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
[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] support label of activations with all atlases 1100 by Remi-Gau
[ENH] add support for session level models #1116 be @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
Changed
[REF] Refactor and update CLI in #1096 @Remi-Gau
Deprecated
Removed
[REF] Remove old CLI in #1096 @Remi-Gau
Fixed
[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
[DIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in #1110 by @Remi-Gau
Security
[3.1.0] - 2023-07-01
Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v3.0.0…v3.1.0
Added
[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
[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] make it possible to update bidspm from any folder in 948 by Remi-Gau
[ENH] add CC0 license by default to all outputs in 898 by Remi-Gau
Changed
Removed
Fixed
[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] 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] 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
[3.0.0] - 2022-12-14
Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v2.3.0…v3.0.0
Changed
Added
[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] 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] 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
[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
[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] error logs are generated upon crash for better bug reports in 808 by Remi-Gau
[ENH] include bids and bids stats model validation if the validators are installed in 787 by Remi-Gau
[ENH] lesion detection will be done by including the CSF TPM too in 778 by Remi-Gau
Fixed
[2.2.0] - 2022-10-29
Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v2.1.0…v2.2.0
Added
Changed
Fixed
[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
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] 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] change default space value in cpp_spm in 699 by Remi-Gau
[FIX] add some warnings to handle several bugs with empty ROIs in 693 by Remi-Gau
[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] 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] prevent some crashes if Model.Input are not passed as arrays in 650 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
[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] 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] update doc on how to filter files and what files gets upsampled by Remi-Gau in 494
[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] Update FAQ and BIDS stats model related doc by Remi-Gau in 626
[ENH] adapt to use fmriprep input with rshrf toolbox by Remi-Gau in 370
[ENH] Add QA functions to plot events file and compute design efficiency by Remi-Gau in 428
[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] Enhancements subject / group level GLM and results by Remi-Gau in 443
[ENH] add elapsedTime function by marcobarilari in 229
[ENH] reports are saved for each subject being processed by Remi-Gau in 448
[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] use BIDS stats model to select input task, space and override options by Remi-Gau in 461
[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] start implementing BIDS stats model transformers by Remi-Gau in 493
[ENH] Replace anat reference by bids filter by Remi-Gau in 497
[ENH] run subject level GLM with no condition by Remi-Gau in 520
[ENH] add workflow for creation of T1map from mp2rage by Remi-Gau in 542
[ENH] automatically generate method sections by Remi-Gau in 572
[ENH] adapt group level analysis to work with BIDS stats model by Remi-Gau in 581
[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] 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] 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
Fixed
[FIX] make sure default BIDS models are usable by Remi-Gau in 459
[FIX] reolve 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] 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