diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 3ccbc00b9..8941f9e8d 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -82,6 +82,7 @@ body: Or check the content of CITATION.cff. options: + - v3.1.0 - v3.0.0 - v2.3.0 - v2.2.0 @@ -95,6 +96,7 @@ body: - v1.1.0 - v1.0.0 - v0.2.0 + - v0.1.1 - v0.1.0 - v0.0.3 - v0.0.2 diff --git a/.gitignore b/.gitignore index 0dcb66f3a..222c49fbe 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,7 @@ lib/spmup +docs/posters/2023_ohbm/poster/betterposter-thumbnail-portrait.png + # General .DS_Store @@ -9,6 +11,8 @@ lib/spmup *.html *.docx *.ps +*.~lock.* +*.ppt* new_events.tsv diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 63c1c3e46..563b3dbcf 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -32,13 +32,14 @@ repos: - id: trailing-whitespace - id: end-of-file-fixer - id: check-yaml - - id: check-added-large-files + - id: check-json + # - id: check-added-large-files - repo: https://github.com/pre-commit/pygrep-hooks rev: v1.10.0 hooks: - - id: rst-backticks # Detect common mistake of using single backticks when writing rst - - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst + - id: rst-backticks + - id: rst-inline-touching-normal - repo: https://github.com/psf/black rev: 23.3.0 @@ -108,11 +109,5 @@ repos: hooks: - id: codespell -# - repo: https://github.com/tcort/markdown-link-check -# rev: v3.11.2 -# hooks: -# - id: markdown-link-check -# args: [-q, -c, .github/workflows/mlc_config.json] - ci: skip: [hadolint-docker] diff --git a/CHANGELOG.md b/CHANGELOG.md index 9e9637e9c..518e81924 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,9 +19,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Security --> -## [Unreleased] + + +### Added + +### Changed + +### Deprecated + +### Removed + +### Fixed + +### Security --> + + +## [3.1.0] - 2023-07-01 + +**Full Changelog**: https://github.com/cpp-lln-lab/bidspm/compare/v3.0.0...v3.1.0 ### Added @@ -49,8 +65,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * [ENH] overwrite files when renaming by default (#1051) @Remi-Gau * [ENH] turn error into warning when no data to copy found (#992) @Remi-Gau -### Deprecated - ### Removed * [ENH] drop rsHRF support (#906) @Remi-Gau diff --git a/CITATION.cff b/CITATION.cff index eb1989c79..1905b409c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,7 +2,7 @@ cff-version: 1.2.0 title: "bidspm" -version: 3.0.0 +version: 3.1.0 abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and analyze BIDS data sets using SPM12. @@ -14,10 +14,13 @@ identifiers: - description: This is the collection of archived snapshots of all releases of bidspm type: doi value: "10.5281/zenodo.3554331" + - description: OHBM 2023 poster + type: doi + value: "10.5281/zenodo.8099835" contact: - affiliation: "Université catholique de Louvain" - email: remi.gau@uclouvain.be + email: remi.gau2@mcgill.ca family-names: Gau given-names: Rémi @@ -25,7 +28,7 @@ authors: - family-names: "Gau" given-names: "Rémi" orcid: "https://orcid.org/0000-0002-1535-9767" - affiliation: "Université catholique de Louvain" + affiliation: "Origami lab, McGill University, Montreal, Québec, Canada" - family-names: "Barilari" given-names: "Marco" @@ -42,11 +45,6 @@ authors: orcid: "https://orcid.org/0000-0002-1866-8645" affiliation: "Université catholique de Louvain" -- family-names: "Collignon" - given-names: "Olivier" - orcid: "https://orcid.org/0000-0003-1882-3550" - affiliation: "Université catholique de Louvain" - - family-names: "Gurtubay" given-names: "Ane" orcid: "https://orcid.org/0000-0003-3824-2219" @@ -105,6 +103,12 @@ authors: affiliation: "Université catholique de Louvain" orcid: "https://orcid.org/0000-0001-9752-3294" +- family-names: "Collignon" + given-names: "Olivier" + orcid: "https://orcid.org/0000-0003-1882-3550" + affiliation: "Université catholique de Louvain" + + license: GPL-3.0 keywords: diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index ad495023b..2dd3fa6c4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -98,3 +98,21 @@ created with: ```bash make update_faq ``` + +### release protocol + +- [ ] create a dedicated branch for the release candidate +- [ ] update version in `citation.cff` +- [ ] documentation related + - [ ] ensure the documentation is up to date + - [ ] make sure the doc builds correctly and fix any error +- [ ] update jupyter books +- [ ] update binder +- [ ] update docker recipes +- [ ] update changelog +- [ ] run `make release` +- [ ] open a pull request (PR) from this release candidate branch targeting the default branch +- [ ] fix any remaining failing continuous integration (test, markdown and code linting...) +- [ ] merge to default branch +- [ ] create a tagged release +- [ ] build and push docker images if necessary diff --git a/README.md b/README.md index 83c956348..1888fb29c 100644 --- a/README.md +++ b/README.md @@ -234,17 +234,19 @@ Please see our ```bibtex @software{bidspm, - author = {Gau, Rémi and Barilari, Marco and Battal, Ceren and Rezk, Mohamed and Collignon, Olivier and Gurtubay, Ane and Falagiarda, Federica and MacLean, Michèle and Cerpelloni, Filippo and Shahzad, Iqra and Nunes, Márcia and Caron-Guyon, Jeanne and Chouinard-Leclaire, Christine and Yang, Ying, and Mattioni, Stefania}, + author = {Gau, Rémi and Barilari, Marco and Battal, Ceren and Rezk, Mohamed and Collignon, Olivier and Gurtubay, Ane and Falagiarda, Federica and MacLean, Michèle and Cerpelloni, Filippo and Shahzad, Iqra and Nunes, Márcia and Caron-Guyon, Jeanne and Chouinard-Leclaire, Christine and Yang, Ying and Mattioni, Stefania and Van Audenhaege, Alice and Matuszewski, Jacek}, license = {GPL-3.0}, - title = {bidspm}, + title = {{bidspm}}, url = {https://github.com/cpp-lln-lab/bidspm}, - version = {3.0.0} - doi = {10.5281/zenodo.3554331}, - publisher = {Zenodo}, - journal = {Software} + version = {3.1.0} } ``` +### Posters + +- [OHBM 2023](https://doi.org/10.5281/zenodo.8099835) + + ## Contributors Thanks goes to these wonderful people diff --git a/docs/bidspm-manual.pdf b/docs/bidspm-manual.pdf new file mode 100644 index 000000000..bf282cd4f Binary files /dev/null and b/docs/bidspm-manual.pdf differ diff --git a/docs/poster/checklist.md b/docs/paper/checklist.md similarity index 100% rename from docs/poster/checklist.md rename to docs/paper/checklist.md diff --git a/docs/poster/metadata.py b/docs/paper/metadata.py similarity index 100% rename from docs/poster/metadata.py rename to docs/paper/metadata.py diff --git a/docs/poster/metadata.yml b/docs/paper/metadata.yml similarity index 100% rename from docs/poster/metadata.yml rename to docs/paper/metadata.yml diff --git a/docs/poster/paper.Rmd b/docs/paper/paper.Rmd similarity index 100% rename from docs/poster/paper.Rmd rename to docs/paper/paper.Rmd diff --git a/docs/poster/paper.bib b/docs/paper/paper.bib similarity index 100% rename from docs/poster/paper.bib rename to docs/paper/paper.bib diff --git a/docs/poster/requirements.txt b/docs/paper/requirements.txt similarity index 100% rename from docs/poster/requirements.txt rename to docs/paper/requirements.txt diff --git a/docs/poster/OHBM_2023.Rmd b/docs/poster/OHBM_2023.Rmd deleted file mode 100644 index 7d3648471..000000000 --- a/docs/poster/OHBM_2023.Rmd +++ /dev/null @@ -1,140 +0,0 @@ ---- -title: "bidspm an SPM centric BIDS app" -author: - - name: Rémi Gau - orcid: 0000-0002-1535-9767 - affiliation: 1 - - name: Marco Barilari - orcid: 0000-0002-3313-3120 - affiliation: 1 - - name: Ceren Battal - orcid: 0000-0002-9844-7630 - affiliation: 1 - - name: Jeanne Caron-Guyon - orcid: 0000-0001-8681-5267 - affiliation: 1 - - name: Filippo Cerpelloni - orcid: 0000-0001-8070-5753 - affiliation: 1 - - name: Federica Falagiarda - orcid: 0000-0001-7844-1605 - affiliation: 1 - - name: Ane Gurtubay - orcid: 0000-0003-3824-2219 - affiliation: 1 - - name: Michèle MacLean - orcid: 0000-0002-0174-9326 - affiliation: 2 - - name: Stefania Mattioni - orcid: 0000-0001-8279-6118 - affiliation: 3 - - name: Mohamed Rezk - orcid: 0000-0002-1866-8645 - affiliation: 1 - - name: Iqra Shahzad - orcid: 0000-0002-8724-7668 - affiliation: 1 - - name: Ying Yang - orcid: 0000-0002-4157-2975 - affiliation: 1 - - name: Olivier Collignon - orcid: 0000-0003-1882-3550 - affiliation: 1 -affiliations: - - name: | - Institute for research in Psychology (IPSY) & Neuroscience (IoNS), Louvain Bionics, Crossmodal Perception and Plasticity Laboratory - University of Louvain (UCLouvain), Louvain, Belgium. - index: 1 - - name: Département de psychologie, Université de Montréal, Montréal, Canada - index: 2 - - name: Experimental Psychology, Ghent University, Ghent, Belgium - index: 3 - - name: Brain and cognition, Leuven Brain Institute, KU Leuven, Belgium - index: 4 -date: "2022-12-17" -output: - word_document: default - pdf_document: default -bibliography: OHBM_2023.bib ---- - -# Abstract - -## Introduction - -Great strides have recently been made in standardizing the format of -neuroimaging data with initiatives such as the Brain Imaging Data Structure -(@bids) and pipelines like fmriprep (@fmriprep). However, the statistical -analysis phase of the typical neuroimaging process requires a significant amount -of flexibility, which often leads to non-reproducible and heterogeneous scripts. -Additionally, scientific publications often lack critical contextual -information, making it hard to replicate the analyses from published studies. -Even when analysis scripts are shared, they may lack transparency, making it -difficult to understand and apply the same model to different datasets. - -To address these issues, the -[BIDS Statistical Model](https://bids-standard.github.io/stats-models/) was -recently developed to promote automated model fitting pipelines (see for example -[fitlins](https://github.com/poldracklab/fitlins)). However, there is no -integration of the BIDS statistical model with SPM12. bidSPM is a BIDS app to -fill this gap and make it easier to leverage this new tool. - -## Methods - -The philosophy of bidSPM is to take standardized data and configuration files as -input and to return standardized outputs. This should minimize how much code -researchers have to write. - -bidSPM uses the BIDS app CLI (@bids_app) to provide a standardized way to run -fMRI analysis of a BIDS dataset with SPM12 and several of its complementary -toolboxes. Analyses can be done at the subject and group level, on the whole -brain or in a region of interest. Additionally, the bidspm pipeline can be a -preparatory step for different kinds of analyses, whether task-free -(resting-state) or task-based univariate and multivariate studies. - -To run a statistical analysis, bidSPM only requires as inputs: - -- a valid raw BIDS dataset -- its BIDS derivatives (preprocessed by fmriprep or by bidSPM itself) -- a bids stats model JSON file. - -The BIDS stats model is used to define the input data, the variables and the -confound variables to include in the general linear model (GLM), the contrasts -to estimates as well as several options for HRF convolution, model estimation, -results to display… - -Having a single JavaScript Object Notation (JSON) file to define one analysis -allows researchers to easily create several models. bidSPM can then help choose -the best model as it can perform bayesian model selection via the model -assessment, comparison and selection (MACS) toolbox (@macs) of SPM12. - -This feature can be relevant to compare 1) different cognitive models for a -given task, 2) denoising strategies. This approach provides a principled way to -choose a model for a given dataset without having to peek at the results, and -thus may also help prevent procedural over-fitting (@choosing). - -## Results - -In the end bidSPM outputs follow the BIDS derivatives conventions and GLM -results are stored in a NIDM results (@nidm_results) allowing researchers to -upload their results to [Neurovault](https://neurovault.org/), (@neurovault) in -a couple of clicks. - -Additionally, bidSPM can easily provide 4D maps of a subject’s GLM output (beta -/ t-maps) to allow further analysis using MVPA classification frameworks or RSA -tools, making it a bridge connecting different frameworks. - -## Conclusion - -bidSPM provides researchers with a flexible way to run statistical analysis -using SPM12 with a single JSON file and only a few lines of code based on data -formatted in BIDS. - -bidSPM can be run on MATLAB or Octave and is also packaged as docker image and -is available on [github](https://github.com/cpp-lln-lab/bidspm) and -[dockerhub](https://hub.docker.com/repository/docker/cpplab/bidspm/). - -We hope that this tool will make it easier for the community to adopt practices -that lead to more reproducible results by relying on standardised pipelines that -are easily shareable. - -## References diff --git a/docs/poster/OHBM_2023.bib b/docs/poster/OHBM_2023.bib deleted file mode 100644 index 5330c0472..000000000 --- a/docs/poster/OHBM_2023.bib +++ /dev/null @@ -1,123 +0,0 @@ - -@article{bids_app, - 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 = {2023-01-13}, - 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}, - file = {Full Text:/home/remi/Zotero/storage/FGYENZJJ/Gorgolewski et al. - 2017 - BIDS apps Improving ease of use, accessibility, a.pdf:application/pdf} -} - -@article{bids, - title = {The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments}, - volume = {3}, - issn = {2052-4463}, - url = {http://www.nature.com/articles/sdata201644}, - doi = {10.1038/sdata.2016.44}, - language = {en}, - number = {1}, - urldate = {2022-10-19}, - 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 = dec, - year = {2016}, - pages = {160044}, - file = {Full Text:/home/remi/Zotero/storage/GS7EW8E9/Gorgolewski et al. - 2016 - The brain imaging data structure, a format for org.pdf:application/pdf} -} - -@article{fmriprep, - title = {{fMRIPrep}: a robust preprocessing pipeline for functional {MRI}}, - volume = {16}, - issn = {1548-7091, 1548-7105}, - shorttitle = {{fMRIPrep}}, - url = {http://www.nature.com/articles/s41592-018-0235-4}, - doi = {10.1038/s41592-018-0235-4}, - language = {en}, - number = {1}, - urldate = {2022-10-19}, - 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}, - file = {Submitted Version:/home/remi/Zotero/storage/EJRS4M2V/Esteban et al. - 2019 - fMRIPrep a robust preprocessing pipeline for func.pdf:application/pdf} -} - -@article{nidm_results, - title = {Sharing brain mapping statistical results with the neuroimaging data model}, - volume = {3}, - issn = {2052-4463}, - url = {https://www.nature.com/articles/sdata2016102}, - doi = {10.1038/sdata.2016.102}, - abstract = {Abstract - - Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices. This standardized representation allows authors to relay methods and results in a platform-independent regularized format that is not tied to a particular neuroimaging software package. Tools are available to export NIDM-Result graphs and associated files from the widely used SPM and FSL software packages, and the NeuroVault repository can import NIDM-Results archives. The specification is publicly available at: - http://nidm.nidash.org/specs/nidm-results.html - .}, - language = {en}, - number = {1}, - urldate = {2023-01-13}, - journal = {Scientific Data}, - author = {Maumet, Camille and Auer, Tibor and Bowring, Alexander and Chen, Gang and Das, Samir and Flandin, Guillaume and Ghosh, Satrajit and Glatard, Tristan and Gorgolewski, Krzysztof J. and Helmer, Karl G. and Jenkinson, Mark and Keator, David B. and Nichols, B. Nolan and Poline, Jean-Baptiste and Reynolds, Richard and Sochat, Vanessa and Turner, Jessica and Nichols, Thomas E.}, - month = dec, - year = {2016}, - pages = {160102}, - file = {Full Text:/home/remi/Zotero/storage/86V8RI9S/Maumet et al. - 2016 - Sharing brain mapping statistical results with the.pdf:application/pdf} -} - - -@article{neurovault, - title = {{NeuroVault}.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain}, - volume = {9}, - issn = {1662-5196}, - shorttitle = {{NeuroVault}.org}, - url = {http://journal.frontiersin.org/article/10.3389/fninf.2015.00008/abstract}, - doi = {10.3389/fninf.2015.00008}, - urldate = {2023-01-13}, - journal = {Frontiers in Neuroinformatics}, - author = {Gorgolewski, Krzysztof J. and Varoquaux, Gael and Rivera, Gabriel and Schwarz, Yannick and Ghosh, Satrajit S. and Maumet, Camille and Sochat, Vanessa V. and Nichols, Thomas E. and Poldrack, Russell A. and Poline, Jean-Baptiste and Yarkoni, Tal and Margulies, Daniel S.}, - month = apr, - year = {2015}, - file = {Full Text:/home/remi/Zotero/storage/MZY6GDJC/Gorgolewski et al. - 2015 - NeuroVault.org a web-based repository for collect.pdf:application/pdf} -} - - -@article{macs, - title={MACS - a new SPM toolbox for model assessment, comparison and selection.}, - author={Soch J, Allefeld C}, - journal={Journal of Neuroscience Methods}, - year={2018}, - volume={306}, - doi={https://doi.org/10.1016/j.jneumeth.2018.05.017} -} - - - -@article{choosing, - title = {Choosing {Prediction} {Over} {Explanation} in {Psychology}: {Lessons} {From} {Machine} {Learning}}, - volume = {12}, - issn = {1745-6916, 1745-6924}, - shorttitle = {Choosing {Prediction} {Over} {Explanation} in {Psychology}}, - url = {http://journals.sagepub.com/doi/10.1177/1745691617693393}, - doi = {10.1177/1745691617693393}, - abstract = {Psychology has historically been concerned, first and foremost, with explaining the causal mechanisms that give rise to behavior. Randomized, tightly controlled experiments are enshrined as the gold standard of psychological research, and there are endless investigations of the various mediating and moderating variables that govern various behaviors. We argue that psychology’s near-total focus on explaining the causes of behavior has led much of the field to be populated by research programs that provide intricate theories of psychological mechanism but that have little (or unknown) ability to predict future behaviors with any appreciable accuracy. We propose that principles and techniques from the field of machine learning can help psychology become a more predictive science. We review some of the fundamental concepts and tools of machine learning and point out examples where these concepts have been used to conduct interesting and important psychological research that focuses on predictive research questions. We suggest that an increased focus on prediction, rather than explanation, can ultimately lead us to greater understanding of behavior.}, - language = {en}, - number = {6}, - urldate = {2023-01-13}, - journal = {Perspectives on Psychological Science}, - author = {Yarkoni, Tal and Westfall, Jacob}, - month = nov, - year = {2017}, - pages = {1100--1122}, - file = {Accepted Version:/home/remi/Zotero/storage/M35DDSAZ/Yarkoni and Westfall - 2017 - Choosing Prediction Over Explanation in Psychology.pdf:application/pdf}, -} diff --git a/docs/poster/OHBM_2023.pdf b/docs/poster/OHBM_2023.pdf deleted file mode 100644 index eeef7a52e..000000000 Binary files a/docs/poster/OHBM_2023.pdf and /dev/null differ diff --git a/docs/print_boilerplate.m b/docs/print_boilerplate.m index 55f903b0e..77b47d140 100644 --- a/docs/print_boilerplate.m +++ b/docs/print_boilerplate.m @@ -35,7 +35,7 @@ % preprocessing boilerplate(opt, 'outputPath', fullfile(WK, 'source', 'examples'), ... - 'pipelineType', 'preproc'); + 'pipelineType', 'preprocess'); % stats opt.model.file = fullfile(face_rep_dir, ... diff --git a/docs/source/CONTRIBUTING.md b/docs/source/CONTRIBUTING.md new file mode 120000 index 000000000..f939e75f2 --- /dev/null +++ b/docs/source/CONTRIBUTING.md @@ -0,0 +1 @@ +../../CONTRIBUTING.md \ No newline at end of file diff --git a/docs/source/default_options.m b/docs/source/default_options.m index 136559c4c..264e53193 100644 --- a/docs/source/default_options.m +++ b/docs/source/default_options.m @@ -47,6 +47,7 @@ opt.query.modality{2} = 'func' ; opt.realign.useUnwarp = 1, ; opt.rename.do = 1, ; +opt.rename.overwrite = 1, ; opt.results.MC = 'FWE' ; opt.results.atlas = 'Neuromorphometrics' ; opt.results.binary = 0, ; diff --git a/docs/source/dev_doc.rst b/docs/source/dev_doc.rst index b9a7f068b..dd3866f31 100644 --- a/docs/source/dev_doc.rst +++ b/docs/source/dev_doc.rst @@ -12,6 +12,8 @@ workflows ========= .. _bidsChangeSuffix: .. autofunction:: src.workflows.bidsChangeSuffix +.. _bidsCheckVoxelSize: +.. autofunction:: src.workflows.bidsCheckVoxelSize .. _bidsCopyInputFolder: .. autofunction:: src.workflows.bidsCopyInputFolder .. _bidsInverseNormalize: @@ -398,6 +400,8 @@ infra .. autofunction:: src.infra.resizeAliMask .. _returnBsmDocURL: .. autofunction:: src.infra.returnBsmDocURL +.. _returnHomeDir: +.. autofunction:: src.infra.returnHomeDir .. _returnRepoURL: .. autofunction:: src.infra.returnRepoURL .. _returnRootDir: diff --git a/docs/source/examples/bidspm.bib b/docs/source/examples/bidspm.bib index c37c874f4..71a47cf28 100644 --- a/docs/source/examples/bidspm.bib +++ b/docs/source/examples/bidspm.bib @@ -3,13 +3,13 @@ @software{bidspm license = {GPL-3.0}, title = {bidspm}, url = {https://github.com/cpp-lln-lab/bidspm}, - version = {3.0.0} + version = {3.1.0} doi = {10.5281/zenodo.3554331}, publisher = {Zenodo}, journal = {Software} } -@article{Corbin2018, +@article{corbin2018, author = {Corbin, Nadège and Todd, Nick and Friston, Karl J. and Callaghan, Martina F.}, title = {Accurate modeling of temporal correlations in rapidly sampled fMRI time series}, journal = {Human Brain Mapping}, @@ -19,3 +19,76 @@ @article{Corbin2018 doi = {10.1002/hbm.24218}, year = {2018} } + +@article{rosenke2020, + author = {Rosenke, Mona and van Hoof, Rick and van den Hurk, Job and Grill-Spector, Kalanit and Goebel, Rainer}, + title = {{A Probabilistic Functional Atlas of Human Occipito-Temporal Visual Cortex}}, + journal = {Cerebral Cortex}, + volume = {31}, + number = {1}, + pages = {603-619}, + year = {2020}, + month = {09}, + issn = {1047-3211}, + doi = {10.1093/cercor/bhaa246}, + url = {https://doi.org/10.1093/cercor/bhaa246}, + eprint = {https://academic.oup.com/cercor/article-pdf/31/1/603/34840143/bhaa246.pdf} +} + +@article{wang2014, + author = {Wang, Liang and Mruczek, Ryan E.B. and Arcaro, Michael J. and Kastner, Sabine}, + title = {{Probabilistic Maps of Visual Topography in Human Cortex}}, + journal = {Cerebral Cortex}, + volume = {25}, + number = {10}, + pages = {3911-3931}, + year = {2014}, + month = {12}, + issn = {1047-3211}, + doi = {10.1093/cercor/bhu277}, + url = {https://doi.org/10.1093/cercor/bhu277}, + eprint = {https://academic.oup.com/cercor/article-pdf/25/10/3911/14102011/bhu277.pdf} +} + +@article{huang2022, + title = {An extended {Human} {Connectome} {Project} multimodal parcellation atlas of the human cortex and subcortical areas}, + volume = {227}, + issn = {1863-2653, 1863-2661}, + url = {https://link.springer.com/10.1007/s00429-021-02421-6}, + doi = {10.1007/s00429-021-02421-6}, + language = {en}, + number = {3}, + urldate = {2022-12-14}, + journal = {Brain Structure and Function}, + author = {Huang, Chu-Chung and Rolls, Edmund T. and Feng, Jianfeng and Lin, Ching-Po}, + month = apr, + year = {2022}, + pages = {763--778}, +} + +@article{glasser2016, + title = {A multi-modal parcellation of human cerebral cortex}, + volume = {536}, + issn = {0028-0836, 1476-4687}, + url = {http://www.nature.com/articles/nature18933}, + doi = {10.1038/nature18933}, + language = {en}, + number = {7615}, + urldate = {2023-05-18}, + journal = {Nature}, + author = {Glasser, Matthew F. and Coalson, Timothy S. and Robinson, Emma C. and Hacker, Carl D. and Harwell, John and Yacoub, Essa and Ugurbil, Kamil and Andersson, Jesper and Beckmann, Christian F. and Jenkinson, Mark and Smith, Stephen M. and Van Essen, David C.}, + month = aug, + year = {2016}, + pages = {171--178}, + file = {Accepted Version:/home/remi/Zotero/storage/6R5464JP/Glasser et al. - 2016 - A multi-modal parcellation of human cerebral corte.pdf:application/pdf}, +} + +@article{brett2002, + title={Region of interest analysis using the MarsBar toolbox for SPM 99}, + author={Brett, Matthew and Anton, Jean-Luc and Valabregue, Romain and Poline, Jean-Baptiste and others}, + journal={Neuroimage}, + volume={16}, + number={2}, + pages={S497}, + year={2002} +} diff --git a/docs/source/examples/preprocess_citation.md b/docs/source/examples/preprocess_citation.md index 7777d25f6..1af267e83 100644 --- a/docs/source/examples/preprocess_citation.md +++ b/docs/source/examples/preprocess_citation.md @@ -1,11 +1,11 @@ ## Pre processing -The (f)MRI data were pre-processed with bidspm (v3.0.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm]) +The (f)MRI data were pre-processed with bidspm (v3.1.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm]) using statistical parametric mapping (SPM12 - 7771; Wellcome Center for Neuroimaging, London, UK; https://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037) using MATLAB 9.4.0.813654 (R2018a) -on a unix computer (Linux version 5.19.0-40-generic (build@lcy02-amd64-047) (x86_64-linux-gnu-gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #41~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 31 16:00:14 UTC 2 +on a unix computer (Linux version 5.19.0-46-generic (build@lcy02-amd64-025) (x86_64-linux-gnu-gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 21 15:35:31 UTC 2 ) . @@ -56,5 +56,5 @@ gaussian kernel (FWHM = 6 mm). ## References This method section was automatically generated using bidspm -(v3.0.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331) +(v3.1.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331) and octache (https://github.com/Remi-Gau/Octache). diff --git a/docs/source/examples/stats_model-resampling_citation.md b/docs/source/examples/stats_model-resampling_citation.md index 3f42484e0..51aad8d28 100644 --- a/docs/source/examples/stats_model-resampling_citation.md +++ b/docs/source/examples/stats_model-resampling_citation.md @@ -1,11 +1,11 @@ ## fMRI statistical analysis -The fMRI data were analysed with bidspm (v3.0.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm]) +The fMRI data were analysed with bidspm (v3.1.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm]) using statistical parametric mapping (SPM12 - 7771; Wellcome Center for Neuroimaging, London, UK; https://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037) using MATLAB 9.4.0.813654 (R2018a) -on a unix computer (Linux version 5.19.0-40-generic (build@lcy02-amd64-047) (x86_64-linux-gnu-gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #41~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 31 16:00:14 UTC 2 +on a unix computer (Linux version 5.19.0-46-generic (build@lcy02-amd64-025) (x86_64-linux-gnu-gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 21 15:35:31 UTC 2 ) The input data were the preprocessed BOLD images in IXI549Space space for the task " facerepetition ". @@ -17,9 +17,7 @@ regression at each voxel of the brain, using generalized least squares with a global AR(1) model to account for temporal auto-correlation and a drift fit with discrete cosine transform basis ( 128 seconds cut-off). -Image intensity scaling was done run-wide before statistical modeling such that -the mean image would have a mean intracerebral intensity of 100. - + Image intensity scaling was done run-wide before statistical modeling such that the mean image would have a mean intracerebral intensity of 100. We modeled the fMRI experiment in a event design with regressors entered into the run-specific design matrix. The onsets were convolved with SPM canonical hemodynamic response function (HRF) @@ -43,5 +41,5 @@ to account for residual motion artefacts, ## References This method section was automatically generated using bidspm -(v3.0.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331) +(v3.1.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331) and octache (https://github.com/Remi-Gau/Octache). diff --git a/docs/source/index.rst b/docs/source/index.rst index 752bf8abe..06928cc1d 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -30,6 +30,7 @@ Welcome to bidspm documentation! docker CHANGELOG links_and_references + CONTRIBUTING dev_doc diff --git a/src/reports/bidspm.bib b/src/reports/bidspm.bib index dcca7c59a..71a47cf28 100644 --- a/src/reports/bidspm.bib +++ b/src/reports/bidspm.bib @@ -3,7 +3,7 @@ @software{bidspm license = {GPL-3.0}, title = {bidspm}, url = {https://github.com/cpp-lln-lab/bidspm}, - version = {3.0.0} + version = {3.1.0} doi = {10.5281/zenodo.3554331}, publisher = {Zenodo}, journal = {Software} diff --git a/version.txt b/version.txt index ad55eb85f..6c8dc7eb2 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -v3.0.0 +v3.1.0