa104}, +} + +@article{karakuzu_qmri-bids_2022, + title = {{qMRI}-{BIDS}: {An} extension to the brain imaging data structure for quantitative magnetic resonance imaging data}, + volume = {9}, + issn = {2052-4463}, + shorttitle = {{qMRI}-{BIDS}}, + url = {https://www.nature.com/articles/s41597-022-01571-4}, + doi = {10.1038/s41597-022-01571-4}, + abstract = {Abstract + + The Brain Imaging Data Structure (BIDS) established community consensus on the organization of data and metadata for several neuroimaging modalities. Traditionally, BIDS had a strong focus on functional magnetic resonance imaging (MRI) datasets and lacked guidance on how to store + multimodal + structural MRI datasets. Here, we present and describe the BIDS Extension Proposal 001 (BEP001), which adds a range of quantitative MRI (qMRI) applications to the BIDS. In general, the aim of qMRI is to characterize brain microstructure by quantifying the physical MR parameters of the tissue via computational, biophysical models. By proposing this new standard, we envision standardization of qMRI through multicenter dissemination of interoperable datasets. This way, BIDS can act as a catalyst of convergence between qMRI methods development and application-driven neuroimaging studies that can help develop quantitative biomarkers for neural tissue characterization. In conclusion, this BIDS extension offers a common ground for developers to exchange novel imaging data and tools, reducing the entrance barrier for qMRI in the field of neuroimaging.}, + language = {en}, + number = {1}, + urldate = {2023-07-03}, + journal = {Scientific Data}, + author = {Karakuzu, Agah and Appelhoff, Stefan and Auer, Tibor and Boudreau, Mathieu and Feingold, Franklin and Khan, Ali R. and Lazari, Alberto and Markiewicz, Chris and Mulder, Martijn and Phillips, Christophe and Salo, Taylor and Stikov, Nikola and Whitaker, Kirstie and De Hollander, Gilles}, + month = aug, + year = {2022}, + pages = {517}, +} + +@article{knudsen_guidelines_2020, + title = {Guidelines for the content and format of {PET} brain data in publications and archives: {A} consensus paper}, + volume = {40}, + issn = {0271-678X, 1559-7016}, + shorttitle = {Guidelines for the content and format of {PET} brain data in publications and archives}, + url = {http://journals.sagepub.com/doi/10.1177/0271678X20905433}, + doi = {10.1177/0271678X20905433}, + abstract = {It is a growing concern that outcomes of neuroimaging studies often cannot be replicated. To counteract this, the magnetic resonance (MR) neuroimaging community has promoted acquisition standards and created data sharing platforms, based on a consensus on how to organize and share MR neuroimaging data. Here, we take a similar approach to positron emission tomography (PET) data. To facilitate comparison of findings across studies, we first recommend publication standards for tracer characteristics, image acquisition, image preprocessing, and outcome estimation for PET neuroimaging data. The co-authors of this paper, representing more than 25 PET centers worldwide, voted to classify information as mandatory, recommended, or optional. Second, we describe a framework to facilitate data archiving and data sharing within and across centers. Because of the high cost of PET neuroimaging studies, sample sizes tend to be small and relatively few sites worldwide have the required multidisciplinary expertise to properly conduct and analyze PET studies. Data sharing will make it easier to combine datasets from different centers to achieve larger sample sizes and stronger statistical power to test hypotheses. The combining of datasets from different centers may be enhanced by adoption of a common set of best practices in data acquisition and analysis.}, + language = {en}, + number = {8}, + urldate = {2023-07-03}, + journal = {Journal of Cerebral Blood Flow \& Metabolism}, + author = {Knudsen, Gitte M and Ganz, Melanie and Appelhoff, Stefan and Boellaard, Ronald and Bormans, Guy and Carson, Richard E and Catana, Ciprian and Doudet, Doris and Gee, Antony D and Greve, Douglas N and Gunn, Roger N and Halldin, Christer and Herscovitch, Peter and Huang, Henry and Keller, Sune H and Lammertsma, Adriaan A and Lanzenberger, Rupert and Liow, Jeih-San and Lohith, Talakad G and Lubberink, Mark and Lyoo, Chul H and Mann, J John and Matheson, Granville J and Nichols, Thomas E and Nørgaard, Martin and Ogden, Todd and Parsey, Ramin and Pike, Victor W and Price, Julie and Rizzo, Gaia and Rosa-Neto, Pedro and Schain, Martin and Scott, Peter Jh and Searle, Graham and Slifstein, Mark and Suhara, Tetsuya and Talbot, Peter S and Thomas, Adam and Veronese, Mattia and Wong, Dean F and Yaqub, Maqsood and Zanderigo, Francesca and Zoghbi, Sami and Innis, Robert B}, + month = aug, + year = {2020}, + pages = {1576--1585}, +} + +@article{clement_asl-bids_2022, + title = {{ASL}-{BIDS}, the brain imaging data structure extension for arterial spin labeling}, + volume = {9}, + issn = {2052-4463}, + url = {https://www.nature.com/articles/s41597-022-01615-9}, + doi = {10.1038/s41597-022-01615-9}, + abstract = {Abstract + Arterial spin labeling (ASL) is a non-invasive MRI technique that allows for quantitative measurement of cerebral perfusion. Incomplete or inaccurate reporting of acquisition parameters complicates quantification, analysis, and sharing of ASL data, particularly for studies across multiple sites, platforms, and ASL methods. There is a strong need for standardization of ASL data storage, including acquisition metadata. Recently, ASL-BIDS, the BIDS extension for ASL, was developed and released in BIDS 1.5.0. This manuscript provides an overview of the development and design choices of this first ASL-BIDS extension, which is mainly aimed at clinical ASL applications. Discussed are the structure of the ASL data, focussing on storage order of the ASL time series and implementation of calibration approaches, unit scaling, ASL-related BIDS fields, and storage of the labeling plane information. Additionally, an overview of ASL-BIDS compatible conversion and ASL analysis software and ASL example datasets in BIDS format is provided. We anticipate that large-scale adoption of ASL-BIDS will improve the reproducibility of ASL research.}, + language = {en}, + number = {1}, + urldate = {2023-07-03}, + journal = {Scientific Data}, + author = {Clement, Patricia and Castellaro, Marco and Okell, Thomas W. and Thomas, David L. and Vandemaele, Pieter and Elgayar, Sara and Oliver-Taylor, Aaron and Kirk, Thomas and Woods, Joseph G. and Vos, Sjoerd B. and Kuijer, Joost P. A. and Achten, Eric and Van Osch, Matthias J. P. and {BIDS maintainers} and Appelhoff, Stefan and Blair, Ross and Feingold, Franklin and Gau, Rémi and Markiewicz, Christopher J. and Salo, Taylor and Detre, John A. and Lu, Hanzhang and Alsop, David C. and Chappell, Michael A. and Hernandez-Garcia, Luis and Petr, Jan and Mutsaerts, Henk J. M. M.}, + month = sep, + year = {2022}, + pages = {543}, +} + +@techreport{luke_fnirs-bids_2023, + type = {preprint}, + title = {{fNIRS}-{BIDS}, the {Brain} {Imaging} {Data} {Structure} {Extended} to {Functional} {Near}-{Infrared} {Spectroscopy}}, + url = {https://osf.io/7nmcp}, + abstract = {Functional near-infrared spectroscopy (fNIRS) is an increasingly popular neuroimaging technique that measures cortical hemodynamic activity in a non-invasive and portable fashion. Although the fNIRS community has been successful in disseminating several open-source processing tools and a standard file format (SNIRF), the development of reproducible research and sharing of fNIRS data amongst researchers has been hindered by a lack of standards and clarity over how study data should be organized and stored. This problem is not new in neuroimaging (and science in general), and it became evident years ago with the proliferation of publicly available functional magnetic resonance imaging (fMRI) datasets.To solve this critical issue, the neuroimaging community created the Brain Imaging Data Structure (BIDS) that specifies standards for how datasets should be organized to facilitates sharing and reproducibility of science. Since then, BIDS has been extended to dozens of neuroimaging modalities including EEG, MEG, PET and many others.In this paper, we present the extension of BIDS for fNIRS data alongside tools that may assist researchers in formatting existing and new data with the goal of promoting public disseminations of fNIRS datasets.}, + urldate = {2023-12-17}, + institution = {Open Science Framework}, + author = {Luke, Robert and Oostenveld, Robert and Cockx, Helena and Niso, Guiomar and Shader, Maureen and Orihuela-Espina, Felipe and Innes-Brown, Hamish and Tucker, Stephen and Boas, David and Gau, Remi and Salo, Taylor and Appelhoff, Stefan and Markiewicz, Christopher Johnson and McAlpine, David and {Bids\_Maintainers} and Pollonini, Luca}, + month = jan, + year = {2023}, + doi = {10.31219/osf.io/7nmcp}, +} + +@techreport{jeung_motion-bids_2023, + type = {preprint}, + title = {Motion-{BIDS}: extending the {Brain} {Imaging} {Data} {Structure} specification to organize motion data for reproducible research}, + shorttitle = {Motion-{BIDS}}, + url = {https://osf.io/w6z79}, + abstract = {We present an extension to the Brain Imaging Data Structure (BIDS) for motion data. Motion data is frequently recordedalongside human brain imaging and electrophysiological data. The goal of Motion-BIDS is to make motion data interoperableacross different laboratories and with other data modalities in human brain and behavioral research. To this end, Motion-BIDSstandardizes the data format and metadata structure. It describes how to document experimental details, taking the diversity ofhardware and software systems for motion data into consideration. This promotes FAIR data sharing and Open Science inhuman motion research.}, + urldate = {2023-12-17}, + institution = {PsyArXiv}, + author = {Jeung, Sein and Cockx, Helena and Appelhoff, Stefan and Berg, Timotheus and Gramann, Klaus and Grothkopp, Sören and Warmerdam, Elke and Hansen, Clint and Oostenveld, Robert and {Bids\_Maintainers} and Welzel, Julius}, + month = nov, + year = {2023}, + doi = {10.31234/osf.io/w6z79}, +} + +@article{poldrack_past_2023, + title = {The {Past}, {Present}, and {Future} of the {Brain} {Imaging} {Data} {Structure} ({BIDS})}, + copyright = {Creative Commons Attribution 4.0 International}, + url = {https://arxiv.org/abs/2309.05768}, + doi = {10.48550/ARXIV.2309.05768}, + abstract = {The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.}, + urldate = {2023-12-19}, + author = {Poldrack, Russell A. and Markiewicz, Christopher J. and Appelhoff, Stefan and Ashar, Yoni K. and Auer, Tibor and Baillet, Sylvain and Bansal, Shashank and Beltrachini, Leandro and Benar, Christian G. and Bertazzoli, Giacomo and Bhogawar, Suyash and Blair, Ross W. and Bortoletto, Marta and Boudreau, Mathieu and Brooks, Teon L. and Calhoun, Vince D. and Castelli, Filippo Maria and Clement, Patricia and Cohen, Alexander L and Cohen-Adad, Julien and D'Ambrosio, Sasha and de Hollander, Gilles and de la iglesia-Vayá, María and de la Vega, Alejandro and Delorme, Arnaud and Devinsky, Orrin and Draschkow, Dejan and Duff, Eugene Paul and DuPre, Elizabeth and Earl, Eric and Esteban, Oscar and Feingold, Franklin W. and Flandin, Guillaume and galassi, anthony and Gallitto, Giuseppe and Ganz, Melanie and Gau, Rémi and Gholam, James and Ghosh, Satrajit S. and Giacomel, Alessio and Gillman, Ashley G and Gleeson, Padraig and Gramfort, Alexandre and Guay, Samuel and Guidali, Giacomo and Halchenko, Yaroslav O. and Handwerker, Daniel A. and Hardcastle, Nell and Herholz, Peer and Hermes, Dora and Honey, Christopher J. and Innis, Robert B. and Ioanas, Horea-Ioan and Jahn, Andrew and Karakuzu, Agah and Keator, David B. and Kiar, Gregory and Kincses, Balint and Laird, Angela R. and Lau, Jonathan C. and Lazari, Alberto and Legarreta, Jon Haitz and Li, Adam and Li, Xiangrui and Love, Bradley C. and Lu, Hanzhang and Maumet, Camille and Mazzamuto, Giacomo and Meisler, Steven L. and Mikkelsen, Mark and Mutsaerts, Henk and Nichols, Thomas E. and Nikolaidis, Aki and Nilsonne, Gustav and Niso, Guiomar and Norgaard, Martin and Okell, Thomas W and Oostenveld, Robert and Ort, Eduard and Park, Patrick J. and Pawlik, Mateusz and Pernet, Cyril R. and Pestilli, Franco and Petr, Jan and Phillips, Christophe and Poline, Jean-Baptiste and Pollonini, Luca and Raamana, Pradeep Reddy and Ritter, Petra and Rizzo, Gaia and Robbins, Kay A. and Rockhill, Alexander P. and Rogers, Christine and Rokem, Ariel and Rorden, Chris and Routier, Alexandre and Saborit-Torres, Jose Manuel and Salo, Taylor and Schirner, Michael and Smith, Robert E. and Spisak, Tamas and Sprenger, Julia and Swann, Nicole C. and Szinte, Martin and Takerkart, Sylvain and Thirion, Bertrand and Thomas, Adam G. and Torabian, Sajjad and Varoquaux, Gael and Voytek, Bradley and Welzel, Julius and Wilson, Martin and Yarkoni, Tal and Gorgolewski, Krzysztof J.}, + year = {2023}, + note = {Publisher: arXiv +Version Number: 1}, + keywords = {FOS: Biological sciences, Other Quantitative Biology (q-bio.OT)}, +} From 316e46afdc1362901caca36ce16cce19908a1150 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 22 Mar 2024 14:20:23 -0400 Subject: [PATCH 4/4] let's try conda --- environment.yml | 16 ++++++++++++++++ readthedocs.yml | 6 +++++- requirements.txt | 9 --------- 3 files changed, 21 insertions(+), 10 deletions(-) create mode 100644 environment.yml delete mode 100644 requirements.txt diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000000..04f4dd5078 --- /dev/null +++ b/environment.yml @@ -0,0 +1,16 @@ +name: bids_spec +channels: + - defaults +dependencies: + - pip + - pypandoc + - numpy + - pip: + - tools/schemacode/[render] + - mkdocs>=1.1 + - mkdocs-material>=5.4 + - pymdown-extensions>=7.0.0 + - mkdocs-branchcustomization-plugin~=0.1.3 + - mkdocs-macros-plugin + - mkdocs-redirects + - mkdocs-bibtex diff --git a/readthedocs.yml b/readthedocs.yml index 5611c59505..b0703e747a 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -5,7 +5,8 @@ build: apt_packages: - jq tools: - python: "3.11" + python: "mambaforge-22.9" + jobs: pre_build: - bst -v export --output src/schema.json @@ -15,6 +16,9 @@ mkdocs: configuration: mkdocs.yml fail_on_warning: true +conda: + environment: environment.yml + python: install: - requirements: requirements.txt diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index cd74f0c5ec..0000000000 --- a/requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -mkdocs>=1.1 -mkdocs-material>=5.4 -pymdown-extensions>=7.0.0 -mkdocs-branchcustomization-plugin~=0.1.3 -mkdocs-macros-plugin -mkdocs-redirects -mkdocs-bibtex -numpy -tools/schemacode/[render]