Package: bidser 0.4.0

bidser: Work with 'BIDS' (Brain Imaging Data Structure) Projects

Tools for working with 'BIDS' (Brain Imaging Data Structure) formatted neuroimaging datasets. The package provides functionality for reading and querying 'BIDS'-compliant projects, creating mock 'BIDS' datasets for testing, and extracting preprocessed data from 'fMRIPrep' derivatives. It supports searching and filtering 'BIDS' files by various entities such as subject, session, task, and run to streamline neuroimaging data workflows. See Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44> for the 'BIDS' specification.

Authors:Bradley Buchsbaum [aut, cre]

bidser_0.4.0.tar.gz
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manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
bidser/json (API)

# Install 'bidser' in R:
install.packages('bidser', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bbuchsbaum/bidser/issues

Pkgdown/docs site:https://bbuchsbaum.github.io

On CRAN:

Conda:

7.04 score 6 stars 61 scripts 277 downloads 84 exports 34 dependencies

Last updated from:54a5d69cab. Checks:6 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK314
source / vignettesOK323
linux-release-x86_64OK262
macos-release-arm64OK198
macos-oldrel-arm64OK204
windows-develERROR303
windows-releaseERROR288
windows-oldrelERROR279
wasm-releaseOK151

Exports:anat_parseras_bids_uribids_check_compliancebids_datatype_specbids_entitiesbids_heatmapbids_indexbids_parserbids_projectbids_reportbids_report_databids_schemabids_schema_versionsbids_subjectbids_subject.bids_projectbids_summarybids_transformbids_uribids_versionbrain_maskbuild_subject_graphcheck_confoundscheck_func_scansclean_confoundsclear_example_bids_cacheconfound_filesconfound_setconfound_strategycreate_mock_bidscreate_preproc_maskcreate_smooth_transformerdataset_descriptiondataset_namedataset_typedecode_bids_entitiesderivative_filesderivative_pipelinesencodeevent_filesfile_pairsflat_listfmap_parserfmriprep_anat_parserfmriprep_func_parserfunc_parserfunc_scansgen_parserget_example_bids_datasetget_metadataget_repetition_timeinfer_tris_bids_urilist_confound_setslist_confound_strategieslist_datatypeslist_pack_bidsload_all_eventsmask_filesn_volumespack_bidsparseparticipantsplot_bidspreproc_scansquery_filesread_confoundsread_dataset_descriptionread_eventsread_func_scans.bids_projectread_participantsread_preproc_scans.bids_projectread_scans_tsvread_sessions_tsvread_sidecarregister_datatyperesolve_bids_urisearch_filessessionssidecarsurface_filestaskstransform_filesunregister_datatypevariables_table

Dependencies:bitbit64clicliprcpp11crayondata.tabledata.treedplyrfsgenericsgluehmsjsonlitelifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readrrlangstringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Working with Confounds and Variables
Building a test dataset | Confound sets: predefined recipes | Reading confounds | Selecting variables by name or wildcard | Flat output for quick modeling | Confound strategies: PCA reduction | Custom strategies | Reading event files | The variables table: one tibble per run | Dataset QA with bids_report() | Putting it together

Last update: 2026-06-02
Started: 2026-03-29

Getting Started with bidser
Introduction to bidser | What is BIDS? | What does bidser do? | Loading a BIDS Dataset | Basic Dataset Queries | Dataset Structure | Finding Files by Type | Filtering by Subject and Task | Working with Multiple Subjects | Working with Event Files | Analyzing Event Data | Working with Metadata Sidecars | Working with Individual Subjects | Advanced Querying with query_files() | Match Modes | Entity Presence, Extension, and Datatype Filters | Tibble Output with Parsed Entities | Scoped Queries and Derivatives | Permissive Loading | Run-Level Variables and Report Data | Full File Paths | Working with fMRIPrep Derivatives

Last update: 2026-06-02
Started: 2020-04-09

Create Mock BIDS Projects for Tests and Examples
What does a small mock project look like? | How do you query raw and derivative files? | How do you inspect injected events and confounds? | How do you pack the project for sharing? | Next Steps

Last update: 2026-04-05
Started: 2026-03-29

Work With Derivatives and Confounds
Where are the derivatives? | How do you pull one derivative run? | How do you read and check confounds? | How do you verify run-level coverage? | How do you turn that into a report? | Next Steps

Last update: 2026-04-05
Started: 2026-03-29

Readme and manuals

Help Manual

Help pageTopics
Anatomical parser constructoranat_parser
Coerce to a BIDS URI objectas_bids_uri as_bids_uri.bids_uri as_bids_uri.character
Basic BIDS Compliance Checksbids_check_compliance
Build a custom BIDS datatype specbids_datatype_spec
Parse BIDS entities from paths into a tibblebids_entities
Create a specialized heatmap visualization of BIDS databids_heatmap
Build or retrieve a persistent file index for a BIDS projectbids_index
BIDS filename parsers using regexbids_parser
Create a BIDS Project Objectbids_project
Create a lightweight text report for a BIDS projectbids_report
Assemble lightweight report data for a BIDS projectbids_report_data
Load and cache the BIDS schemabids_schema
List available BIDS schema versionsbids_schema_versions
Access a single subject from a BIDS projectbids_subject bids_subject.bids_project
Summarize a BIDS datasetbids_summary
Apply a transformation to BIDS filesbids_transform
Construct a BIDS URI objectbids_uri
Get the BIDS version of a datasetbids_version bids_version.bids_dataset_description bids_version.bids_project bids_version.mock_bids_project
Retrieve a brain mask for a subjectbrain_mask brain_mask.bids_project
Build Subject Graph Structurebuild_subject_graph build_subject_graph.bids_project build_subject_graph.mock_bids_project
Check and clean confound tablescheck_confounds clean_confounds
Check Functional Scans in a BIDS Projectcheck_func_scans
Clear Example BIDS Dataset Cacheclear_example_bids_cache
Get confound files from a BIDS projectconfound_files confound_files.bids_project confound_files.mock_bids_project
Convenience confound sets for fMRIPrepconfound_set
Confound denoising strategiesconfound_strategy
Create a Mock BIDS Project Objectcreate_mock_bids
Create a preprocessing mask from BIDS datacreate_preproc_mask
Create a binary brain mask from preprocessed scanscreate_preproc_mask.bids_project
Create Preprocessing Mask (Mock Implementation)create_preproc_mask.mock_bids_project
Create a simple smoothing transformercreate_smooth_transformer
Get the dataset_description object from a BIDS projectdataset_description dataset_description.bids_project
Get fields from a BIDS dataset descriptiondataset_name dataset_type
Decode BIDS entities back into a filenamedecode_bids_entities
Query derivative files from a BIDS projectderivative_files
List derivative pipelines in a BIDS projectderivative_pipelines
Encode a string into a BIDS key-value listencode encode.character
Get event files from a BIDS projectevent_files event_files.bids_project event_files.mock_bids_project
Find File Pairs in a BIDS Projectfile_pairs
Get "flat" representation of BIDS Projectflat_list flat_list.bids_project
Fieldmap parser constructorfmap_parser
fMRIPrep anatomical parser constructorfmriprep_anat_parser
fMRIPrep functional parser constructorfmriprep_func_parser
Functional parser constructorfunc_parser
Get functional scans from a BIDS projectfunc_scans func_scans.mock_bids_project
Get Functional Scans from a BIDS Projectfunc_scans.bids_project
Generate a parser from a specgen_parser
Download Example BIDS Datasetget_example_bids_dataset
Resolve metadata for a BIDS fileget_metadata get_metadata.bids_project
Get Repetition Time (TR) from a sidecar JSONget_repetition_time
Infer TR (Repetition Time) from a BOLD file or sidecarinfer_tr infer_tr.character
Test whether an object is a BIDS URIis_bids_uri
List available confound setslist_confound_sets
List available confound strategieslist_confound_strategies
List registered BIDS datatypeslist_datatypes
List Contents of Packed BIDS Archivelist_pack_bids
Load All Event Filesload_all_events load_all_events.bids_project
Query Mask Files from a BIDS Projectmask_files mask_files.bids_project mask_files.mock_bids_project
Get the number of volumes in functional scansn_volumes n_volumes.bids_project n_volumes.character
Pack BIDS Project with Stub or Downsampled Imaging Filespack_bids
Parse a file-name into BIDS componentsparse
Get participants from a BIDS projectparticipants participants.bids_project
Get Participants from Mock BIDS Projectparticipants.mock_bids_project
Plot a comprehensive visual overview of a BIDS projectplot_bids
Plot PCA confoundsplot.bids_confounds
Plot a BIDS project as a dendrogramplot.bids_project plot.mock_bids_project
Get preprocessed functional MRI scanspreproc_scans
Get preprocessed scans from a BIDS projectpreproc_scans.bids_project
Print Mock BIDS Project Summaryprint.mock_bids_project
Query files in BIDS structure with explicit semanticsquery_files query_files.bids_project query_files.mock_bids_project
Read Confound Files from a BIDS Projectread_confounds
Read confound filesread_confounds.bids_project
Read Confound Files (Mock Implementation)read_confounds.mock_bids_project
Read the dataset_description.json for a BIDS projectread_dataset_description read_dataset_description.bids_project read_dataset_description.character
Read Event Files from a BIDS Projectread_events
Read event files from a BIDS projectread_events.bids_project
Read Event Files from Mock BIDS Projectread_events.mock_bids_project
Read in a set of four-dimensional functional scansread_func_scans.bids_project
Read participants.tsv as a typed tabular objectread_participants read_participants.bids_project read_participants.character
Read preprocessed functional MRI scans from a BIDS projectread_preproc_scans.bids_project
Read a scans.tsv file for a subjectread_scans_tsv read_scans_tsv.bids_project
Read a sessions.tsv file for a subjectread_sessions_tsv read_sessions_tsv.bids_project
Read sidecar JSON files and return metadata as a tidy tibbleread_sidecar
Register a custom BIDS datatyperegister_datatype
Resolve a BIDS URI to a local or remote pathresolve_bids_uri resolve_bids_uri.bids_uri resolve_bids_uri.character
Search files in BIDS structuresearch_files search_files.bids_project search_files.mock_bids_project
Get sessions from a BIDS projectsessions sessions.bids_project
Get Sessions from Mock BIDS Projectsessions.mock_bids_project
Get the sidecar metadata attached to a tabular BIDS objectsidecar sidecar.bids_tabular
Query Surface Files from a BIDS Projectsurface_files surface_files.bids_project surface_files.mock_bids_project
Get tasks from a BIDS projecttasks tasks.bids_project
Get Tasks from Mock BIDS Projecttasks.mock_bids_project
Query Transform Files from a BIDS Projecttransform_files transform_files.bids_project transform_files.mock_bids_project
Unregister a custom BIDS datatypeunregister_datatype
Create a tidy run-level variables tablevariables_table