v3.1.0

[3.1.0] - 2023-07-01

Full Changelog: v3.0.0...v3.1.0

Added

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

Changed

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

Removed

• [ENH] drop rsHRF support (#906) @Remi-Gau

Fixed

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

v3.0.0

Release Notes

• [REL] version 3.0.0 (#886) @Remi-Gau

BREAKING CHANGES

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

CHANGES

• improve CLI and add a python CLI

• [ENH] include roi based calls in CLI (#880) @Remi-Gau
• [ENH] add copy dataset to CLI (#842) @Remi-Gau
• [ENH] add smoothing to CLI (#841) @Remi-Gau
• [ENH] create docker image of bids app - Octave (#837) @Remi-Gau
• [ENH] use python based CLI to run bidspm with octave (#832) @Remi-Gau*

MINOR CHANGES

• [ENH] update CPP_ROI (#885) @Remi-Gau
• [ENH] add extra files to derivatives datasets (#883) @Remi-Gau
• [ENH] incorporate opt.results in bids stats model (#879) @Remi-Gau
• [ENH] add option to ignore creating dataset level node in default model (#871) @Remi-Gau
• [ENH] implement logger (#867) @Remi-Gau
• [ENH] add function to return contrast filename for a certain contrast name (#866) @Remi-Gau

FIXES

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

MISC

• [MNT] set up tests on NARPS dataset (#877) @Remi-Gau
• [REF] refactor CI workflows (#878) @Remi-Gau
• [DOC] update FAQ to explain how to change subject level GLM folder name (#872) @Remi-Gau
• [INFRA] add integration test roi based glm (#861) @Remi-Gau
• [MNT] reorganize folders (#864) @Remi-Gau
• [MNT] replace isfolder by isdir (#863) @Remi-Gau

v2.3.0

Release Notes

Main changes:

• bidspm main function:
  • error logs are generated upon crash for better bug reports
  • saving options are saved to help with bug report
  • can create default BIDS stats model
  • generate method section in reports folder when running preprocess or statistics
  • include bids and bids stats model validation if the validators are installed
• add inverse normalize workflow
• smoothing workflow will also try to smooth the corresponding anat data too
• lesion detection will be done by including the CSF TPM too

CHANGES

• [ENH] add design only to CLI #772
• [ENH] add smoothing for anat files
• [ENH] save skipped ROIs and concat beta maps (#823) @Remi-Gau
• [ENH] add boilerplate to CLI (#822) @Remi-Gau
• [ENH] add error.log (#808) @Remi-Gau
• [ENH] Use CLI to create default model (#804) @Remi-Gau
• [ENH] improve bids validation (#787) @Remi-Gau
• [ENH] add inverse normalize workflow (#784) @Remi-Gau
• [ENH] add csf tpm to lesion detection and update submodules (#778) @Remi-Gau

Fixes

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

Documentation

• [DOC] add Stefania Mattioni as contributor (#828) @Remi-Gau
• [DOC] add auto label of activation info (#821) @Remi-Gau
• [DOC] improve bids model warning (#820) @Remi-Gau
• [DOC] add all functions to doc (#819) @Remi-Gau
• [DOC] add Manon-56 as a contributor for bug (#807) @allcontributors

Maintenance

• [MNT] Test notebooks (#788) @Remi-Gau
• [MNT] improve docker, version, release handling (#785) @Remi-Gau
• [MNT] update submodules
• [MNT] improve doc generation and remove dead code (#790) @Remi-Gau
• [MNT] use github action to validate citation cff #771
• [MNT] update CI and fix tests #762

v2.2.0

Release Notes

CHANGES

• [FIX] fixes workflow timing (#773) @Remi-Gau
• [ENH] add design only to CLI (#772) @Remi-Gau
• [MNT] use github action to validate citation cff (#771) @Remi-Gau
• [MNT] update CI and fix tests (#762) @Remi-Gau
• [FIX] related to #763 and testing through CI if the patch breaks things (reopened) (#765) @marcobarilari
• [ENH] Update bidspm path (#752) @Remi-Gau
• [DOC] use new copyright format (#750) @Remi-Gau
• [ENH] add functions to help select fmriprep regressors (#748) @Remi-Gau
• [ENH] start switching to bidspm (#747) @Remi-Gau
• [DOC] improve stats doc and warnings (#746) @Remi-Gau
• [DEP] update bids matlab (#734) @Remi-Gau
• [MNT] start implement CLI (#733) @Remi-Gau
• [ENH] use inputs from several datasets for lesion abnormality detection (#730) @Remi-Gau

v2.1.0

Release Notes

CHANGES

• [REL] v2.1.0 (#728) @Remi-Gau
• [FIX] fix lesion segmentation output (and refactor) (#727) @Remi-Gau
• [FIX] add more explicit error message for input parsing of getData (#726) @Remi-Gau
• [FIX] support globbing patterns to specify conditions in design matrix (#716) @Remi-Gau
• [FIX] fix ALI toolbox issues (#723) @Remi-Gau
• [MNT] update citation file (#721) @Remi-Gau
• [ENH] add possibility to use AAL for labelling of activations (#717) @Remi-Gau
• docs: add christine0903 as a contributor for ideas (#720) @allcontributors
• [pre-commit.ci] pre-commit autoupdate (#718) @pre-commit-ci
• [FIX] improve warning selecting too many masks (#715) @Remi-Gau
• [FIX] fix and refactor demos, and update help sections (#701) @Remi-Gau
• [pre-commit.ci] pre-commit autoupdate (#714) @pre-commit-ci
• [FIX] add guard clauses to run ROI based analysis only when requested (#708) @Remi-Gau
• [FIX] convert nan to zeros in confounds (#700) @Remi-Gau
• [FIX] change default space value in cpp_spm (#699) @Remi-Gau
• docs: add JeanneCaronGuyon as a contributor for bug (#697) @allcontributors
• [FIX] various bug fixes (#694) @Remi-Gau
• [FIX] add some warnings to handle several bugs with empty ROIs (#693) @Remi-Gau
• [INFRA] fix octave tests (#692) @Remi-Gau
• [FIX] re enable octave tests CI (#686) @Remi-Gau
• [FIX] patches for #682 and #683 (#687) @mwmaclean
• docs: add mwmaclean as a contributor for bug (#688) @allcontributors
• [DOC] update FAQ to help structure data to run stats on fmriprep (#685) @Remi-Gau
• [DEP] update bids matlab (#680) @Remi-Gau
• [FIX] ensure that bidsResults does not run if we don't have the proper options (#679) @Remi-Gau
• [DOC] add demo for ds002799 (#678) @Remi-Gau
• [DOC] add DIY section to documtation (#677) @Remi-Gau
• [FIX] returnRootDir only relies on fullpaths (#676) @Remi-Gau
• [FIX] set minimum compatible fmriprep version (#675) @Remi-Gau
• [DOC] improve description of stats output and of bids stats model (#670) @Remi-Gau
• [FIX] renaming of design matrix images at group level (#668) @Remi-Gau
• [FIX] make sure 2 sample ttest can run more than one contrasts (#665) @Remi-Gau
• [FIX] label actiation: csv results file witrh no significant voxels are ignored with a warning (#663) @Remi-Gau
• [INFRA] improve issue template (#661) @Remi-Gau
• [FIX] onsets and confounds are saved in the proper dir when there are several tasks (#659) @Remi-Gau
• [FIX] fix silent dry run override (#657) @Remi-Gau
• [FIX] use proper subject background for montage (#656) @Remi-Gau
• [FIX] allow extra BIDS entities to be integrated in glm dir name (#654) @Remi-Gau
• [FIX] make GLM path more consistent (#652) @Remi-Gau
• [FIX] prevent some crashes if Model.Input are not passed as arrays (#650) @Remi-Gau
• [FIX] fix printing of of path (#649) @Remi-Gau
• [pre-commit.ci] pre-commit autoupdate (#641) @pre-commit-ci
• [FIX] properly skip segment and sullstrip (#638) @Remi-Gau
• [FIX] use unix format when priting path to screen (#634) @Remi-Gau
• [FIX] getEnvInfo for windows (#631) @Remi-Gau

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 https://github.com/cpp-lln-...

v1.1.5

What's Changed

• docs: add iqrashahzad14 as a contributor for bug, doc, question, review, userTesting by @allcontributors in #483
• docs: add marcobarilari as a contributor for userTesting by @allcontributors in #485
• docs: add CerenB as a contributor for userTesting by @allcontributors in #486
• docs: add fcerpe as a contributor for userTesting by @allcontributors in #487
• docs: add mwmaclean as a contributor for userTesting by @allcontributors in #488
• docs: add fedefalag as a contributor for userTesting by @allcontributors in #489
• [DOC] update contributors by @Remi-Gau in #519
• [ENH] change default to not run GLM QA by @Remi-Gau in #529
• [ENH] add checks and more verbose ouput for subject level GLM specification by @Remi-Gau in #530
• [INFRA] fix tests main by @Remi-Gau in #553

Full Changelog: v1.1.4...v1.1.5

CPP SPM - v1.1.4

What's Changed

• docs: add fcerpe as a contributor for bug, test by @allcontributors in #460
• rc1.1.4 by @Remi-Gau in #479

Full Changelog: v1.1.3...v1.1.4

CPP SPM - v1.1.3

What's Changed

• bidsConcatBetaTmaps. fix by @CerenB in #425

Full Changelog: v1.1.2...v1.1.3

CPP SPM - v1.1.2

fixes

• remove extra submodules
• make sure that run wise contrasts are computed
• update CPP_ROI and bids-matlab submodule and fix code accordingly