{ "_id": "6a1f9bcfb401979e73430b7a", "Package": "bidser", "Version": "0.4.0", "Title": "Work with 'BIDS' (Brain Imaging Data Structure) Projects", "Description": "Tools for working with 'BIDS' (Brain Imaging Data\nStructure) formatted neuroimaging datasets. The package\nprovides functionality for reading and querying\n'BIDS'-compliant projects, creating mock 'BIDS' datasets for\ntesting, and extracting preprocessed data from 'fMRIPrep'\nderivatives. It supports searching and filtering 'BIDS' files\nby various entities such as subject, session, task, and run to\nstreamline neuroimaging data workflows. See Gorgolewski et al.\n(2016) for the 'BIDS'\nspecification.", "Authors@R": "person(\"Bradley\", \"Buchsbaum\", , \"brad.buchsbaum@gmail.com\", c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1108-4866\"))", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "ByteCompile": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://github.com/bbuchsbaum/bidser,\nhttps://bbuchsbaum.github.io/bidser/", "BugReports": "https://github.com/bbuchsbaum/bidser/issues", "Config/Needs/website": "albersdown", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libx11-dev", "Repository": "https://bbuchsbaum.r-universe.dev", "Date/Publication": "2026-06-02 23:56:48 UTC", "RemoteUrl": "https://github.com/bbuchsbaum/bidser", "RemoteRef": "HEAD", "RemoteSha": "3cb7bf763214e6a4c93d24e485e4f46492eeb8d0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 03:07:25 UTC", "User": "root" }, "Author": "Bradley Buchsbaum [aut, cre] (ORCID:\n)", "Maintainer": "Bradley Buchsbaum ", "MD5sum": "c5572aa8c2545e614f6a7c14deb2a10e", "_user": "bbuchsbaum", "_type": "src", "_file": "bidser_0.4.0.tar.gz", "_fileid": "88562b5c407f692acda92d277e3353d73c50f1357b2c9be05e0ca75fdc191630", "_filesize": 983084, "_sha256": "88562b5c407f692acda92d277e3353d73c50f1357b2c9be05e0ca75fdc191630", "_created": "2026-06-03T03:07:25.000Z", "_published": "2026-06-03T03:13:19.857Z", "_distro": "noble", "_jobs": [ { "job": 79215155654, "time": 269, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7374996058" }, { "job": 79215155616, "time": 236, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7374989325" }, { "job": 79215155649, "time": 164, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7374973825" }, { "job": 79215155670, "time": 164, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7374973848" }, { "job": 79214672173, "time": 294, 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"extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/bbuchsbaum/bidser", "_realowner": "bbuchsbaum", "_cranurl": true, "_releases": [ { "version": "0.2.0", "date": "2026-02-19" } ], "_exports": [ "anat_parser", "as_bids_uri", "bids_check_compliance", "bids_datatype_spec", "bids_heatmap", "bids_index", "bids_parser", "bids_project", "bids_report", "bids_report_data", "bids_schema", "bids_schema_versions", "bids_subject", "bids_subject.bids_project", "bids_summary", "bids_transform", "bids_uri", "bids_version", "brain_mask", "build_subject_graph", "check_confounds", "check_func_scans", "clean_confounds", "clear_example_bids_cache", "confound_files", "confound_set", "confound_strategy", "create_mock_bids", "create_preproc_mask", "create_smooth_transformer", "dataset_description", "dataset_name", "dataset_type", "decode_bids_entities", "derivative_files", "derivative_pipelines", "encode", "event_files", "file_pairs", "flat_list", "fmap_parser", "fmriprep_anat_parser", "fmriprep_func_parser", "func_parser", "func_scans", "gen_parser", "get_example_bids_dataset", "get_metadata", "get_repetition_time", "infer_tr", "is_bids_uri", "list_confound_sets", "list_confound_strategies", "list_datatypes", "list_pack_bids", "load_all_events", "mask_files", "pack_bids", "parse", "participants", "plot_bids", "preproc_scans", "query_files", "read_confounds", "read_dataset_description", "read_events", "read_func_scans.bids_project", "read_participants", "read_preproc_scans.bids_project", "read_scans_tsv", "read_sessions_tsv", "read_sidecar", "register_datatype", "resolve_bids_uri", "search_files", "sessions", "sidecar", "surface_files", "tasks", "transform_files", "unregister_datatype", "variables_table" ], "_help": [ { "page": "anat_parser", "title": "Anatomical parser constructor", "topics": [ "anat_parser" ] }, { "page": "as_bids_uri", "title": "Coerce to a BIDS URI object", "topics": [ "as_bids_uri", "as_bids_uri.bids_uri", "as_bids_uri.character" ] }, { "page": "bids_check_compliance", "title": "Basic BIDS Compliance Checks", "topics": [ "bids_check_compliance" ] }, { "page": "bids_datatype_spec", "title": "Build a custom BIDS datatype spec", "topics": [ "bids_datatype_spec" ] }, { "page": "bids_heatmap", "title": "Create a specialized heatmap visualization of BIDS data", "topics": [ "bids_heatmap" ] }, { "page": "bids_index", "title": "Build or retrieve a persistent file index for a BIDS project", "topics": [ "bids_index" ] }, { "page": "bids_parser", "title": "BIDS filename parsers using regex", "topics": [ "bids_parser" ] }, { "page": "bids_project", "title": "Create a BIDS Project Object", "topics": [ "bids_project" ] }, { "page": "bids_report", "title": "Create a lightweight text report for a BIDS project", "topics": [ "bids_report" ] }, { "page": "bids_report_data", "title": "Assemble lightweight report data for a BIDS project", "topics": [ "bids_report_data" ] }, { "page": "bids_schema", "title": "Load and cache the BIDS schema", "topics": [ "bids_schema" ] }, { "page": "bids_schema_versions", "title": "List available BIDS schema versions", "topics": [ "bids_schema_versions" ] }, { "page": "bids_subject", "title": "Access a single subject from a BIDS project", "topics": [ "bids_subject", "bids_subject.bids_project" ] }, { "page": "bids_summary", "title": "Summarize a BIDS dataset", "topics": [ "bids_summary" ] }, { "page": "bids_transform", "title": "Apply a transformation to BIDS files", "topics": [ "bids_transform" ] }, { "page": "bids_uri", "title": "Construct a BIDS URI object", "topics": [ "bids_uri" ] }, { "page": "bids_version", "title": "Get the BIDS version of a dataset", "topics": [ "bids_version", "bids_version.bids_dataset_description", "bids_version.bids_project", "bids_version.mock_bids_project" ] }, { "page": "brain_mask", "title": "Retrieve a brain mask for a subject", "topics": [ "brain_mask", "brain_mask.bids_project" ] }, { "page": "build_subject_graph", "title": "Build Subject Graph Structure", "topics": [ "build_subject_graph", "build_subject_graph.bids_project", "build_subject_graph.mock_bids_project" ] }, { "page": "check_confounds", "title": "Check and clean confound tables", "topics": [ "check_confounds", "clean_confounds" ] }, { "page": "check_func_scans", "title": "Check Functional Scans in a BIDS Project", "topics": [ "check_func_scans" ] }, { "page": "clear_example_bids_cache", "title": "Clear Example BIDS Dataset Cache", "topics": [ "clear_example_bids_cache" ] }, { "page": "confound_files-method", "title": "Get confound files from a BIDS project", "topics": [ "confound_files", "confound_files.bids_project", "confound_files.mock_bids_project" ] }, { "page": "confound_set", "title": "Convenience confound sets for fMRIPrep", "topics": [ "confound_set" ] }, { "page": "confound_strategy", "title": "Confound denoising strategies", "topics": [ "confound_strategy" ] }, { "page": "create_mock_bids", "title": "Create a Mock BIDS Project Object", "topics": [ "create_mock_bids" ] }, { "page": "create_preproc_mask", "title": "Create a preprocessing mask from BIDS data", "topics": [ "create_preproc_mask" ] }, { "page": "create_preproc_mask.bids_project", "title": "Create a binary brain mask from preprocessed scans", "topics": [ "create_preproc_mask.bids_project" ] }, { "page": "create_preproc_mask-method", "title": "Create Preprocessing Mask (Mock Implementation)", "topics": [ "create_preproc_mask.mock_bids_project" ] }, { "page": "create_smooth_transformer", "title": "Create a simple smoothing transformer", "topics": [ "create_smooth_transformer" ] }, { "page": "dataset_description", "title": "Get the dataset_description object from a BIDS project", "topics": [ "dataset_description", "dataset_description.bids_project" ] }, { "page": "dataset_name", "title": "Get fields from a BIDS dataset description", "topics": [ "dataset_name", "dataset_type" ] }, { "page": "decode_bids_entities", "title": "Decode BIDS entities back into a filename", "topics": [ "decode_bids_entities" ] }, { "page": "derivative_files", "title": "Query derivative files from a BIDS project", "topics": [ "derivative_files" ] }, { "page": "derivative_pipelines", "title": "List derivative pipelines in a BIDS project", "topics": [ "derivative_pipelines" ] }, { "page": "encode", "title": "Encode a string into a BIDS key-value list", "topics": [ "encode", "encode.character" ] }, { "page": "event_files-method", "title": "Get event files from a BIDS project", "topics": [ "event_files", "event_files.bids_project", "event_files.mock_bids_project" ] }, { "page": "file_pairs", "title": "Find File Pairs in a BIDS Project", "topics": [ "file_pairs" ] }, { "page": "flat_list-method", "title": "Get \"flat\" representation of BIDS Project", "topics": [ "flat_list", "flat_list.bids_project" ] }, { "page": "fmap_parser", "title": "Fieldmap parser constructor", "topics": [ "fmap_parser" ] }, { "page": "fmriprep_anat_parser", "title": "fMRIPrep anatomical parser constructor", "topics": [ "fmriprep_anat_parser" ] }, { "page": "fmriprep_func_parser", "title": "fMRIPrep functional parser constructor", "topics": [ "fmriprep_func_parser" ] }, { "page": "func_parser", "title": "Functional parser constructor", "topics": [ "func_parser" ] }, { "page": "func_scans", "title": "Get functional scans from a BIDS project", "topics": [ "func_scans", "func_scans.mock_bids_project" ] }, { "page": "func_scans.bids_project", "title": "Get Functional Scans from a BIDS Project", "topics": [ "func_scans.bids_project" ] }, { "page": "gen_parser", "title": "Generate a parser from a spec", "topics": [ "gen_parser" ] }, { "page": "get_example_bids_dataset", "title": "Download Example BIDS Dataset", "topics": [ "get_example_bids_dataset" ] }, { "page": "get_metadata", "title": "Resolve metadata for a BIDS file", "topics": [ "get_metadata", "get_metadata.bids_project" ] }, { "page": "get_repetition_time", "title": "Get Repetition Time (TR) from a sidecar JSON", "topics": [ "get_repetition_time" ] }, { "page": "infer_tr", "title": "Infer TR (Repetition Time) from a BOLD file or sidecar", "topics": [ "infer_tr", "infer_tr.character" ] }, { "page": "is_bids_uri", "title": "Test whether an object is a BIDS URI", "topics": [ "is_bids_uri" ] }, { "page": "list_confound_sets", "title": "List available confound sets", "topics": [ "list_confound_sets" ] }, { "page": "list_confound_strategies", "title": "List available confound strategies", "topics": [ "list_confound_strategies" ] }, { "page": "list_datatypes", "title": "List registered BIDS datatypes", "topics": [ "list_datatypes" ] }, { "page": "list_pack_bids", "title": "List Contents of Packed BIDS Archive", "topics": [ "list_pack_bids" ] }, { "page": "load_all_events-method", "title": "Load All Event Files", "topics": [ "load_all_events", "load_all_events.bids_project" ] }, { "page": "mask_files", "title": "Query Mask Files from a BIDS Project", "topics": [ "mask_files", "mask_files.bids_project", "mask_files.mock_bids_project" ] }, { "page": "pack_bids", "title": "Pack BIDS Project with Stub or Downsampled Imaging Files", "topics": [ "pack_bids" ] }, { "page": "parse-method", "title": "Parse a file-name into BIDS components", "topics": [ "parse" ] }, { "page": "participants-method", "title": "Get participants from a BIDS project", "topics": [ "participants", "participants.bids_project" ] }, { "page": "participants.mock_bids_project", "title": "Get Participants from Mock BIDS Project", "topics": [ "participants.mock_bids_project" ] }, { "page": "plot_bids", "title": "Plot a comprehensive visual overview of a BIDS project", "topics": [ "plot_bids" ] }, { "page": "plot.bids_confounds", "title": "Plot PCA confounds", "topics": [ "plot.bids_confounds" ] }, { "page": "plot.bids_project", "title": "Plot a BIDS project as a dendrogram", "topics": [ "plot.bids_project", "plot.mock_bids_project" ] }, { "page": "preproc_scans-method", "title": "Get preprocessed functional MRI scans", "topics": [ "preproc_scans" ] }, { "page": "preproc_scans.bids_project", "title": "Get preprocessed scans from a BIDS project", "topics": [ "preproc_scans.bids_project" ] }, { "page": "print.mock_bids_project", "title": "Print Mock BIDS Project Summary", "topics": [ "print.mock_bids_project" ] }, { "page": "query_files", "title": "Query files in BIDS structure with explicit semantics", "topics": [ "query_files", "query_files.bids_project", "query_files.mock_bids_project" ] }, { "page": "read_confounds", "title": "Read Confound Files from a BIDS Project", "topics": [ "read_confounds" ] }, { "page": "read_confounds.bids_project", "title": "Read confound files", "topics": [ "read_confounds.bids_project" ] }, { "page": "read_confounds-method", "title": "Read Confound Files (Mock Implementation)", "topics": [ "read_confounds.mock_bids_project" ] }, { "page": "read_dataset_description", "title": "Read the dataset_description.json for a BIDS project", "topics": [ "read_dataset_description", "read_dataset_description.bids_project", "read_dataset_description.character" ] }, { "page": "read_events", "title": "Read Event Files from a BIDS Project", "topics": [ "read_events" ] }, { "page": "read_events.bids_project", "title": "Read event files from a BIDS project", "topics": [ "read_events.bids_project" ] }, { "page": "read_events-method", "title": "Read Event Files from Mock BIDS Project", "topics": [ "read_events.mock_bids_project" ] }, { "page": "read_func_scans", "title": "Read in a set of four-dimensional functional scans", "topics": [ "read_func_scans.bids_project" ] }, { "page": "read_participants", "title": "Read participants.tsv as a typed tabular object", "topics": [ "read_participants", "read_participants.bids_project", "read_participants.character" ] }, { "page": "read_preproc_scans.bids_project", "title": "Read preprocessed functional MRI scans from a BIDS project", "topics": [ "read_preproc_scans.bids_project" ] }, { "page": "read_scans_tsv", "title": "Read a scans.tsv file for a subject", "topics": [ "read_scans_tsv", "read_scans_tsv.bids_project" ] }, { "page": "read_sessions_tsv", "title": "Read a sessions.tsv file for a subject", "topics": [ "read_sessions_tsv", "read_sessions_tsv.bids_project" ] }, { "page": "read_sidecar", "title": "Read sidecar JSON files and return metadata as a tidy tibble", "topics": [ "read_sidecar" ] }, { "page": "register_datatype", "title": "Register a custom BIDS datatype", "topics": [ "register_datatype" ] }, { "page": "resolve_bids_uri", "title": "Resolve a BIDS URI to a local or remote path", "topics": [ "resolve_bids_uri", "resolve_bids_uri.bids_uri", "resolve_bids_uri.character" ] }, { "page": "search_files", "title": "Search files in BIDS structure", "topics": [ "search_files", "search_files.bids_project", "search_files.mock_bids_project" ] }, { "page": "sessions-method", "title": "Get sessions from a BIDS project", "topics": [ "sessions", "sessions.bids_project" ] }, { "page": "sessions.mock_bids_project", "title": "Get Sessions from Mock BIDS Project", "topics": [ "sessions.mock_bids_project" ] }, { "page": "sidecar", "title": "Get the sidecar metadata attached to a tabular BIDS object", "topics": [ "sidecar", "sidecar.bids_tabular" ] }, { "page": "surface_files", "title": "Query Surface Files from a BIDS Project", "topics": [ "surface_files", "surface_files.bids_project", "surface_files.mock_bids_project" ] }, { "page": "tasks-method", "title": "Get tasks from a BIDS project", "topics": [ "tasks", "tasks.bids_project" ] }, { "page": "tasks.mock_bids_project", "title": "Get Tasks from Mock BIDS Project", "topics": [ "tasks.mock_bids_project" ] }, { "page": "transform_files", "title": "Query Transform Files from a BIDS Project", "topics": [ "transform_files", "transform_files.bids_project", "transform_files.mock_bids_project" ] }, { "page": "unregister_datatype", "title": "Unregister a custom BIDS datatype", "topics": [ "unregister_datatype" ] }, { 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