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Changelog

Source: NEWS.md

bidser 0.5.0

  • read_sidecar(inherit = TRUE) now anchors on the imaging scans matching the query and resolves each scan’s effective metadata via BIDS inheritance, returning one row per scan. Previously it anchored on JSON sidecar files, so an inheritance-aware query for a subject whose scans only had higher-level (task/dataset) sidecars returned an empty tibble. inherit = FALSE is unchanged (one row per JSON file).

  • Windows: normalize project and resolved paths with forward slashes (winslash = "/") so full paths returned by query_files(full_path = TRUE), func_scans(), n_volumes(), and resolve_bids_uri() use a consistent separator instead of mixing \ and /. Fixes several R CMD check test failures on Windows.

  • Make query_files() reuse the index built when the project was constructed instead of re-scanning the filesystem on every call. Repeated queries are now roughly two orders of magnitude faster (an indexed lookup rather than a full stat of the dataset on each query). The default query surface is a snapshot; use refresh = TRUE to re-scan the manifest and pick up additions, content changes, and removals without rebuilding the project object. query_files() also now honours index = "none" and prefers each project’s own construction-time snapshot, so two project objects sharing a path no longer perturb each other’s query results.

  • Build the query manifest from a direct filesystem path scan instead of only the parsed data tree. This keeps bidser’s tree-focused accessors intact while making query_files() and broad search_files() see pybids-visible layout files such as README, CHANGES, dataset_description.json, participants.tsv, *_scans.tsv, JSON sidecars, root .bval/.bvec files, and extensionless files under subject datatypes. On ds005, the raw file-count parity surface is now 142/142 against vendored pybids.

  • Make indexed query_files() honour strict = TRUE for missing entity filters, so broad subject/task queries do not accidentally include root layout files.

  • Fix wildcard entity filters such as task = ".*" in fallback/no-index query_files() calls so they match indexed query semantics, and remove the unused tree-derived manifest builder left behind by the filesystem-backed manifest path.

  • Fix require_entity = TRUE being silently ignored on the indexed query_files() path when an entity filter used the .* wildcard (e.g. task = ".*"). It now requires the entity to be present as documented, matching the non-indexed path, so entity-less files (such as anatomical scans, which lack task) are correctly excluded.

  • Add raw DWI files as a built-in datatype, so bids_project() and query_files() index dwi/ files (.nii.gz, .nii, .json, .bval, .bvec) without user-side register_datatype() setup.

  • Speed up index construction by deriving manifest/sidecar entities directly from paths and by lazily ingesting JSON sidecar contents only when metadata APIs need them. This keeps query-oriented project construction focused on the file manifest while preserving indexed metadata inheritance on demand.

  • Speed up bids_project() construction by replacing generic tree/table conversions and repeated tree searches with leaf-specific extractors, by using vectorized manifest row construction, and by trimming parser/directory-listing overhead in constructor hot paths.

  • Further speed up indexed query_files() by avoiding per-query manifest re-finalization and by applying indexed filters with a single logical mask.

  • Add tools/benchmark-pybids-parity.R, a repeatable local harness for comparing bidser construction/query timings and basic file-count parity against the vendored pybids checkout via uv.

bidser 0.4.0

  • Add bids_entities() for vectorized path-to-entity parsing, returning one typed tibble row per path.
  • Add n_volumes() for reading functional scan volume counts from NIfTI headers, with a bids_project method for raw or preprocessed scan discovery.
  • Make search_files() fall back to a filesystem regex scan when the parsed BIDS tree has no match, so ad hoc regex searches can find valid but currently unparsed files such as masks.
  • Expose common filtering arguments on the read_events() and read_confounds() generics, and have read_events() return bare metadata aliases alongside the legacy dotted columns.
  • Change confound_set("dvars") to select only std_dvars, with explicit std_dvars, raw_dvars, non_std_dvars, and vx_wisestd_dvars selectors for callers that want a specific variant.
  • Add confound_set("legacy_default"), a public, version-robust handle for the 26 canonical confound names historically exposed only as the unexported bidser:::DEFAULT_CVARS2. Code that depended on bidser:::DEFAULT_CVARS2 should switch to confound_set("legacy_default"), which returns the identical set. DEFAULT_CVARS2 is retained (unexported) for now but is superseded.
  • Express the read_confounds() cvars default via confound_set("legacy_default") and remove the internal DEFAULT_CVARS constant. The default now resolves through canonical confound names; the set of columns returned for a no-cvars call is unchanged in practice on fMRIPrep outputs. ?read_confounds now documents the recommended modern default confound_strategy("pcabasic80") (noting it is not equivalent to the legacy default) and cross-references the confound_set()/confound_strategy()/list_confound_sets()/ list_confound_strategies() helpers.
  • Change read_preproc_scans() to return a file-ordered list of NeuroVec objects, one per matched preprocessed scan, instead of collapsing multiple files into a single container.
  • Fix derivative discovery and legacy fMRIPrep helpers for datasets that place derivative subject folders directly under derivatives/ with prep_dir = "derivatives".
  • Make read_confounds() raise informative, selection-aware errors when no matching participants, confound files, or usable requested confounds are found.
  • Add run-level confound diagnostics and cleaning via check_confounds(), clean_confounds(), and read_confounds(..., clean = ), with zero-variance confounds dropped by default and recorded in a confound_diagnostics attribute.
  • Fix create_preproc_mask() to ignore matching JSON sidecars and only read actual NIfTI mask images.
  • Add query_files() as the recommended explicit query API for new workflows, with match_mode, require_entity, and raw/derivatives scope controls.
  • Add get_metadata() for inheritance-aware BIDS metadata resolution with deterministic nearest-sidecar precedence.
  • Extend read_sidecar() with inheritance-aware resolution via inherit and inherit_scope.
  • Add permissive bids_project(..., strict_participants = FALSE) loading for datasets that omit participants.tsv, while keeping compliance reporting explicit.
  • Add derivative discovery via bids_project(..., derivatives = "auto") and derivative_pipelines(), while preserving legacy fmriprep helpers when an fMRIPrep pipeline is present.
  • Add persistent file indexing with bids_index() and indexed query_files() lookups.
  • Add variables_table() and bids_report_data() / bids_report() for tidy run-level inventory and lightweight dataset reporting.
  • Expand acceptance coverage for metadata inheritance, missing-sidecar cases, conflict handling, and derivative-scope behavior.
  • Keep search_files() available for backward compatibility while steering new examples and docs toward query_files().

bidser 0.3.0

  • Fix load_all_events() and read_events() to use tab delimiter for BIDS TSV event files instead of space delimiter.
  • Fix read_sidecar() to handle JSON sidecars containing vector-valued fields (e.g. SliceTiming) by storing them as list-columns instead of failing with a “differing number of rows” error.

bidser 0.2.0

CRAN release: 2026-02-19

  • TBD.

bidser 0.1.0

  • Initial CRAN release.
  • Read, validate, and query BIDS-compliant neuroimaging projects.
  • Support for fMRIPrep derivatives including confound tables, preprocessed scans, and brain masks.
  • Mock BIDS project creation for testing (create_mock_bids()).
  • Confound processing with PCA reduction and canonical variable aliasing.
  • Visualization of PCA confound scores and loadings (plot.bids_confounds()).
  • Search and filter BIDS files by subject, session, task, run, space, and other entities.