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Common principles

Definitions

The keywords "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in [RFC2119].

Throughout this specification we use a list of terms and abbreviations. To avoid misunderstanding we clarify them here.

  1. Dataset - a set of neuroimaging and behavioral data acquired for a purpose of a particular study. A dataset consists of data acquired from one or more subjects, possibly from multiple sessions.

  2. Subject - a person or animal participating in the study. Used interchangeably with term Participant.

  3. Session - a logical grouping of neuroimaging and behavioral data consistent across subjects. Session can (but doesn't have to) be synonymous to a visit in a longitudinal study. In general, subjects will stay in the scanner during one session. However, for example, if a subject has to leave the scanner room and then be re-positioned on the scanner bed, the set of MRI acquisitions will still be considered as a session and match sessions acquired in other subjects. Similarly, in situations where different data types are obtained over several visits (for example fMRI on one day followed by DWI the day after) those can be grouped in one session. Defining multiple sessions is appropriate when several identical or similar data acquisitions are planned and performed on all -or most- subjects, often in the case of some intervention between sessions (for example, training). In the PET context, a session may also indicate a group of related scans, taken in one or more visits.

  4. Sample - a sample pertaining to a subject such as tissue, primary cell or cell-free sample. The sample-<label> key/value pair is used to distinguish between different samples from the same subject. The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.

  5. Data acquisition - a continuous uninterrupted block of time during which a brain scanning instrument was acquiring data according to particular scanning sequence/protocol.

  6. Data type - a functional group of different types of data. BIDS defines the following data types:

    1. func (task based and resting state functional MRI)
    2. dwi (diffusion weighted imaging)
    3. fmap (field inhomogeneity mapping data such as field maps)
    4. anat (structural imaging such as T1, T2, PD, and so on)
    5. perf (perfusion)
    6. meg (magnetoencephalography)
    7. eeg (electroencephalography)
    8. ieeg (intracranial electroencephalography)
    9. beh (behavioral)
    10. pet (positron emission tomography)
    11. micr (microscopy)

    Data files are contained in a directory named for the data type. In raw datasets, the data type directory is nested inside subject and (optionally) session directories.

  7. Task - a set of structured activities performed by the participant. Tasks are usually accompanied by stimuli and responses, and can greatly vary in complexity. For the purpose of this specification we consider the so-called "resting state" a task. In the context of brain scanning, a task is always tied to one data acquisition. Therefore, even if during one acquisition the subject performed multiple conceptually different behaviors (with different sets of instructions) they will be considered one (combined) task.

  8. Event - something that happens or may be perceived by a test subject as happening at a particular instant during the recording. Events are most commonly associated with on- or offset of stimulus presentations, or with the distinct marker of on- or offset of a subject's response or motor action. Other events may include unplanned incidents (for example, sudden onset of noise and vibrations due to construction work, laboratory device malfunction), changes in task instructions (for example, switching the response hand), or experiment control parameters (for example, changing the stimulus presentation rate over experimental blocks), and noted data feature occurrences (for example, a recording electrode producing noise). In BIDS, each event has an onset time and duration. Note that not all tasks will have recorded events (for example, "resting state").

  9. Run - an uninterrupted repetition of data acquisition that has the same acquisition parameters and task (however events can change from run to run due to different subject response or randomized nature of the stimuli). Run is a synonym of a data acquisition. Note that "uninterrupted" may look different by modality due to the nature of the recording. For example, in MRI or MEG, if a subject leaves the scanner, the acquisition must be restarted. For some types of PET acquisitions, a subject may leave and re-enter the scanner without interrupting the scan.

  10. Modality - the category of brain data recorded by a file. For MRI data, different pulse sequences are considered distinct modalities, such as T1w, bold or dwi. For passive recording techniques, such as EEG, MEG or iEEG, the technique is sufficiently uniform to define the modalities eeg, meg and ieeg. When applicable, the modality is indicated in the suffix. The modality may overlap with, but should not be confused with the data type.

  11. <index> - a nonnegative integer, possibly prefixed with arbitrary number of 0s for consistent indentation, for example, it is 01 in run-01 following run-<index> specification.

  12. <label> - an alphanumeric value, possibly prefixed with arbitrary number of 0s for consistent indentation, for example, it is rest in task-rest following task-<label> specification. Note that labels MUST not collide when casing is ignored (see Case collision intolerance).

  13. suffix - an alphanumeric value, located after the key-value_ pairs (thus after the final _), right before the File extension, for example, it is eeg in sub-05_task-matchingpennies_eeg.vhdr.

  14. File extension - a portion of the filename after the left-most period (.) preceded by any other alphanumeric. For example, .gitignore does not have a file extension, but the file extension of test.nii.gz is .nii.gz. Note that the left-most period is included in the file extension.

  15. DEPRECATED - A "deprecated" entity or metadata field SHOULD NOT be used in the generation of new datasets. It remains in the standard in order to preserve the interpretability of existing datasets. Validating software SHOULD warn when deprecated practices are detected and provide a suggestion for updating the dataset to preserve the curator's intent.

Compulsory, optional, and additional data and metadata

The following standard describes a way of arranging data and writing down metadata for a subset of neuroimaging experiments. Some aspects of the standard are compulsory. For example a particular filename format is required when storing structural scans. Some aspects are regulated but optional. For example a T2 volume does not need to be included, but when it is available it should be saved under a particular filename specified in the standard. This standard aspires to describe a majority of datasets, but acknowledges that there will be cases that do not fit. In such cases one can include additional files and subdirectories to the existing directory structure following common sense. For example one may want to include eye tracking data in a vendor specific format that is not covered by this standard. The most sensible place to put it is next to the continuous recording file with the same naming scheme but different extensions. The solutions will change from case to case and publicly available datasets will be reviewed to include common data types in the future releases of the BIDS specification.

File name structure

A filename consists of a chain of entities, or key-value pairs, a suffix and an extension. Two prominent examples of entities are subject and session.

For a data file that was collected in a given session from a given subject, the filename MUST begin with the string sub-<label>_ses-<label>. If the session level is omitted in the directory structure, the filename MUST begin with the string sub-<label>, without ses-<label>.

Note that sub-<label> corresponds to the subject entity because it has the sub- "key" and<label> "value", where <label> would in a real data file correspond to a unique identifier of that subject, such as 01. The same holds for the session entity with its ses- key and its <label> value.

The extra session layer (at least one /ses-<label> subdirectory) SHOULD be added for all subjects if at least one subject in the dataset has more than one session. If a /ses-<label> subdirectory is included as part of the directory hierarchy, then the same ses-<label> key/value pair MUST also be included as part of the filenames themselves. Acquisition time of session can be defined in the sessions file.

A chain of entities, followed by a suffix, connected by underscores (_) produces a human readable filename, such as sub-01_task-rest_eeg.edf. It is evident from the filename alone that the file contains resting state data from subject 01. The suffix eeg and the extension .edf depend on the imaging modality and the data format and indicate further details of the file's contents.

Entities within a filename MUST be unique. For example, the following filename is not valid because it uses the acq entity twice: sub-01_acq-laser_acq-uneven_electrodes.tsv

In cases where entities duplicate metadata, the presence of an entity should not be used as a replacement for the corresponding metadata field. For instance, in echo-planar imaging MRI, the dir-<label> entity MAY be used to distinguish files with different phase-encoding directions, but the file's PhaseEncodingDirection can only be specified as metadata.

A summary of all entities in BIDS and the order in which they MUST be specified is available in the entity table in the appendix.

Entity-linked file collections

An entity-linked file collection is a set of files that are related to each other based on a repetitive acquisition of sequential data by changing acquisition parameters one (or multiple) at a time or by being inherent components of the same data. Entity-linked collections are identified by a common suffix, indicating the group of files that should be considered a logical unit. Within each collection, files MUST be distinguished from each other by at least one entity (for example, echo) that corresponds to an altered acquisition parameter (EchoTime) or that defines a component relationship (for example, part). Note that these entities MUST be described by the specification and the parameter changes they declare MUST NOT invalidate the definition of the accompanying suffix. For example, the use of the echo entity along with the T1w suffix casts doubt on the validity of the identified contrast weighting. Provided the conditions above are satisfied, any suffix (such as bold) can identify an entity-linked file collection, although certain suffixes are exclusive for this purpose (for example, MP2RAGE). Use cases concerning this convention are compiled in the file collections appendix. This convention is mainly intended for but not limited to MRI modalities.

Case collision intolerance

File name components are case sensitive, but collisions MUST be avoided when casing is ignored. For example, a dataset cannot contain both sub-s1 and sub-S1, as the labels would collide on a case-insensitive filesystem. Additionally, because the suffix eeg is defined, then the suffix EEG will not be added to future versions of the standard.

Source vs. raw vs. derived data

BIDS was originally designed to describe and apply consistent naming conventions to raw (unprocessed or minimally processed due to file format conversion) data. During analysis such data will be transformed and partial as well as final results will be saved. Derivatives of the raw data (other than products of DICOM to NIfTI conversion) MUST be kept separate from the raw data. This way one can protect the raw data from accidental changes by file permissions. In addition it is easy to distinguish partial results from the raw data and share the latter. See Storage of derived datasets for more on organizing derivatives.

Similar rules apply to source data, which is defined as data before harmonization, reconstruction, and/or file format conversion (for example, E-Prime event logs or DICOM files). Storing actual source files with the data is preferred over links to external source repositories to maximize long term preservation, which would suffer if an external repository would not be available anymore. This specification currently does not go into the details of recommending a particular naming scheme for including different types of source data (such as the raw event logs or parameter files, before conversion to BIDS). However, in the case that these data are to be included:

  1. These data MUST be kept in separate sourcedata directory with a similar directory structure as presented below for the BIDS-managed data. For example: sourcedata/sub-01/ses-pre/func/sub-01_ses-pre_task-rest_bold.dicom.tgz or sourcedata/sub-01/ses-pre/func/MyEvent.sce.

  2. A README file SHOULD be found at the root of the sourcedata directory or the derivatives directory, or both. This file should describe the nature of the raw data or the derived data. We RECOMMEND including the PDF print-out with the actual sequence parameters generated by the scanner in the sourcedata directory.

Alternatively one can organize their data in the following way

└─ my_dataset-1/
   ├─ sourcedata 
   ├─ ... 
   ├─ rawdata/
   │  ├─ dataset_description.json 
   │  ├─ participants.tsv 
   │  ├─ sub-01/
   │  ├─ sub-02/
   │  └─ ... 
   └─ derivatives/
      ├─ pipeline_1/
      ├─ pipeline_2/
      └─ ... 

In this example, where sourcedata and derivatives are not nested inside rawdata, only the rawdata subdirectory needs to be a BIDS-compliant dataset. The subdirectories of derivatives MAY be BIDS-compliant derivatives datasets (see Non-compliant derivatives for further discussion). This specification does not prescribe anything about the contents of sourcedata directories in the above example - nor does it prescribe the sourcedata, derivatives, or rawdata directory names. The above example is just a convention that can be useful for organizing raw, source, and derived data while maintaining BIDS compliance of the raw data directory. When using this convention it is RECOMMENDED to set the SourceDatasets field in dataset_description.json of each subdirectory of derivatives to:

{
  "SourceDatasets": [ {"URL": "file://../../rawdata/"} ]
}

Storage of derived datasets

Derivatives can be stored/distributed in two ways:

  1. Under a derivatives/ subdirectory in the root of the source BIDS dataset directory to make a clear distinction between raw data and results of data processing. A data processing pipeline will typically have a dedicated directory under which it stores all of its outputs. Different components of a pipeline can, however, also be stored under different subdirectories. There are few restrictions on the directory names; it is RECOMMENDED to use the format <pipeline>-<variant> in cases where it is anticipated that the same pipeline will output more than one variant (for example, AFNI-blurring and AFNI-noblurring). For the sake of consistency, the subdirectory name SHOULD be the GeneratedBy.Name field in data_description.json, optionally followed by a hyphen and a suffix (see Derived dataset and pipeline description).

    Example of derivatives with one directory per pipeline:

    <dataset>/derivatives/fmriprep-v1.4.1/sub-0001
    <dataset>/derivatives/spm/sub-0001
    <dataset>/derivatives/vbm/sub-0001
    

    Example of a pipeline with split derivative directories:

    <dataset>/derivatives/spm-preproc/sub-0001
    <dataset>/derivatives/spm-stats/sub-0001
    

    Example of a pipeline with nested derivative directories:

    <dataset>/derivatives/spm-preproc/sub-0001
    <dataset>/derivatives/spm-preproc/derivatives/spm-stats/sub-0001
    
  2. As a standalone dataset independent of the source (raw or derived) BIDS dataset. This way of specifying derivatives is particularly useful when the source dataset is provided with read-only access, for publishing derivatives as independent bodies of work, or for describing derivatives that were created from more than one source dataset. The sourcedata/ subdirectory MAY be used to include the source dataset(s) that were used to generate the derivatives. Likewise, any code used to generate the derivatives from the source data MAY be included in the code/ subdirectory.

    Example of a derivative dataset including the raw dataset as source:

└─ my_processed_data/
   ├─ code/
   │  ├─ processing_pipeline-1.0.0.img 
   │  ├─ hpc_submitter.sh 
   │  └─ ... 
   ├─ sourcedata/
   │  ├─ sub-01/
   │  ├─ sub-02/
   │  └─ ... 
   ├─ sub-01/
   ├─ sub-02/
   └─ ... 

Throughout this specification, if a section applies particularly to derivatives, then Case 1 will be assumed for clarity in templates and examples, but removing /derivatives/<pipeline> from the template name will provide the equivalent for Case 2. In both cases, every derivatives dataset is considered a BIDS dataset and must include a dataset_description.json file at the root level (see Dataset description). Consequently, files should be organized to comply with BIDS to the full extent possible (that is, unless explicitly contradicted for derivatives). Any subject-specific derivatives should be housed within each subject’s directory; if session-specific derivatives are generated, they should be deposited under a session subdirectory within the corresponding subject directory; and so on.

Non-compliant derivatives

Nothing in this specification should be interpreted to disallow the storage/distribution of non-compliant derivatives of BIDS datasets. In particular, if a BIDS dataset contains a derivatives/ subdirectory, the contents of that directory may be a heterogeneous mix of BIDS Derivatives datasets and non-compliant derivatives.

File Formation specification

Imaging files

All imaging data MUST be stored using the NIfTI file format. We RECOMMEND using compressed NIfTI files (.nii.gz), either version 1.0 or 2.0. Imaging data SHOULD be converted to the NIfTI format using a tool that provides as much of the NIfTI header information (such as orientation and slice timing information) as possible. Since the NIfTI standard offers limited support for the various image acquisition parameters available in DICOM files, we RECOMMEND that users provide additional meta information extracted from DICOM files in a sidecar JSON file (with the same filename as the .nii[.gz] file, but with a .json extension). Extraction of BIDS compatible metadata can be performed using dcm2niix and dicm2nii DICOM to NIfTI converters. The BIDS-validator will check for conflicts between the JSON file and the data recorded in the NIfTI header.

Tabular files

Tabular data MUST be saved as tab delimited values (.tsv) files, that is, CSV files where commas are replaced by tabs. Tabs MUST be true tab characters and MUST NOT be a series of space characters. Each TSV file MUST start with a header line listing the names of all columns (with the exception of physiological and other continuous recordings). Names MUST be separated with tabs. It is RECOMMENDED that the column names in the header of the TSV file are written in snake_case with the first letter in lower case (for example, variable_name, not Variable_name). String values containing tabs MUST be escaped using double quotes. Missing and non-applicable values MUST be coded as n/a. Numerical values MUST employ the dot (.) as decimal separator and MAY be specified in scientific notation, using e or E to separate the significand from the exponent. TSV files MUST be in UTF-8 encoding.

Example:

onset   duration    response_time   correct stop_trial  go_trial
200 200 0   n/a n/a n/a

Note: The TSV examples in this document (like the one above this note) are occasionally formatted using space characters instead of tabs to improve human readability. Directly copying and then pasting these examples from the specification for use in new BIDS datasets can lead to errors and is discouraged.

Tabular files MAY be optionally accompanied by a simple data dictionary in the form of a JSON object within a JSON file. The JSON files containing the data dictionaries MUST have the same name as their corresponding tabular files but with .json extensions. If a data dictionary is provided, it MAY contain one or more fields describing the columns found in the TSV file (in addition to any other metadata one wishes to include that describe the file as a whole). Note that if a field name included in the data dictionary matches a column name in the TSV file, then that field MUST contain a description of the corresponding column, using an object containing the following fields:

Key name Requirement Level Data type Description
Description RECOMMENDED string Free-form natural language description. The description of the column.
HED OPTIONAL string or object of strings Hierarchical Event Descriptor (HED) information, see: Appendix III for details.
Levels RECOMMENDED object of strings For categorical variables: An object of possible values (keys) and their descriptions (values).
LongName OPTIONAL string Long (unabbreviated) name of the column.
TermURL RECOMMENDED string URL pointing to a formal definition of this type of data in an ontology available on the web.
Units RECOMMENDED string Measurement units for the associated file. SI units in CMIXF formatting are RECOMMENDED (see Units).

Please note that while both Units and Levels are RECOMMENDED, typically only one of these two fields would be specified for describing a single TSV file column.

Example:

{
  "test": {
    "LongName": "Education level",
    "Description": "Education level, self-rated by participant",
    "Levels": {
      "1": "Finished primary school",
      "2": "Finished secondary school",
      "3": "Student at university",
      "4": "Has degree from university"
    }
  },
  "bmi": {
    "LongName": "Body mass index",
    "Units": "kg/m^2",
    "TermURL": "https://purl.bioontology.org/ontology/SNOMEDCT/60621009"
  }
}

Key/value files (dictionaries)

JavaScript Object Notation (JSON) files MUST be used for storing key/value pairs. JSON files MUST be in UTF-8 encoding. Extensive documentation of the format can be found at https://www.json.org/, and at https://tools.ietf.org/html/std90. Several editors have built-in support for JSON syntax highlighting that aids manual creation of such files. An online editor for JSON with built-in validation is available at https://jsoneditoronline.org. It is RECOMMENDED that keys in a JSON file are written in CamelCase with the first letter in upper case (for example, SamplingFrequency, not samplingFrequency). Note however, when a JSON file is used as an accompanying sidecar file for a TSV file, the keys linking a TSV column with their description in the JSON file need to follow the exact formatting as in the TSV file.

Example of a hypothetical *_bold.json file, accompanying a *_bold.nii file:

{
  "RepetitionTime": 3,
  "Instruction": "Lie still and keep your eyes open"
}

Example of a hypothetical *_events.json file, accompanying an *_events.tsv file. Note that the JSON file contains a key describing an arbitrary column stim_presentation_side in the TSV file it accompanies. See task events section for more information.

{
  "stim_presentation_side": {
    "Levels": {
      "1": "stimulus presented on LEFT side",
      "2": "stimulus presented on RIGHT side"
    }
  }
}

The Inheritance Principle

  1. Any metadata file (such as .json, .bvec or .tsv) MAY be defined at any directory level.

  2. For a given data file, any metadata file is applicable to that data file if:

    1. It is stored at the same directory level or higher;
    2. The metadata and the data filenames possess the same suffix;
    3. The metadata filename does not include any entity absent from the data filename.
  3. A metadata file MUST NOT have a filename that would be otherwise applicable to some data file based on rules 2.b and 2.c but is made inapplicable based on its location in the directory structure as per rule 2.a.

  4. There MUST NOT be multiple metadata files applicable to a data file at one level of the directory hierarchy.

  5. If multiple metadata files satisfy criteria 2.a-c above:

    1. For tabular files and other simple metadata files (for instance, bvec / bval files for diffusion MRI), accessing metadata associated with a data file MUST consider only the applicable file that is lowest in the filesystem hierarchy.

    2. For JSON files, key-values are loaded from files from the top of the directory hierarchy downwards, such that key-values from the top level are inherited by all data files at lower levels to which it is applicable unless overridden by a value for the same key present in another metadata file at a lower level (though it is RECOMMENDED to minimize the extent of such overrides).

Corollaries:

  1. As per rule 3, metadata files applicable only to a specific participant / session MUST be defined in or below the directory corresponding to that participant / session; similarly, a metadata file that is applicable to multiple participants / sessions MUST NOT be placed within a directory corresponding to only one such participant / session.

  2. It is permissible for a single metadata file to be applicable to multiple data files at that level of the hierarchy or below. Where such metadata content is consistent across multiple data files, it is RECOMMENDED to store metadata in this way, rather than duplicating that metadata content across multiple metadata files.

  3. Where multiple applicable JSON files are loaded as per rule 5.b, key-values can only be overwritten by files lower in the filesystem hierarchy; the absence of a key-value in a later file does not imply the "unsetting" of that field (indeed removal of existing fields is not possible).

Example 1: Demonstration of inheritance principle

├─ sub-01/
│  └─ func/
│     ├─ sub-01_task-rest_acq-default_bold.nii.gz 
│     ├─ sub-01_task-rest_acq-longtr_bold.nii.gz 
│     └─ sub-01_task-rest_acq-longtr_bold.json 
└─ task-rest_bold.json 

Contents of file task-rest_bold.json:

{
    "EchoTime": 0.040,
    "RepetitionTime": 1.0
}

Contents of file sub-01/func/sub-01_task-rest_acq-longtr_bold.json:

{
    "RepetitionTime": 3.0
}

When reading image sub-01/func/sub-01_task-rest_acq-default_bold.nii.gz, only metadata file task-rest_bold.json is read; file sub-01/func/sub-01_task-rest_acq-longtr_bold.json is inapplicable as it contains entity "acq-longtr" that is absent from the image path (rule 2.c). When reading image sub-01/func/sub-01_task-rest_acq-longtr_bold.nii.gz, metadata file task-rest_bold.json at the top level is read first, followed by file sub-01/func/sub-01_task-rest_acq-longtr_bold.json at the bottom level (rule 5.b); the value for field "RepetitionTime" is therefore overridden to the value 3.0. The value for field "EchoTime" remains applicable to that image, and is not unset by its absence in the metadata file at the lower level (rule 5.b; corollary 3).

Example 2: Impermissible use of multiple metadata files at one directory level (rule 4)

└─ sub-01/
   └─ ses-test/
      ├─ anat/
      │  └─ sub-01_ses-test_T1w.nii.gz 
      └─ func/
         ├─ sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz 
         ├─ sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz 
         ├─ sub-01_ses-test_task-overtverbgeneration_bold.json 
         └─ sub-01_ses-test_task-overtverbgeneration_run-2_bold.json 

Example 3: Modification of filesystem structure from Example 2 to satisfy inheritance principle requirements

└─ sub-01/
   └─ ses-test/
      ├─ sub-01_ses-test_task-overtverbgeneration_bold.json 
      ├─ anat/
      │  └─ sub-01_ses-test_T1w.nii.gz 
      └─ func/
         ├─ sub-01_ses-test_task-overtverbgeneration_run-1_bold.nii.gz 
         ├─ sub-01_ses-test_task-overtverbgeneration_run-2_bold.nii.gz 
         └─ sub-01_ses-test_task-overtverbgeneration_run-2_bold.json 

Example 4: Single metadata file applying to multiple data files (corollary 2)

└─ sub-01/
   ├─ anat/
   └─ func/
      ├─ sub-01_task-xyz_acq-test1_run-1_bold.nii.gz 
      ├─ sub-01_task-xyz_acq-test1_run-2_bold.nii.gz 
      └─ sub-01_task-xyz_acq-test1_bold.json 

Participant names and other labels

BIDS allows for custom user-defined <label>s and <index>es for example, for naming of participants, sessions, acquisition schemes. Note that they MUST consist only of allowed characters as described in Definitions above. In <index>es we RECOMMEND using zero padding (for example, 01 instead of 1 if you have more than nine subjects) to make alphabetical sorting more intuitive. Note that zero padding SHOULD NOT be used to merely maintain uniqueness of <index>es.

Please note that a given label or index is distinct from the "prefix" it refers to. For example sub-01 refers to the sub entity (a subject) with the label 01. The sub- prefix is not part of the subject label, but must be included in filenames (similarly to other key names).

Specification of paths

Several metadata fields in BIDS require the specification of paths, that is, a string of characters used to uniquely identify a location in a directory structure. For example the IntendedFor or AssociatedEmptyroom metadata fields.

Throughout BIDS all such paths MUST be specified using the slash character (/), regardless of the operating system that a particular dataset is curated on or used on.

Paths SHOULD NOT be absolute local paths, because these might break when a dataset is used on a different machine. It is RECOMMENDED that all paths specified in a BIDS dataset are relative paths, as specified in the respective descriptions of metadata fields that require the use of paths.

Uniform Resource Indicator

A Uniform Resource Indicator (URI) is a string referring to a resource and SHOULD have the form <scheme>:[//<authority>]<path>[?<query>][#<fragment>], as specified in RFC 3986. This applies to URLs and other common URIs, including Digital Object Identifiers (DOIs), which may be fully specified as doi:<path>, for example, doi:10.5281/zenodo.3686061. A given resource may have multiple URIs. When selecting URIs to add to dataset metadata, it is important to consider specificity and persistence.

Several fields are designated for DOIs, for example, DatasetDOI in dataset_description.json. DOI values SHOULD be fully specified URIs such as doi:10.18112/openneuro.ds000001.v1.0.0. Bare DOIs such as 10.18112/openneuro.ds000001.v1.0.0 are DEPRECATED.

Units

All units SHOULD be specified as per International System of Units (abbreviated as SI, from the French Système international (d'unités)) and can be SI units or SI derived units. In case there are valid reasons to deviate from SI units or SI derived units, the units MUST be specified in the sidecar JSON file. In case data is expressed in SI units or SI derived units, the units MAY be specified in the sidecar JSON file. In case non-standard prefixes are added to SI or non-SI units, these non-standard prefixed units MUST be specified in the JSON file. See Appendix V for a list of standard units and prefixes. Note also that for the formatting of SI units, the CMIXF-12 convention for encoding units is RECOMMENDED. CMIXF provides a consistent system for all units and prefix symbols with only basic characters, avoiding symbols that can cause text encoding problems; for example the CMIXF formatting for "micro volts" is uV, "degrees Celsius" is oC and "Ohm" is Ohm. See Appendix V for more information.

For additional rules, see below:

  • Elapsed time SHOULD be expressed in seconds. Please note that some DICOM parameters have been traditionally expressed in milliseconds. Those need to be converted to seconds.

  • Frequency SHOULD be expressed in Hertz.

  • Arbitrary units SHOULD be indicated with the string "arbitrary".

Describing dates and timestamps:

  • Date time information MUST be expressed in the following format YYYY-MM-DDThh:mm:ss[.000000][Z] (year, month, day, hour (24h), minute, second, optional fractional seconds, and optional UTC time indicator). This is almost equivalent to the RFC3339 "date-time" format, with the exception that UTC indicator Z is optional and non-zero UTC offsets are not indicated. If Z is not indicated, time zone is always assumed to be the local time of the dataset viewer. No specific precision is required for fractional seconds, but the precision SHOULD be consistent across the dataset. For example 2009-06-15T13:45:30.

  • Time stamp information MUST be expressed in the following format: hh:mm:ss[.000000] For example 13:45:30.

  • Note that, depending on local ethics board policy, date time information may not need to be fully detailed. For example, it is permissible to set the time to 00:00:00 if reporting the exact recording time is undesirable. However, for privacy protection reasons, it is RECOMMENDED to shift dates, as described below, without completely removing time information, as time information can be useful for research purposes.

  • Dates can be shifted by a random number of days for privacy protection reasons. To distinguish real dates from shifted dates, is is RECOMMENDED to set shifted dates to the year 1925 or earlier. Note that some data formats do not support arbitrary recording dates. For example, the EDF data format can only contain recording dates after 1985. For longitudinal studies dates MUST be shifted by the same number of days within each subject to maintain the interval information. For example: 1867-06-15T13:45:30

  • WARNING: The Neuromag/Elekta/MEGIN file format for MEG (.fif) does not support recording dates earlier than 1902 roughly. Some analysis software packages (for example, MNE-Python) handle their data as .fif internally and will break if recording dates are specified prior to 1902, even if the original data format is not .fif. See MEG-file-formats for more information.

  • Age SHOULD be given as the number of years since birth at the time of scanning (or first scan in case of multi session datasets). Using higher accuracy (weeks) should in general be avoided due to privacy protection, unless when appropriate given the study goals, for example, when scanning babies.

Directory structure

Single session example

This is an example of the directory and file structure. Because there is only one session, the session level is not required by the format. For details on individual files see descriptions in the next section:

├─ sub-control01/
│  ├─ anat/
│  │  ├─ sub-control01_T1w.nii.gz 
│  │  ├─ sub-control01_T1w.json 
│  │  ├─ sub-control01_T2w.nii.gz 
│  │  └─ sub-control01_T2w.json 
│  ├─ func/
│  │  ├─ sub-control01_task-nback_bold.nii.gz 
│  │  ├─ sub-control01_task-nback_bold.json 
│  │  ├─ sub-control01_task-nback_events.tsv 
│  │  ├─ sub-control01_task-nback_physio.tsv.gz 
│  │  ├─ sub-control01_task-nback_physio.json 
│  │  └─ sub-control01_task-nback_sbref.nii.gz 
│  ├─ dwi/
│  │  ├─ sub-control01_dwi.nii.gz 
│  │  ├─ sub-control01_dwi.bval 
│  │  └─ sub-control01_dwi.bvec 
│  └─ fmap/
│     ├─ sub-control01_phasediff.nii.gz 
│     ├─ sub-control01_phasediff.json 
│     └─ sub-control01_magnitude1.nii.gz 
├─ code/
│  └─ deface.py 
├─ derivatives/
├─ README 
├─ participants.tsv 
├─ dataset_description.json 
└─ CHANGES 

Unspecified data

Additional files and directories containing raw data MAY be added as needed for special cases. All non-standard file entities SHOULD conform to BIDS-style naming conventions, including alphabetic entities and suffixes and alphanumeric labels/indices. Non-standard suffixes SHOULD reflect the nature of the data, and existing entities SHOULD be used when appropriate. For example, an ASSET calibration scan might be named sub-01_acq-ASSET_calibration.nii.gz.

Non-standard files and directories should be named with care. Future BIDS efforts may standardize new entities and suffixes, changing the meaning of filenames and setting requirements on their contents or metadata. Validation and parsing tools MAY treat the presence of non-standard files and directories as an error, so consult the details of these tools for mechanisms to suppress warnings or provide interpretations of your filenames.