Crate bids 

Comprehensive Rust tools for BIDS (Brain Imaging Data Structure) datasets.

This is the umbrella crate that re-exports all bids-* sub-crates, providing a single dependency for full BIDS dataset support. It is the Rust equivalent of the PyBIDS Python package.

Quick Start

use bids::{BidsLayout, BidsFile};

let layout = BidsLayout::new("/path/to/bids/dataset").unwrap();
let files = layout.get()
    .suffix("bold")
    .extension(".nii.gz")
    .subject("01")
    .collect()
    .unwrap();

for f in &files {
    println!("{}: {:?}", f.filename, f.entities);
}

Crate Organization

• Core (core) — Fundamental types: files, entities, metadata, config, errors
• I/O (io) — TSV/JSON reading, path building, file writing
• Layout (layout) — Dataset indexing and fluent query API
• Variables (variables) — BIDS variable system for statistical modeling
• Modeling (modeling) — BIDS-StatsModels, HRF functions, transformations
• Reports (reports) — Auto-generated methods sections
• Domain crates — Modality-specific support (EEG, MEG, PET, etc.)
• Infrastructure — NIfTI parsing, signal filtering, formula parsing, schema validation

Feature Flags

Feature	Description
ndarray	Enable ndarray integration for EEG (Array2) and NIfTI (ArrayD)
safetensors	Enable safetensors export for ML frameworks
mmap	Enable memory-mapped NIfTI access via memmap2
arrow	Enable Apache Arrow / Parquet export for dataset manifests

Re-exports

pub use bids_core as core;

pub use bids_io as io;

pub use bids_layout as layout;

pub use bids_variables as variables;

pub use bids_validate as validate;

pub use bids_derive as derive;

pub use bids_modeling as modeling;

pub use bids_reports as reports;

pub use bids_beh as beh;

pub use bids_eeg as eeg;

pub use bids_ieeg as ieeg;

pub use bids_meg as meg;

pub use bids_micr as micr;

pub use bids_motion as motion;

pub use bids_mrs as mrs;

pub use bids_nirs as nirs;

pub use bids_perf as perf;

pub use bids_pet as pet;

pub use bids_dataset as dataset;

pub use bids_filter as filter;

pub use bids_formula as formula;

pub use bids_inflect as inflect;

pub use bids_nifti as nifti;

pub use bids_schema as schema;

Modules

prelude

Convenience prelude importing the most commonly used types.

Structs

BidsFile

Represents a single file in a BIDS dataset.

BidsLayout

The main entry point for interacting with a BIDS dataset.

BidsMetadata

Ordered metadata dictionary for a BIDS file.

BidsReport

Generate publication-quality data acquisition methods from a BIDS dataset.

BidsVersion

A parsed BIDS specification version (SemVer).

Config

Configuration for a BIDS layout, defining entities and path patterns.

ContrastInfo

Information about a statistical contrast.

DatasetDescription

Contents of a BIDS dataset_description.json file.

Entity

Represents a single entity defined in configuration.

GradientTable

Combined b-value + b-vector gradient table for a DWI acquisition.

PaddedInt

Integer type that preserves zero-padding.

QueryFilter

A filter for querying files by entity values.

StatsModelsGraph

Rooted directed acyclic graph representing a BIDS-StatsModel specification.

Enums

BidsError

Errors that can occur when working with BIDS datasets.

Compatibility

Result of checking a dataset’s BIDS version against the library’s supported version.

CopyMode

How to copy a file to a new location.

EntityValue

A typed entity value, preserving the original representation where needed.

HrfModel

Hemodynamic Response Function (HRF) model type.

InvalidFilters

How to handle unrecognized entity names in query filters.

Query

Special query values for entity filtering.

Scope

Scope for queries.

Constants

MIN_COMPATIBLE_VERSION

The minimum BIDS version that this release can read without data loss.

SUPPORTED_BIDS_VERSION

The BIDS specification version that this release of bids-rs targets.

Traits

TimeSeries

Trait for read-only access to multichannel time-series data.

Functions

collect_associated_files

Group BIDSFiles with multiple files per acquisition (multi-echo, multi-part, etc.).

convert_json_keys

Convert CamelCase keys to snake_case recursively in a JSON value.

matches_entities

Check whether a file’s entities match the target entities.

Type Aliases

Entities

A map from entity names to their typed values for a single file.

Result

A specialized Result type for BIDS operations.

StringEntities

A map from entity names to string values (used in variables/collections).