v2.0.0

What's Changed

• [FIX] adapt to the new bids-matlab "dev" by @Remi-Gau in #366
• [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
• try silencing pre-commit-ci runs on lib folder by @Remi-Gau in #383
• add test to workflows by @Remi-Gau in #384
• Rename preprocessing output to bids by @Remi-Gau in #395
• [ENH] ROI tSNR pipeline by @Remi-Gau in #401
• prepare binder and basic jupyter notebook by @Remi-Gau in #155
• [ENH] allow fMRIprep input for GLM by @Remi-Gau in #367
• [FIX] apply #418 to dev by @Remi-Gau in #419
• [FIX] Update binder by @Remi-Gau in #413
• [INFRA] update dockerfiles by @Remi-Gau in #420
• [STY] apply miss_hit naming parameters rule by @Remi-Gau in #391
• [INFRA] speed up tests by using smaller dummy dataset by @Remi-Gau in #421
• [FIX] apply #425 to dev by @Remi-Gau in #426
• [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
• [INFRA] set matlab ci by @Remi-Gau in #431
• [ENH] add a function to deinitialize CPP SPM and make sure there is just one instance in the path by @Remi-Gau in #435
• [INFRA] update CI by @Remi-Gau in #436
• [FIX] Fix facerep demo by @Remi-Gau in #438
• [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
• add elapsedTime function by @marcobarilari in #229
• [REF] refactor elapsedTime and integrate it into the code base by @Remi-Gau in #445
• [DOC] general doc update by @Remi-Gau in #446
• [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
• [INFRA] replace zenodo.json by citation.cff file by @Remi-Gau in #450
• [ENH] add possibility to limit maximum number of volumes per run in a subject level GLM by @Remi-Gau in #451
• [INFRA] add tests and error handling for results workflow by @Remi-Gau in #452
• [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
• [DOC] update templates by @Remi-Gau in #455
• change MNI to SPM default IXI549Space by @Remi-Gau in #456
• [ENH] add metadata consistency checks by @Remi-Gau in #457
• [FIX] make sure default BIDS models are usable by @Remi-Gau in #459
• [ENH] use BIDS stats model to select input task, space and override options by @Remi-Gau in #461
• [FIX] reolve issues to get anat file from a different session from the func data by @Remi-Gau in #462
• [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
• [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
• [DOC] improve resuls doc and associated how to by @Remi-Gau in #470
• [ENH] enhancements for ROI based GLM by @Remi-Gau in #477
• [REF / FIX / ENH] misc by @Remi-Gau in #478
• [ENH] save jobs as m file by @Remi-Gau in #482
• [DOC] Misc doc updates by @Remi-Gau in #484
• [ENH] filter file volume by @Remi-Gau in #492
• [ENH] start implementing BIDS stats model transformers by @Remi-Gau in #493
• [DOC] update doc on how to filter files and what files gets upsampled by @Remi-Gau in #494
• [ENH] Bump bids matlab by @Remi-Gau in #495
• [ENH] Replace anat reference by bids filter by @Remi-Gau in #497
• CI-run system test on dev branch and cron job every 15 days by @Remi-Gau in #499
• [FIX] returnRootDir did not return the root dir by @Remi-Gau in #498
• [INFRA] Update system tests by @Remi-Gau in #500
• [FIX] throw error when no repetition time was found by @Remi-Gau in #509
• [ENH] start creating main API by @Remi-Gau in #511
• [FIX] update vismotion demo by @Remi-Gau in #513
• [FIX] Misc bug squashing 🐛 💀 by @Remi-Gau in #515
• [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
• [REF] Refactor volume splicing by @Remi-Gau in #526
• [ENH] transformers 2 by @Remi-Gau in #522
• [ENH] rename output func qa by @Remi-Gau in #533
• [REF] Transfer some BIDS stats model function to bids matlab by @Remi-Gau in #536
• [ENH] drop stats folder by @Remi-Gau in #539
• [ENH] stats model and results by @Remi-Gau in #541
• [ENH] add workflow for creation of T1map from mp2rage by @Remi-Gau in #542
• Fix typos in the sh run file of vismotion demo by @marcobarilari in #524
• fix #545 add more options for segmentation batch by @marcobarilari in #547
• [FIX] fix test dev by @Remi-Gau in #556
• [DOC] add MyST for the doc and add list of default options in the doc by @Remi-Gau in #557
• [ENH] only save batches as .m files by @Remi-Gau in #559
• docs: add mcgnunes as a contributor for bug by @allcontributors in #561
• [FIX] creates BIDS valid filename for ROIs in individual space by @Remi-Gau in #562
• [ENH] create a BIDS app API by @Remi-Gau in #564
• [REF] rename variables and using bids.File instead on bids.matlab internals by @Remi-Gau in #567
• [DOC] update RTD with a symlink to README by @Remi-Gau in #569
• [DEP] update bids matlab by @Remi-Gau in #570
• [ENH] skullstripping fixes and options by @Remi-Gau in #571
• [ENH] automatically generate method sections by @Remi-Gau in #572
• [INFRA] misc by @Remi-Gau in #573
• [ENH] Update submodules by @Remi-Gau in #575
• [ENH] fix some issue on model selection by @Remi-Gau in #574
• [ENH] properly rely on BIDS stats model to specify subject level contrast by @Remi-Gau in #576
• [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
• [INFRA] CI and system tests improvements by @Remi-Gau in #586
• [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
• [FIX & ENH] misc by @Remi-Gau in #590
• [ENH] misc improvements at the run level GLM by @Remi-Gau in #592
• [ENH] improve reports by @Remi-Gau in #595
• [DOC] fmriprep stats demo by @Remi-Gau in #594
• [FIX] fix system test and silence ALI warning by @Remi-Gau in #596
• [ENH] add two sample t test group level batch by @Remi-Gau in #597
• [INFRA & FIX] system test and figure duplicate by @Remi-Gau in #598
• Changes by create-pull-request action by @github-actions in #599
• [DOC] Update getRegressorIdx.m by @Remi-Gau in #601
• [FIX & ENH] Spatial preprocessing normalizes output of skullstripping by @Remi-Gau in #602
• [ENH] use official HRF model from bids stats model by @Remi-Gau in #604
• [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
• [ENH] misc by @Remi-Gau in #608
• [REF] refactor roi related functions by @Remi-Gau in #609
• [INFRA] add validation workflow for citation.cff by @Remi-Gau in #613
• [DOC] update where references are stored by @Remi-Gau in #614
• [FIX] GLM: allow to filter input files based on BIDS entities for bold files by @Remi-Gau in #611
• [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
• [DOC] update vismotion demo by @Remi-Gau in #624
• [DOC] Update FAQ and BIDS stats model related doc by @Remi-Gau in #626
• rc2.0.0 by @Remi-Gau in #538

Full Changelog: v1.1.5...v2.0.0