Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of bidspm

bidspm - 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 by Remi-Gau
  • [ENH] add support for one-way ANOVA across groups at the group level 1296 by 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 by Remi-Gau
  • [ENH] make addConfoundsToDesignMatrix a method of BidsModel 1294 by by Remi-Gau
  • [ENH] add Apptainer definition 1254 by by Remi-Gau and by monique2208
  • [ENH] allow to copy anat only on raw datasets 1181 by by Remi-Gau
  • [ENH] add option to concatenate runs at subject level to facilite running PPI analysis 1133 by by Remi-Gau
  • [ENH] allow to run substeps of the bayesian model selection [1145]untagged-295695efb0c123726a81(https://github.com/cpp-lln-lab/bidspm/pull/1145) by 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 by Remi-Gau
  • [ENH] add several confound strategies to add to bids stats model and a function to create family of models 1126 by by Remi-Gau
  • [ENH] add CLI to run bayesian model selection 1121 by 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 by d-ni374
  • [FIX] update {func}createDefaultStatsModel to use proper GroupBy at the dataset level 1248 by by d-ni374
  • [FIX] make {func}getAcquisitionTime less brittle 1248 by by d-ni374
  • [FIX] fix regular expression in {func}bidsResults to identify contrasts 1248 by by d-ni374 and 1275 by 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 by Remi-Gau
  • [FIX] add java and zip to container recipes to allow using nidm results with octave 1265 by by Remi-Gau
  • [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation 1203 by by Remi-Gau
  • [FIX] save onsets.mat directly in subject stats folder 1187 by by Remi-Gau
  • [FIX] do not compute subject level contrast when running dataset level 1102 by by Remi-Gau
  • [FIX] copy RepetitionTime in sidecar JSON after running smoothing in 1099 by by Remi-Gau
  • [FIX] rename results files (csv, tsv, png, nii) of each contrasts 1104 by 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 by Remi-Gau

Full Changelog: https://github.com/cpp-lln-lab/bidspm/compare/v3.1.0...v4.0.0

- MATLAB
Published by release-drafter[bot] over 1 year ago

bidspm - v3.1.0

[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 (#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

- MATLAB
Published by release-drafter[bot] over 2 years ago

bidspm - 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

- MATLAB
Published by Remi-Gau about 3 years ago

bidspm - 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

- MATLAB
Published by release-drafter[bot] over 3 years ago

bidspm - 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

- MATLAB
Published by release-drafter[bot] over 3 years ago

bidspm - 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

- MATLAB
Published by release-drafter[bot] over 3 years ago

bidspm - v2.0.0

What's Changed

  • [FIX] adapt to the new bids-matlab "dev" by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/366
  • [ENH] adapt workflows to new bids-matlab by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/368
  • [ENH] adapt to use fmriprep input with rshrf toolbox by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/370
  • [ENH] add verbosity control by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/381
  • try silencing pre-commit-ci runs on lib folder by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/383
  • add test to workflows by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/384
  • Rename preprocessing output to bids by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/395
  • [ENH] ROI tSNR pipeline by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/401
  • prepare binder and basic jupyter notebook by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/155
  • [ENH] allow fMRIprep input for GLM by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/367
  • [FIX] apply #418 to dev by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/419
  • [FIX] Update binder by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/413
  • [INFRA] update dockerfiles by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/420
  • [STY] apply misshit naming parameters rule by @Remi-Gau in https://github.com/cpp-lln-lab/CPPSPM/pull/391
  • [INFRA] speed up tests by using smaller dummy dataset by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/421
  • [FIX] apply #425 to dev by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/426
  • [ENH] Add QA functions to plot events file and compute design efficiency by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/428
  • [ENH] compute tSNR for a given mask by @mwmaclean in https://github.com/cpp-lln-lab/CPP_SPM/pull/402
  • [INFRA] set matlab ci by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/431
  • [ENH] add a function to deinitialize CPP SPM and make sure there is just one instance in the path by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/435
  • [INFRA] update CI by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/436
  • [FIX] Fix facerep demo by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/438
  • [ENH] Allow for multi tasks processing by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/439
  • [ENH] Update BIDS stats model by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/441
  • [ENH] Enhancements subject / group level GLM and results by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/443
  • add elapsedTime function by @marcobarilari in https://github.com/cpp-lln-lab/CPP_SPM/pull/229
  • [REF] refactor elapsedTime and integrate it into the code base by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/445
  • [DOC] general doc update by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/446
  • [ENH] drop support for parfor loops by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/447
  • [ENH] reports are saved for each subject being processed by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/448
  • [ENH] drop nifti tools dependency by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/449
  • [INFRA] replace zenodo.json by citation.cff file by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/450
  • [ENH] add possibility to limit maximum number of volumes per run in a subject level GLM by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/451
  • [INFRA] add tests and error handling for results workflow by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/452
  • [ENH] save group stats in separate derivatives folder by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/453
  • [ENH] improve confounds inclusion in design matrix by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/454
  • [DOC] update templates by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/455
  • change MNI to SPM default IXI549Space by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/456
  • [ENH] add metadata consistency checks by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/457
  • [FIX] make sure default BIDS models are usable by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/459
  • [ENH] use BIDS stats model to select input task, space and override options by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/461
  • [FIX] reolve issues to get anat file from a different session from the func data by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/462
  • [DOC] Add figures for some workflows by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/463
  • [DOC] adds link and references to other SPM material by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/464
  • [ENH] update roi based glm by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/465
  • [ENH] integrates anat and func QA as part of bidsSpatialPrepro by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/466
  • [ENH] create an anat only spatial preprocessing by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/467
  • [ENH] add workflow to perform model selection using the MACS toolbox by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/472
  • [DOC] improve resuls doc and associated how to by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/470
  • [ENH] enhancements for ROI based GLM by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/477
  • [REF / FIX / ENH] misc by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/478
  • [ENH] save jobs as m file by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/482
  • [DOC] Misc doc updates by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/484
  • [ENH] filter file volume by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/492
  • [ENH] start implementing BIDS stats model transformers by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/493
  • [DOC] update doc on how to filter files and what files gets upsampled by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/494
  • [ENH] Bump bids matlab by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/495
  • [ENH] Replace anat reference by bids filter by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/497
  • CI-run system test on dev branch and cron job every 15 days by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/499
  • [FIX] returnRootDir did not return the root dir by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/498
  • [INFRA] Update system tests by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/500
  • [FIX] throw error when no repetition time was found by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/509
  • [ENH] start creating main API by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/511
  • [FIX] update vismotion demo by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/513
  • [FIX] Misc bug squashing :bug: :skull: by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/515
  • [ENH] change verbosity levels by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/507
  • [ENH] Add change suffix workflow by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/516
  • [ENH] run subject level GLM with no condition by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/520
  • [ENH] add remove dummies workflow by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/521
  • [REF] Refactor volume splicing by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/526
  • [ENH] transformers 2 by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/522
  • [ENH] rename output func qa by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/533
  • [REF] Transfer some BIDS stats model function to bids matlab by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/536
  • [ENH] drop stats folder by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/539
  • [ENH] stats model and results by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/541
  • [ENH] add workflow for creation of T1map from mp2rage by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/542
  • Fix typos in the sh run file of vismotion demo by @marcobarilari in https://github.com/cpp-lln-lab/CPP_SPM/pull/524
  • fix #545 add more options for segmentation batch by @marcobarilari in https://github.com/cpp-lln-lab/CPP_SPM/pull/547
  • [FIX] fix test dev by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/556
  • [DOC] add MyST for the doc and add list of default options in the doc by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/557
  • [ENH] only save batches as .m files by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/559
  • docs: add mcgnunes as a contributor for bug by @allcontributors in https://github.com/cpp-lln-lab/CPP_SPM/pull/561
  • [FIX] creates BIDS valid filename for ROIs in individual space by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/562
  • [ENH] create a BIDS app API by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/564
  • [REF] rename variables and using bids.File instead on bids.matlab internals by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/567
  • [DOC] update RTD with a symlink to README by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/569
  • [DEP] update bids matlab by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/570
  • [ENH] skullstripping fixes and options by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/571
  • [ENH] automatically generate method sections by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/572
  • [INFRA] misc by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/573
  • [ENH] Update submodules by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/575
  • [ENH] fix some issue on model selection by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/574
  • [ENH] properly rely on BIDS stats model to specify subject level contrast by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/576
  • [ENH] simplify and extend bidsResults by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/577
  • [ENH] adapt group level analysis to work with BIDS stats model by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/581
  • [ENH] add F test by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/584
  • [ENH] Add parametric modulation to run / subject level GLM by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/585
  • [INFRA] CI and system tests improvements by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/586
  • [ENH] use native resolution for segmentation for lesion detection by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/588
  • [ENH] add "force" parameter to bidsCopyInputFolder by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/589
  • [ENH] add metadata to preprocessed derivatives by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/580
  • [FIX & ENH] misc by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/590
  • [ENH] misc improvements at the run level GLM by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/592
  • [ENH] improve reports by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/595
  • [DOC] fmriprep stats demo by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/594
  • [FIX] fix system test and silence ALI warning by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/596
  • [ENH] add two sample t test group level batch by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/597
  • [INFRA & FIX] system test and figure duplicate by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/598
  • Changes by create-pull-request action by @github-actions in https://github.com/cpp-lln-lab/CPP_SPM/pull/599
  • [DOC] Update getRegressorIdx.m by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/601
  • [FIX & ENH] Spatial preprocessing normalizes output of skullstripping by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/602
  • [ENH] use official HRF model from bids stats model by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/604
  • [FIX] fix several issues for GLM at the subject level by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/606
  • [FIX] fix several issues related to getting the correct files for the GLM by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/607
  • [ENH] misc by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/608
  • [REF] refactor roi related functions by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/609
  • [INFRA] add validation workflow for citation.cff by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/613
  • [DOC] update where references are stored by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/614
  • [FIX] GLM: allow to filter input files based on BIDS entities for bold files by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/611
  • [ENH] allow to run "contrasts" and "results" from main API by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/615
  • [ENH] improve group level analysis by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/620
  • [ENH] make it possible to run models / contrasts using other columns than trialtype by @Remi-Gau in https://github.com/cpp-lln-lab/CPPSPM/pull/621
  • [ENH] add neuromorphometrics label to bidsResults output when in MNI space by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/622
  • [DOC] update vismotion demo by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/624
  • [DOC] Update FAQ and BIDS stats model related doc by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/626
  • rc2.0.0 by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/538

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

- MATLAB
Published by Remi-Gau over 3 years ago

bidspm - v1.1.5

What's Changed

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

Full Changelog: https://github.com/cpp-lln-lab/CPP_SPM/compare/v1.1.4...v1.1.5

- MATLAB
Published by Remi-Gau almost 4 years ago

bidspm - CPP SPM - v1.1.4

What's Changed

  • docs: add fcerpe as a contributor for bug, test by @allcontributors in https://github.com/cpp-lln-lab/CPP_SPM/pull/460
  • rc1.1.4 by @Remi-Gau in https://github.com/cpp-lln-lab/CPP_SPM/pull/479

Full Changelog: https://github.com/cpp-lln-lab/CPP_SPM/compare/v1.1.3...v1.1.4

- MATLAB
Published by Remi-Gau about 4 years ago

bidspm - CPP SPM - v1.1.3

What's Changed

  • bidsConcatBetaTmaps. fix by @CerenB in https://github.com/cpp-lln-lab/CPP_SPM/pull/425

Full Changelog: https://github.com/cpp-lln-lab/CPP_SPM/compare/v1.1.2...v1.1.3

- MATLAB
Published by Remi-Gau over 4 years ago

bidspm - 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

- MATLAB
Published by Remi-Gau over 4 years ago

bidspm - CPP SPM - v1.1.1

fixes

  • set the minimum SPM version needed to run CPP_SPM

- MATLAB
Published by Remi-Gau over 4 years ago

bidspm - CPP SPM - v1.1.0

new feature

  • add workflows to deal with lesion detection

fixes

  • fix skull stripping

infra

  • add pre-commit

- MATLAB
Published by Remi-Gau over 4 years ago

bidspm - CPP SPM - v1.0.0 - "For those about to ROI"

breaking change

  • subject level GLM names and structure has been changed

new features

  • possibility to run anat workflow only
  • add tools to deal with ROIs (CPP_ROI and marsbar)
  • add workflows for ALI toolbox (lesion detection)
  • add slice display with "dual coding" (beta and t values shown on the same slice)
  • add possibility to create specify name of GLM directory
  • GLM analysis can now be run in a entirely separate dataset structure independent of the preprocessed data

minor changes

  • improve initialization
  • simplify test suite
  • save a "label tsv" when creating 4D volume from GLM output to use for MVPA (to be merged)
  • make name of GLM output file more BIDS like

- MATLAB
Published by Remi-Gau almost 5 years ago

bidspm - CPP SPM BIDS - v0.2.0

Main changes

  • add carpet plot to QA
  • add 3Dto4D batch
  • update documentation
  • switch to only using bids-matlab for interacting with BIDS data set
  • add demo to run SPM "face dataset"
  • add more functionalities for BIDS model
  • add batches for basic fmap handling and VDM creation
  • update GLM QA
  • improve bidsCopyRaw
  • allow to create montage figure of results
  • add parfor loop where possible

- MATLAB
Published by Remi-Gau about 5 years ago

bidspm - CPP SPM BIDS - v0.1.0

- MATLAB
Published by Remi-Gau over 5 years ago

bidspm - best release for workshop 2019

  • fix RFX
  • add credits
  • add zenodo DOI

- MATLAB
Published by Remi-Gau over 6 years ago

bidspm - better release for workshop 2019

Add a licence

- MATLAB
Published by Remi-Gau over 6 years ago

bidspm - release for workshop 2019

- MATLAB
Published by Remi-Gau over 6 years ago