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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[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 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 be 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 by 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 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] support label of activations with all atlases 1100 by Remi-Gau
  • [ENH] add support for session level models 1116 be by 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 by 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 by Remi-Gau
  • [DOC] change theme and structure of the documentation 1256 by Remi-Gau
  • [REF] refactor and update CLI in 1096 by Remi-Gau
  • [ENH] {func}getData only loads anat data when requested 1257 by Remi-Gau
  • [ENH] the python CLI now uses sub-commands instead of the named parameter --action 1292 by Remi-Gau

Removed

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 by 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

[3.1.0] - 2023-07-01

Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v3.0.0...v3.1.0

Added

  • [DOC] add changelog in 1056 by Remi-Gau
  • [DOC] minor doc fixes in 1020 by Remi-Gau
  • [DOC] Improve doc example out stats in 1014 by Remi-Gau
  • [DOC] update doc regarding FAST model as default in 985 by Remi-Gau
  • [DOC] update contributors and default options in doc in 981 by Remi-Gau
  • [DOC] add doc to link to transformations in 942 by Remi-Gau
  • [DOC] add demo code from workshop in 935 by Remi-Gau
  • [DOC] abstract OHBM 2023 in 934 by Remi-Gau
  • [DOC] add argument groups to python cli in 907 by Remi-Gau
  • [DOC] update FAQ in 897 by Remi-Gau
  • [ENH] add proper error when a column cannot be found in participants.tsv in 1050 by Remi-Gau
  • [ENH] update CPP ROI and add methods section for ROI creation in 1026 by Remi-Gau
  • [ENH] update rename to store original spm name of a file in metadata in 987 by Remi-Gau
  • [ENH] add hemisphere parameter to CLI in 950 by Remi-Gau
  • [ENH] make it possible to update bidspm from any folder in 948 by Remi-Gau
  • [ENH] use filtering of layout in 944 by Remi-Gau
  • [ENH] make reports more silent in 939 by Remi-Gau
  • [ENH] add CC0 license by default to all outputs in 898 by Remi-Gau

Changed

  • [ENH] overwrite files when renaming by default in 1051 by Remi-Gau
  • [ENH] turn error into warning when no data to copy found in 992 by Remi-Gau

Removed

Fixed

  • [FIX] fix vismotion demo in 1070 by Remi-Gau
  • [FIX] Exclude from GLM specification events with onsets longer than the run duration in 1060 by Remi-Gau
  • [FIX] remove dummies from preproc dataset and not raw dataset when using CLI in 1057 by Remi-Gau
  • [FIX] skip smoothing when running bidspm prepoc in dryRun in 1054 by Remi-Gau
  • [FIX] handle phase entity in filename in 1034 by Remi-Gau
  • [FIX] fix group level results after contrasts smoothing in 1021 by Remi-Gau
  • [FIX] copy to derivatives handles bids filter file and minimize re copying files that already exist in 1015 by Remi-Gau
  • [FIX] allow cli to run constrat smoothing in 1012 by Remi-Gau
  • [FIX] Force copy of data from fmriprep folder even if bidspm-preproc folder exists in 1009 by marcobarilari
  • [FIX] report proper fold number in labelfold.tsv in 989 by Remi-Gau
  • [FIX] inconsistent slice timing throw errors and not warnings in 982 by Remi-Gau
  • [FIX] validate condition names early to avoid downstream error in 983 by Remi-Gau
  • [FIX] validate content results structure in 980 by Remi-Gau
  • [FIX] missing variable for a Filter transform should not lead to a crash in 970 by Remi-Gau
  • [FIX] display error when impossible slice timing values are given in 969 by Remi-Gau
  • [FIX] fix QA failures in 941 by Remi-Gau
  • [FIX] bug fix 892 in 936 by Remi-Gau
  • [FIX] fix python cli in 888 by Remi-Gau

[3.0.0] - 2022-12-14

Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v2.3.0...v3.0.0

Changed

  • [DEP] deprecate slice order in options in 882 by Remi-Gau
  • [ENH] change the way parametric models are run in 873 by Remi-Gau*

Added

  • [ENH] include roi based calls in CLI in 880 by Remi-Gau
  • [ENH] add copy dataset to CLI in 842 by Remi-Gau
  • [ENH] add smoothing to CLI in 841 by Remi-Gau
  • [ENH] create docker image of bids app - Octave in 837 by Remi-Gau
  • [ENH] use python based CLI to run bidspm with octave in 832 by Remi-Gau
  • [ENH] update CPP_ROI in 885 by Remi-Gau
  • [ENH] add extra files to derivatives datasets in 883 by Remi-Gau
  • [ENH] incorporate opt.results in bids stats model in 879 by Remi-Gau
  • [ENH] add option to ignore creating dataset level node in default model in 871 by Remi-Gau
  • [ENH] implement logger in 867 by Remi-Gau
  • [ENH] add function to return contrast filename for a certain contrast name in 866 by Remi-Gau
  • [DOC] update FAQ to explain how to change subject level GLM folder name in 872 by Remi-Gau

Fixed

  • [FIX] better handle metadata when changing suffix in 884 by Remi-Gau
  • [FIX] exit with a warning and not an error when no contrast specified in 870 by Remi-Gau
  • [FIX] fix SPM loading in returnContrastImageFile in 869 by Remi-Gau
  • [FIX] fix make file in 868 by Remi-Gau

[2.3.0] - 2022-11-22

Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v2.2.0...v2.3.0

  • bidspm main function:
    • saving options are saved to help with bug report
    • generate method section in reports folder when running preprocess or statistics

Added

  • [DOC] add auto label of activation info in 821 by Remi-Gau
  • [DOC] improve bids model warning in 820 by Remi-Gau
  • [DOC] add all functions to doc in 819 by Remi-Gau
  • [ENH] add design only to CLI 772
  • [ENH] smoothing workflow will also try to smooth the corresponding anat data too
  • [ENH] save skipped ROIs and concat beta maps in 823 by Remi-Gau
  • [ENH] add boilerplate to CLI in 822 by Remi-Gau
  • [ENH] error logs are generated upon crash for better bug reports in 808 by Remi-Gau
  • [ENH] Use CLI to create default model in 804 by Remi-Gau
  • [ENH] include bids and bids stats model validation if the validators are installed in 787 by Remi-Gau
  • [ENH] add inverse normalize workflow in 784 by Remi-Gau
  • [ENH] lesion detection will be done by including the CSF TPM too in 778 by Remi-Gau

Fixed

  • [FIX] fix printing of windows path in 812 by Remi-Gau
  • [FIX] use glob patterns to define dummy contrasts in 826 by Remi-Gau
  • [FIX] rm desc when renamining some files in lesion segemtation in 817 by Remi-Gau
  • [FIX] avoid duplicate contrasts in 816 by Remi-Gau
  • [FIX] make collecting of OS version on windows more robust in 806 by Remi-Gau
  • [FIX] throw warning when no results are asked in 795 by Remi-Gau
  • [FIX] fix windows bugs in 792 by Remi-Gau
  • [FIX] fix spelling in 789 by Remi-Gau
  • [FIX] fix and tidy failing workflows in 774 by Remi-Gau

[2.2.0] - 2022-10-29

Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v2.1.0...v2.2.0

Added

  • [DOC] use new copyright format in 750 by Remi-Gau
  • [DOC] improve stats doc and warnings in 746 by Remi-Gau
  • [ENH] add design only to CLI in 772 by Remi-Gau
  • [ENH] add functions to help select fmriprep regressors in 748 by Remi-Gau
  • [ENH] start switching to bidspm in 747 by Remi-Gau
  • [ENH] use inputs from several datasets for lesion abnormality detection in 730 by Remi-Gau
  • [ENH] Update bidspm path in 752 by Remi-Gau

Changed

Fixed

  • [FIX] fixes workflow timing in 773 by Remi-Gau
  • [FIX] related to 763 and testing through CI if the patch breaks things (reopened) in 765 by marcobarilari

[2.1.0] - 2022-07-21

Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v2.0.0...v2.1.0

Added

  • [ENH] add possibility to use AAL for labelling of activations in 717 by Remi-Gau
  • [DOC] update FAQ to help structure data to run stats on fmriprep in 685 by Remi-Gau
  • [DOC] add demo for ds002799 in 678 by Remi-Gau
  • [DOC] add DIY section to documtation in 677 by Remi-Gau
  • [DOC] improve description of stats output and of bids stats model in 670 by Remi-Gau

Changed

Fixed

  • [FIX] fix lesion segmentation output (and refactor) in 727 by Remi-Gau
  • [FIX] add more explicit error message for input parsing of getData in 726 by Remi-Gau
  • [FIX] support globbing patterns to specify conditions in design matrix in 716 by Remi-Gau
  • [FIX] fix ALI toolbox issues in 723 by Remi-Gau
  • [FIX] improve warning selecting too many masks in 715 by Remi-Gau
  • [FIX] fix and refactor demos, and update help sections in 701 by Remi-Gau
  • [FIX] add guard clauses to run ROI based analysis only when requested in 708 by Remi-Gau
  • [FIX] convert nan to zeros in confounds in 700 by Remi-Gau
  • [FIX] change default space value in cpp_spm in 699 by Remi-Gau
  • [FIX] various bug fixes in 694 by Remi-Gau
  • [FIX] add some warnings to handle several bugs with empty ROIs in 693 by Remi-Gau
  • [FIX] re enable octave tests CI in 686 by Remi-Gau
  • [FIX] patches for 682 and 683 (687) by mwmaclean
  • [FIX] ensure that bidsResults does not run if we don't have the proper options in 679 by Remi-Gau
  • [FIX] returnRootDir only relies on fullpaths in 676 by Remi-Gau
  • [FIX] set minimum compatible fmriprep version in 675 by Remi-Gau
  • [FIX] renaming of design matrix images at group level in 668 by Remi-Gau
  • [FIX] make sure 2 sample ttest can run more than one contrasts in 665 by Remi-Gau
  • [FIX] label actiation: csv results file with no significant voxels are ignored with a warning in 663 by Remi-Gau
  • [FIX] onsets and confounds are saved in the proper dir when there are several tasks in 659 by Remi-Gau
  • [FIX] fix silent dry run override in 657 by Remi-Gau
  • [FIX] use proper subject background for montage in 656 by Remi-Gau
  • [FIX] allow extra BIDS entities to be integrated in glm dir name in 654 by Remi-Gau
  • [FIX] make GLM path more consistent in 652 by Remi-Gau
  • [FIX] prevent some crashes if Model.Input are not passed as arrays in 650 by Remi-Gau
  • [FIX] fix printing of of path in 649 by Remi-Gau
  • [FIX] properly skip segment and sullstrip in 638 by Remi-Gau
  • [FIX] use unix format when printing path to screen in 634 by Remi-Gau
  • [FIX] getEnvInfo for windows in 631 by Remi-Gau

[2.0.0] - 2022-07-10

Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v1.1.5...v2.0.0

Added

  • [DOC] prepare binder and basic jupyter notebook by Remi-Gau in 155
  • [DOC] general doc update by Remi-Gau in 446
  • [DOC] Add figures for some workflows by Remi-Gau in 463
  • [DOC] adds link and references to other SPM material by Remi-Gau in 464
  • [DOC] improve results doc and associated how to by Remi-Gau in 470
  • [DOC] Misc doc updates by Remi-Gau in 484
  • [DOC] update doc on how to filter files and what files gets upsampled by Remi-Gau in 494
  • [DOC] update templates by Remi-Gau in 455
  • [DOC] add MyST for the doc and add list of default options in the doc by Remi-Gau in 557
  • [DOC] update RTD with a symlink to README by Remi-Gau in 569
  • [DOC] fmriprep stats demo by Remi-Gau in 594
  • [DOC] Update getRegressorIdx.m by Remi-Gau in 601
  • [DOC] update where references are stored by Remi-Gau in 614
  • [DOC] update vismotion demo by Remi-Gau in 624
  • [DOC] Update FAQ and BIDS stats model related doc by Remi-Gau in 626
  • [ENH] adapt workflows to new bids-matlab by Remi-Gau in 368
  • [ENH] adapt to use fmriprep input with rshrf toolbox by Remi-Gau in 370
  • [ENH] add verbosity control by Remi-Gau in 381
  • [ENH] ROI tSNR pipeline by Remi-Gau in 401
  • [ENH] allow fMRIprep input for GLM by Remi-Gau in 367
  • [ENH] update dockerfiles by Remi-Gau in 420
  • [ENH] Add QA functions to plot events file and compute design efficiency by Remi-Gau in 428
  • [ENH] compute tSNR for a given mask by mwmaclean in 402
  • [ENH] add a function to deinitialize CPP SPM and make sure there is just one instance in the path by Remi-Gau in 435
  • [ENH] Allow for multi tasks processing by Remi-Gau in 439
  • [ENH] Update BIDS stats model by Remi-Gau in 441
  • [ENH] Enhancements subject / group level GLM and results by Remi-Gau in 443
  • [ENH] add elapsedTime function by marcobarilari in 229
  • [ENH] drop support for parfor loops by Remi-Gau in 447
  • [ENH] reports are saved for each subject being processed by Remi-Gau in 448
  • [ENH] drop nifti tools dependency by Remi-Gau in 449
  • [ENH] add possibility to limit maximum number of volumes per run in a subject level GLM by Remi-Gau in 451
  • [ENH] save group stats in separate derivatives folder by Remi-Gau in 453
  • [ENH] improve confounds inclusion in design matrix by Remi-Gau in 454
  • [ENH] add metadata consistency checks by Remi-Gau in 457
  • [ENH] use BIDS stats model to select input task, space and override options by Remi-Gau in 461
  • [ENH] update roi based glm by Remi-Gau in 465
  • [ENH] integrates anat and func QA as part of bidsSpatialPrepro by Remi-Gau in 466
  • [ENH] create an anat only spatial preprocessing by Remi-Gau in 467
  • [ENH] add workflow to perform model selection using the MACS toolbox by Remi-Gau in 472
  • [ENH] enhancements for ROI based GLM by Remi-Gau in 477
  • [ENH] save jobs as m file by Remi-Gau in 482
  • [ENH] filter file volume by Remi-Gau in 492
  • [ENH] start implementing BIDS stats model transformers by Remi-Gau in 493
  • [ENH] Replace anat reference by bids filter by Remi-Gau in 497
  • [ENH] start creating main API by Remi-Gau in 511
  • [ENH] change verbosity levels by Remi-Gau in 507
  • [ENH] Add change suffix workflow by Remi-Gau in 516
  • [ENH] run subject level GLM with no condition by Remi-Gau in 520
  • [ENH] add remove dummies workflow by Remi-Gau in 521
  • [ENH] transformers 2 by Remi-Gau in 522
  • [ENH] rename output func qa by Remi-Gau in 533
  • [ENH] stats model and results by Remi-Gau in 541
  • [ENH] add workflow for creation of T1map from mp2rage by Remi-Gau in 542
  • [ENH] only save batches as .m files by Remi-Gau in 559
  • [ENH] create a BIDS app API by Remi-Gau in 564
  • [ENH] skullstripping fixes and options by Remi-Gau in 571
  • [ENH] automatically generate method sections by Remi-Gau in 572
  • [ENH] fix some issue on model selection by Remi-Gau in 574
  • [ENH] simplify and extend bidsResults by Remi-Gau in 577
  • [ENH] adapt group level analysis to work with BIDS stats model by Remi-Gau in 581
  • [ENH] add F test by Remi-Gau in 584
  • [ENH] Add parametric modulation to run / subject level GLM by Remi-Gau in 585
  • [ENH] use native resolution for segmentation for lesion detection by Remi-Gau in 588
  • [ENH] add "force" parameter to bidsCopyInputFolder by Remi-Gau in 589
  • [ENH] add metadata to preprocessed derivatives by Remi-Gau in 580
  • [ENH] misc improvements at the run level GLM by Remi-Gau in 592
  • [ENH] improve reports by Remi-Gau in 595
  • [ENH] add two sample t test group level batch by Remi-Gau in 597
  • [ENH] allow to run "contrasts" and "results" from main API by Remi-Gau in 615
  • [ENH] improve group level analysis by Remi-Gau in 620
  • [ENH] make it possible to run models / contrasts using other columns than trial_type by Remi-Gau in 621
  • [ENH] add neuromorphometrics label to bidsResults output when in MNI space by Remi-Gau in 622

Changed

  • [DEP] update bids matlab by Remi-Gau in 570
  • [ENH] Rename preprocessing output to bids by Remi-Gau in 395
  • [ENH] use official HRF model from bids stats model by Remi-Gau in 604
  • [ENH] properly rely on BIDS stats model to specify subject level contrast by Remi-Gau in 576
  • [ENH] Update submodules by Remi-Gau in 575
  • [ENH] Bump bids matlab by Remi-Gau in 495
  • [ENH] drop stats folder by Remi-Gau in 539
  • [ENH] change MNI to SPM default IXI549Space by Remi-Gau in 456

Fixed

  • [FIX] adapt to the new bids-matlab "dev" by Remi-Gau in 366
  • [FIX] apply 418 to dev by Remi-Gau in 419
  • [FIX] Update binder by Remi-Gau in 413
  • [FIX] apply 425 to dev by Remi-Gau in 426
  • [FIX] Fix facerep demo by Remi-Gau in 438
  • [FIX] make sure default BIDS models are usable by Remi-Gau in 459
  • [FIX] resolve issues to get anat file from a different session from the func data by Remi-Gau in 462
  • [FIX] returnRootDir did not return the root dir by Remi-Gau in 498
  • [FIX] throw error when no repetition time was found by Remi-Gau in 509
  • [FIX] update vismotion demo by Remi-Gau in 513
  • [FIX] Misc bug squashing 🐛 💀 by Remi-Gau in 515
  • [FIX] Fix typos in the sh run file of vismotion demo by marcobarilari in 524
  • [FIX] fix 545 add more options for segmentation batch by marcobarilari in 547
  • [FIX] creates BIDS valid filename for ROIs in individual space by Remi-Gau in 562
  • [FIX] fix system test and silence ALI warning by Remi-Gau in 596
  • [FIX] Spatial preprocessing normalizes output of skullstripping by Remi-Gau in 602
  • [FIX] fix several issues for GLM at the subject level by Remi-Gau in 606
  • [FIX] fix several issues related to getting the correct files for the GLM by Remi-Gau in 607
  • [FIX] GLM: allow to filter input files based on BIDS entities for bold files by Remi-Gau in 611