diff --git a/CHANGELOG.md b/CHANGELOG.md index 73f4958f..55646185 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,63 +19,71 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Security --> -## [Unreleased] +## [unreleased] +### Added + +### Changed + +### Deprecated + +### Removed + +### Fixed + +### Security + +## [v4.0.0] - 2024-09-11 + +**Full Changelog**: https://github.com/cpp-lln-lab/bidspm/compare/v3.1.0...v4.0.0 ### 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](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] 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 [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 [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] allow for 2 sample T-Test, within group T-Test and one-way ANOVA to be 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 [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 [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] add Apptainer definition [1254](https://github.com/cpp-lln-lab/bidspm/pull/1254) 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 [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 [Remi-Gau](https://github.com/Remi-Gau) +* [ENH] allow to run substeps of the bayesian model selection [1145](https://github.com/cpp-lln-lab/bidspm/pull/1145) 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 [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 [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 [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](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](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](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) +* [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](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](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] ensure that {func}`setBatchCoregistrationFuncToAnat` takes into account bids_filter [1295](https://github.com/cpp-lln-lab/bidspm/pull/1295) 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 [d-ni374](https://github.com/d-ni374) +* [FIX] make {func}`getAcquisitionTime` less brittle [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) 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 [d-ni374](https://github.com/d-ni374) and [1275](https://github.com/cpp-lln-lab/bidspm/pull/1275) 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 - +* [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 [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 [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 [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 [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 [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 [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 [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 [Remi-Gau](https://github.com/Remi-Gau) ## [3.1.0] - 2023-07-01 diff --git a/CITATION.cff b/CITATION.cff index 61f36fb8..abea5aea 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,7 +2,7 @@ cff-version: 1.2.0 title: bidspm -version: 4.0.0 +version: 4.0.0dev abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and analyze BIDS data sets using SPM12. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 8105f2c3..44ac49b2 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -96,7 +96,7 @@ New questions must be added to `docs/questions` and the main FAQ.md can be created with: ```bash -make update_faq +make -C doc update_faq ``` ### release protocol @@ -110,11 +110,15 @@ make update_faq - [ ] update binder - [ ] update docker recipes - [ ] update changelog + - [ ] change from `[unreleased]` to the version number + - [ ] remove unused sections (like `security`) - [ ] 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 +- [ ] create a github tagged release - [ ] build and push docker images if necessary - [ ] after release - [ ] set version in `citation.cff` to dev + - [ ] update changelog + - [ ] add an `[unreleased]` section diff --git a/version.txt b/version.txt index 857572fc..71910403 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -v4.0.0 +v4.0.0dev