From d8518c33235bed7cee0d7dfd43fc6b8a74154bc8 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 5 Sep 2024 15:48:00 +0200 Subject: [PATCH] prepare release --- CHANGELOG.md | 66 +++--- CITATION.cff | 197 +++++++++--------- CONTRIBUTING.md | 2 + Makefile | 29 +-- README.md | 2 +- docs/Makefile | 7 +- docs/create_manual.sh | 18 -- docs/source/examples/bidspm.bib | 2 +- docs/source/examples/preprocess_citation.md | 6 +- .../stats_model-resampling_citation.md | 6 +- src/reports/bidspm.bib | 2 +- version.txt | 2 +- 12 files changed, 150 insertions(+), 189 deletions(-) delete mode 100644 docs/create_manual.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index 55087afe8..73f4958fc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,55 +24,55 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -* [ENH] add QA workflow `bidsQA` to find outliers in MRIQC output or to view number of outlier timepoints (for a given metric and threshold) in each functional run #1297 by @Remi-Gau -* [ENH] add support for one-way ANOVA across groups at the group level #1296 by @Remi-Gau -* [ENH] allow for 2 sample T-Test, within group T-Test and one-way ANOVA to ne more flexible with respect to what praticipants.tsv column to use to allocate subjects in each group #1296 by @Remi-Gau -* [ENH] make `addConfoundsToDesignMatrix` a method of `BidsModel` #1294 by @Remi-Gau -* [ENH] add Apptainer definition #1254 by @Remi-Gau and @monique2208 -* [ENH] allow to copy anat only on raw datasets #1181 by @Remi-Gau -* [ENH] add option to concatenate runs at subject level to facilite running PPI analysis #1133 by @Remi-Gau -* [ENH] allow to run substeps of substeps of the bayesian model selection #1145 by @Remi-Gau -* [ENH] add quality control for GLM using the MACS toolbox to give a goodness of fit and several other information criteria (AIC, BIC) (MATLAB only) #1135 by @Remi-Gau -* [ENH] add several confound strategies to add to bids stats model and a function to create family of models #1126 by @Remi-Gau -* [ENH] add CLI to run bayesian model selection #1121 by @Remi-Gau +* [ENH] add QA workflow `bidsQA` to find outliers in MRIQC output or to view number of outlier timepoints (for a given metric and threshold) in each functional run [1297](https://github.com/cpp-lln-lab/bidspm/pull/1297) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] add support for one-way ANOVA across groups at the group level [1296](https://github.com/cpp-lln-lab/bidspm/pull/1296) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] allow for 2 sample T-Test, within group T-Test and one-way ANOVA to ne more flexible with respect to what praticipants.tsv column to use to allocate subjects in each group [1296](https://github.com/cpp-lln-lab/bidspm/pull/1296) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] make `addConfoundsToDesignMatrix` a method of `BidsModel` [1294](https://github.com/cpp-lln-lab/bidspm/pull/1294) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] add Apptainer definition [1254](https://github.com/cpp-lln-lab/bidspm/pull/1254) by by [Remi-Gau](https://github.com/Remi-Gau) and by [monique2208](https://github.com/monique2208) +* [ENH] allow to copy anat only on raw datasets [1181](https://github.com/cpp-lln-lab/bidspm/pull/1181) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] add option to concatenate runs at subject level to facilite running PPI analysis [1133](https://github.com/cpp-lln-lab/bidspm/pull/1133) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] allow to run substeps of substeps of the bayesian model selection [1145](https://github.com/cpp-lln-lab/bidspm/pull/1145) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] add quality control for GLM using the MACS toolbox to give a goodness of fit and several other information criteria (AIC, BIC) (MATLAB only) [1135](https://github.com/cpp-lln-lab/bidspm/pull/1135) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] add several confound strategies to add to bids stats model and a function to create family of models [1126](https://github.com/cpp-lln-lab/bidspm/pull/1126) by by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] add CLI to run bayesian model selection [1121](https://github.com/cpp-lln-lab/bidspm/pull/1121) by by [Remi-Gau](https://github.com/Remi-Gau) * [ENH] support label of activations with all atlases [1100](https://github.com/cpp-lln-lab/bidspm/pull/1100) by [Remi-Gau](https://github.com/Remi-Gau) -* [ENH] add support for session level models #1116 be @Remi-Gau +* [ENH] add support for session level models [1116](https://github.com/cpp-lln-lab/bidspm/pull/1116) be by [Remi-Gau](https://github.com/Remi-Gau) - allow to pass dummy contrasts to session level - allow inter session contrasts to be computed at the subject level - improve naming of contrast to mention bids ses and run -* [ENH] add Bayesian model selection to the python CLI #1292 @Remi-Gau +* [ENH] add Bayesian model selection to the python CLI [1292](https://github.com/cpp-lln-lab/bidspm/pull/1292) by [Remi-Gau](https://github.com/Remi-Gau) ### Changed -* [ENH] align specification of F contrasts on the BIDS stats model: they should now be specified as a 2D matrix and not a 1D vector. #1276 @Remi-Gau -* [DOC] change theme and structure of the documentation #1256 @Remi-Gau -* [REF] Refactor and update CLI in #1096 @Remi-Gau -* [ENH] {func}`getData` only loads anat data when requested #1257 @Remi-Gau -* [ENH] the python CLI now uses sub-commands instead of the named parameter `--action` #1292 @Remi-Gau +* [ENH] align specification of F contrasts on the BIDS stats model: they should now be specified as a 2D matrix and not a 1D vector. [1276](https://github.com/cpp-lln-lab/bidspm/pull/1276) by [Remi-Gau](https://github.com/Remi-Gau) +* [DOC] change theme and structure of the documentation [1256](https://github.com/cpp-lln-lab/bidspm/pull/1256) by [Remi-Gau](https://github.com/Remi-Gau) +* [REF] Refactor and update CLI in [1096](https://github.com/cpp-lln-lab/bidspm/pull/1096) by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] {func}`getData` only loads anat data when requested [1257](https://github.com/cpp-lln-lab/bidspm/pull/1257) by [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] the python CLI now uses sub-commands instead of the named parameter `--action` [1292](https://github.com/cpp-lln-lab/bidspm/pull/1292) by [Remi-Gau](https://github.com/Remi-Gau) ### Deprecated ### Removed -* [REF] Remove old CLI in #1096 @Remi-Gau +* [REF] Remove old CLI in [1096](https://github.com/cpp-lln-lab/bidspm/pull/1096) by [Remi-Gau](https://github.com/Remi-Gau) ### Fixed -* [FIX] ensure that {func}`setBatchCoregistrationFuncToAnat` takes into account bids_filter #1295 by @d-ni374 -* [FIX] update {func}`createDefaultStatsModel` to use proper `GroupBy` at the dataset level #1248 by @d-ni374 -* [FIX] make {func}`getAcquisitionTime` less brittle #1248 by @d-ni374 -* [FIX] fix regular expression in {func}`bidsResults` to identify contrasts #1248 by @d-ni374 and #1275 by @Remi-Gau -* [FIX] pass analysis level to stats actions when using python CLI #1258 @Remi-Gau -* [FIX] remove goodness of fit from dataset level analysis as it is not supported by the MACS toolbox #1265 by @Remi-Gau -* [FIX] add java and zip to container recipes to allow using nidm results with octave #1265 by @Remi-Gau -* [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation #1203 by @Remi-Gau -* [FIX] save `onsets.mat` directly in subject stats folder #1187 by @Remi-Gau -* [FIX] do not compute subject level contrast when running dataset level #1102 by @Remi-Gau -* [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in #1099 by @Remi-Gau -* [FIX] rename results files (csv, tsv, png, nii) of each contrasts #1104 by @Remi-Gau -* [FIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in #1110 by @Remi-Gau +* [FIX] ensure that {func}`setBatchCoregistrationFuncToAnat` takes into account bids_filter [1295](https://github.com/cpp-lln-lab/bidspm/pull/1295) by by [d-ni374](https://github.com/d-ni374) +* [FIX] update {func}`createDefaultStatsModel` to use proper `GroupBy` at the dataset level [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374) +* [FIX] make {func}`getAcquisitionTime` less brittle [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374) +* [FIX] fix regular expression in {func}`bidsResults` to identify contrasts [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374) and [1275](https://github.com/cpp-lln-lab/bidspm/pull/1275) by by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] pass analysis level to stats actions when using python CLI [1258](https://github.com/cpp-lln-lab/bidspm/pull/1258) by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] remove goodness of fit from dataset level analysis as it is not supported by the MACS toolbox [1265](https://github.com/cpp-lln-lab/bidspm/pull/1265) by by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] add java and zip to container recipes to allow using nidm results with octave [1265](https://github.com/cpp-lln-lab/bidspm/pull/1265) by by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation [1203](https://github.com/cpp-lln-lab/bidspm/pull/1203) by by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] save `onsets.mat` directly in subject stats folder [1187](https://github.com/cpp-lln-lab/bidspm/pull/1187) by by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] do not compute subject level contrast when running dataset level [1102](https://github.com/cpp-lln-lab/bidspm/pull/1102) by by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in [1099](https://github.com/cpp-lln-lab/bidspm/pull/1099) by by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] rename results files (csv, tsv, png, nii) of each contrasts [1104](https://github.com/cpp-lln-lab/bidspm/pull/1104) by by [Remi-Gau](https://github.com/Remi-Gau) +* [FIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in [1110](https://github.com/cpp-lln-lab/bidspm/pull/1110) by by [Remi-Gau](https://github.com/Remi-Gau) ### Security @@ -252,7 +252,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * [FIX] various bug fixes in [694](https://github.com/cpp-lln-lab/bidspm/pull/694) by [Remi-Gau](https://github.com/Remi-Gau) * [FIX] add some warnings to handle several bugs with empty ROIs in [693](https://github.com/cpp-lln-lab/bidspm/pull/693) by [Remi-Gau](https://github.com/Remi-Gau) * [FIX] re enable octave tests CI in [686](https://github.com/cpp-lln-lab/bidspm/pull/686) by [Remi-Gau](https://github.com/Remi-Gau) -* [FIX] patches for [682](https://github.com/cpp-lln-lab/bidspm/pull/682) and [683](https://github.com/cpp-lln-lab/bidspm/pull/683) (#687) by [mwmaclean](https://github.com/mwmaclean) +* [FIX] patches for [682](https://github.com/cpp-lln-lab/bidspm/pull/682) and [683](https://github.com/cpp-lln-lab/bidspm/pull/683) ([687](https://github.com/cpp-lln-lab/bidspm/pull/687)) by [mwmaclean](https://github.com/mwmaclean) * [FIX] ensure that bidsResults does not run if we don't have the proper options in [679](https://github.com/cpp-lln-lab/bidspm/pull/679) by [Remi-Gau](https://github.com/Remi-Gau) * [FIX] returnRootDir only relies on fullpaths in [676](https://github.com/cpp-lln-lab/bidspm/pull/676) by [Remi-Gau](https://github.com/Remi-Gau) * [FIX] set minimum compatible fmriprep version in [675](https://github.com/cpp-lln-lab/bidspm/pull/675) by [Remi-Gau](https://github.com/Remi-Gau) diff --git a/CITATION.cff b/CITATION.cff index b8da0ae4b..61f36fb8e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,120 +1,121 @@ cff-version: 1.2.0 -title: "bidspm" +title: bidspm -version: 3.1.0dev +version: 4.0.0 -abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and analyze BIDS data sets using SPM12. +abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and + analyze BIDS data sets using SPM12. -message: "If you use this software, please cite it as below." +message: If you use this software, please cite it as below. -repository-code: "https://github.com/cpp-lln-lab/bidspm" +repository-code: https://github.com/cpp-lln-lab/bidspm identifiers: - description: This is the collection of archived snapshots of all releases of bidspm type: doi - value: "10.5281/zenodo.3554331" + value: 10.5281/zenodo.3554331 - description: OHBM 2023 poster type: doi - value: "10.5281/zenodo.8099835" + value: 10.5281/zenodo.8099835 contact: - - affiliation: "Université catholique de Louvain" + - affiliation: Université catholique de Louvain email: remi.gau2@mcgill.ca family-names: Gau given-names: Rémi authors: -- family-names: "Gau" - given-names: "Rémi" - orcid: "https://orcid.org/0000-0002-1535-9767" - affiliation: "Origami lab, McGill University, Montreal, Québec, Canada" - -- family-names: "Barilari" - given-names: "Marco" - orcid: "https://orcid.org/0000-0002-3313-3120" - affiliation: "Université catholique de Louvain" - -- family-names: "Battal" - given-names: "Ceren" - orcid: "https://orcid.org/0000-0002-9844-7630" - affiliation: "Université catholique de Louvain" - -- family-names: "Rezk" - given-names: "Mohamed" - orcid: "https://orcid.org/0000-0002-1866-8645" - affiliation: "Université catholique de Louvain" - -- family-names: "Gurtubay" - given-names: "Ane" - orcid: "https://orcid.org/0000-0003-3824-2219" - affiliation: "Université catholique de Louvain" - -- family-names: "Falagiarda" - given-names: "Federica" - orcid: "https://orcid.org/0000-0001-7844-1605" - affiliation: "Université catholique de Louvain" - -- family-names: "MacLean" - given-names: "Michèle" - orcid: "https://orcid.org/0000-0002-0174-9326" - affiliation: "Université de Montréal" - -- family-names: "Cerpelloni" - given-names: "Filippo" - orcid: "https://orcid.org/0000-0001-8070-5753" - affiliation: "Université catholique de Louvain" - -- family-names: "Shahzad" - given-names: "Iqra" - orcid: "https://orcid.org/0000-0002-8724-7668" - affiliation: "Université catholique de Louvain" - -- family-names: "Nunes" - given-names: "Márcia" - -- family-names: "Caron-Guyon" - given-names: "Jeanne" - orcid: "https://orcid.org/0000-0001-8681-5267" - affiliation: "Université catholique de Louvain" - -- family-names: "Chouinard-Leclaire" - given-names: "Christine" - orcid: "https://orcid.org/0000-0002-1066-6266" - affiliation: "Université de Montréal" - -- family-names: "Yang" - given-names: "Ying" - orcid: "https://orcid.org/0000-0002-4157-2975" - affiliation: "Université catholique de Louvain" - -- family-names: "Mattioni" - given-names: "Stefania" - affiliation: "University of Gent" - orcid: "https://orcid.org/0000-0001-8279-6118" - -- family-names: Huber - given-names: Daniel - affiliation: University of Innsbruck - -- family-names: "Van Audenhaege" - given-names: "Alice" - affiliation: "Université catholique de Louvain" - orcid: "https://orcid.org/0000-0002-5276-8818" - -- family-names: "Matuszewski" - given-names: "Jacek" - 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" - -- family-names: "Denissen" - given-names: "Monique" - + - family-names: Van Audenhaege + given-names: Alice + affiliation: Université catholique de Louvain + orcid: https://orcid.org/0000-0002-5276-8818 + + - family-names: Gurtubay + given-names: Ane + orcid: https://orcid.org/0000-0003-3824-2219 + affiliation: Université catholique de Louvain + + - family-names: Battal + given-names: Ceren + orcid: https://orcid.org/0000-0002-9844-7630 + affiliation: Université catholique de Louvain + + - family-names: Chouinard-Leclaire + given-names: Christine + orcid: https://orcid.org/0000-0002-1066-6266 + affiliation: Université de Montréal + + - family-names: Huber + given-names: Daniel + affiliation: University of Innsbruck + + - family-names: Falagiarda + given-names: Federica + orcid: https://orcid.org/0000-0001-7844-1605 + affiliation: Université catholique de Louvain + + - family-names: Cerpelloni + given-names: Filippo + orcid: https://orcid.org/0000-0001-8070-5753 + affiliation: Université catholique de Louvain + + - family-names: Shahzad + given-names: Iqra + orcid: https://orcid.org/0000-0002-8724-7668 + affiliation: Université catholique de Louvain + + - family-names: Matuszewski + given-names: Jacek + affiliation: Université catholique de Louvain + orcid: https://orcid.org/0000-0001-9752-3294 + + - family-names: Caron-Guyon + given-names: Jeanne + orcid: https://orcid.org/0000-0001-8681-5267 + affiliation: Université catholique de Louvain + + - family-names: Barilari + given-names: Marco + orcid: https://orcid.org/0000-0002-3313-3120 + affiliation: Université catholique de Louvain + + - family-names: MacLean + given-names: Michèle + orcid: https://orcid.org/0000-0002-0174-9326 + affiliation: Université de Montréal + + - family-names: Rezk + given-names: Mohamed + orcid: https://orcid.org/0000-0002-1866-8645 + affiliation: Université catholique de Louvain + + - family-names: Denissen + given-names: Monique + + + - family-names: Nunes + given-names: Márcia + + - family-names: Collignon + given-names: Olivier + orcid: https://orcid.org/0000-0003-1882-3550 + affiliation: Université catholique de Louvain + + - family-names: Gau + given-names: Rémi + orcid: https://orcid.org/0000-0002-1535-9767 + affiliation: Origami lab, McGill University, Montreal, Québec, Canada + + - family-names: Mattioni + given-names: Stefania + affiliation: University of Gent + orcid: https://orcid.org/0000-0001-8279-6118 + + - family-names: Yang + given-names: Ying + orcid: https://orcid.org/0000-0002-4157-2975 + affiliation: Université catholique de Louvain license: GPL-3.0 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index ce1ef8a4b..8105f2c39 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -116,3 +116,5 @@ make update_faq - [ ] merge to default branch - [ ] create a tagged release - [ ] build and push docker images if necessary +- [ ] after release + - [ ] set version in `citation.cff` to dev diff --git a/Makefile b/Makefile index 7c31770b9..e503d73f5 100644 --- a/Makefile +++ b/Makefile @@ -61,37 +61,14 @@ fix_submodule: ## Fix any submodules that would not be checked out prepare_release: python tools/citation_cff_maint.py - python tools/tools/add_links_to_changelog.py + python tools/add_links_to_changelog.py python tools/bump_version.py + cd docs && make release validate_cff: ## Validate the citation file cffconvert --validate -release: validate_cff prepare_release lint manual - - -################################################################################ -# doc - -clean_doc: - cd docs && make clean - -manual: update_faq ## Build PDF version of the doc - cd docs && sh create_manual.sh - - -################################################################################ -# lint - -lint: lint_matlab lint_python ## Clean MATLAB and python code - -lint_matlab: ## Clean MATLAB code - mh_style --fix && mh_metric --ci && mh_lint - -lint_python: ## Clean python code - black *.py src tests docs - flake8 *.py src tests docs - mypy *.py src +release: validate_cff prepare_release ################################################################################ # test diff --git a/README.md b/README.md index 92985a4fb..9ba8b09db 100644 --- a/README.md +++ b/README.md @@ -169,7 +169,7 @@ Please see our [documentation](https://bidspm.readthedocs.io/en/latest/index.htm license = {GPL-3.0}, title = {{bidspm}}, url = {https://github.com/cpp-lln-lab/bidspm}, - version = {3.1.0dev} + version = {4.0.0} } ``` diff --git a/docs/Makefile b/docs/Makefile index 878e08b3c..14ed781bf 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -33,11 +33,13 @@ help: clean: rm -rf $(BUILDDIR) - rm -f bidspm-manual.pdf view: $(BROWSER) build/html/index.html +release: update_faq boilerplate clean_default_options default_mapping + python generate_doc.py + update_faq: cd faq/bids && faqtory build cd faq/general && faqtory build @@ -46,9 +48,6 @@ update_faq: cd faq/spm && faqtory build cd faq/stats && faqtory build -bidspm-manual.pdf: update_faq - bash create_manual.sh - boilerplate: $(MATLAB) $(ARG) -r "print_boilerplate; exit()" rm -fr reports diff --git a/docs/create_manual.sh b/docs/create_manual.sh deleted file mode 100644 index ecfa6896f..000000000 --- a/docs/create_manual.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash - -make boilerplate -make clean_default_options -make default_mapping - -# needed to ignore svg badges -sed -i 's//.. only:: not latex/g' ../README.md -sed -i 's/\[!\[/ \[!\[/g' ../README.md - -python generate_doc.py - -sphinx-build -M latexpdf source build - -cp build/latex/bidspm.pdf bidspm-manual.pdf - -sed -i 's/.. only:: not latex//g' ../README.md -sed -i 's/ \[!\[/\[!\[/g' ../README.md diff --git a/docs/source/examples/bidspm.bib b/docs/source/examples/bidspm.bib index 71a47cf28..11ab25cbe 100644 --- a/docs/source/examples/bidspm.bib +++ b/docs/source/examples/bidspm.bib @@ -3,7 +3,7 @@ @software{bidspm license = {GPL-3.0}, title = {bidspm}, url = {https://github.com/cpp-lln-lab/bidspm}, - version = {3.1.0} + version = {4.0.0} doi = {10.5281/zenodo.3554331}, publisher = {Zenodo}, journal = {Software} diff --git a/docs/source/examples/preprocess_citation.md b/docs/source/examples/preprocess_citation.md index 265d07b80..f3b16709c 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 (v3.1.0dev; 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 (v4.0.; 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 6.5.0-41-generic (buildd@lcy02-amd64-120) (x86_64-linux-gnu-gcc-12 (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #41~22.04.2-Ubuntu SMP PREEMPT_DYNAMIC Mon Jun 3 11:32:55 UTC 2 +on a unix computer (Linux version 6.8.0-40-generic (buildd@lcy02-amd64-078) (x86_64-linux-gnu-gcc-12 (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 ) . @@ -56,5 +56,5 @@ gaussian kernel (FWHM = 6 mm). ## References This method section was automatically generated using bidspm -(v3.1.0dev; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331) +(v4.0.; 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 cc372e692..e4d58f8d7 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 (v3.1.0dev; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm]) +The fMRI data were analysed with bidspm (v4.0.; 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 6.5.0-41-generic (buildd@lcy02-amd64-120) (x86_64-linux-gnu-gcc-12 (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #41~22.04.2-Ubuntu SMP PREEMPT_DYNAMIC Mon Jun 3 11:32:55 UTC 2 +on a unix computer (Linux version 6.8.0-40-generic (buildd@lcy02-amd64-078) (x86_64-linux-gnu-gcc-12 (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 ) The input data were the preprocessed BOLD images in IXI549Space space for the task " facerepetition ". @@ -41,5 +41,5 @@ to account for residual motion artefacts, ## References This method section was automatically generated using bidspm -(v3.1.0dev; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331) +(v4.0.; 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/src/reports/bidspm.bib b/src/reports/bidspm.bib index e054d3486..11ab25cbe 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 = {3.1.0dev} + version = {4.0.0} doi = {10.5281/zenodo.3554331}, publisher = {Zenodo}, journal = {Software} diff --git a/version.txt b/version.txt index aea64d506..857572fcd 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -v3.1.0dev +v4.0.0