Templates:
dataset_description.jsonREADMECHANGESLICENSE
The file dataset_description.json is a JSON file describing the dataset.
Every dataset MUST include this file with the following fields:
{{ MACROS___make_metadata_table( { "Name": "REQUIRED", "BIDSVersion": "REQUIRED", "HEDVersion": "RECOMMENDED", "DatasetLinks": "REQUIRED if BIDS URIs are used", "DatasetType": "RECOMMENDED", "License": "RECOMMENDED", "Authors": "RECOMMENDED", "Acknowledgements": "OPTIONAL", "HowToAcknowledge": "OPTIONAL", "Funding": "OPTIONAL", "EthicsApprovals": "OPTIONAL", "ReferencesAndLinks": "OPTIONAL", "DatasetDOI": "OPTIONAL", "GeneratedBy": "RECOMMENDED", "SourceDatasets": "RECOMMENDED", } ) }}
Each object in the GeneratedBy array includes the following REQUIRED, RECOMMENDED
and OPTIONAL keys:
| Key name | Requirement level | Data type | Description |
|---|---|---|---|
| Name | REQUIRED | string | Name of the pipeline or process that generated the outputs. Use "Manual" to indicate the derivatives were generated by hand, or adjusted manually after an initial run of an automated pipeline. |
| Version | RECOMMENDED | string | Version of the pipeline. |
| Description | OPTIONAL | string | Plain-text description of the pipeline or process that generated the outputs. RECOMMENDED if Name is "Manual". |
| CodeURL | OPTIONAL | string | URL where the code used to generate the dataset may be found. |
| Container | OPTIONAL | object | Used to specify the location and relevant attributes of software container image used to produce the dataset. Valid keys in this object include Type, Tag and URI with string values. |
Example:
{
"Name": "The mother of all experiments",
"BIDSVersion": "1.6.0",
"DatasetType": "raw",
"License": "CC0",
"Authors": [
"Paul Broca",
"Carl Wernicke"
],
"Acknowledgements": "Special thanks to Korbinian Brodmann for help in formatting this dataset in BIDS. We thank Alan Lloyd Hodgkin and Andrew Huxley for helpful comments and discussions about the experiment and manuscript; Hermann Ludwig Helmholtz for administrative support; and Claudius Galenus for providing data for the medial-to-lateral index analysis.",
"HowToAcknowledge": "Please cite this paper: https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
"Funding": [
"National Institute of Neuroscience Grant F378236MFH1",
"National Institute of Neuroscience Grant 5RMZ0023106"
],
"EthicsApprovals": [
"Army Human Research Protections Office (Protocol ARL-20098-10051, ARL 12-040, and ARL 12-041)"
],
"ReferencesAndLinks": [
"https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
"Alzheimer A., & Kraepelin, E. (2015). Neural correlates of presenile dementia in humans. Journal of Neuroscientific Data, 2, 234001. doi:1920.8/jndata.2015.7"
],
"DatasetDOI": "doi:10.0.2.3/dfjj.10",
"HEDVersion": "8.0.0",
"GeneratedBy": [
{
"Name": "reproin",
"Version": "0.6.0",
"Container": {
"Type": "docker",
"Tag": "repronim/reproin:0.6.0"
}
}
],
"SourceDatasets": [
{
"URL": "s3://dicoms/studies/correlates",
"Version": "April 11 2011"
}
]
}As for any BIDS dataset, a dataset_description.json file MUST be found at the
top level of every derived dataset:
<dataset>/derivatives/<pipeline_name>/dataset_description.json.
In contrast to raw BIDS datasets, derived BIDS datasets MUST include a
GeneratedBy key:
{{ MACROS___make_metadata_table( { "GeneratedBy": "REQUIRED" } ) }}
If a derived dataset is stored as a subdirectory of the raw dataset, then the Name field
of the first GeneratedBy object MUST be a substring of the derived dataset directory name.
That is, in a directory <dataset>/derivatives/<pipeline>[-<variant>]/, the first
GeneratedBy object should have a Name of <pipeline>.
Example:
{
"Name": "FMRIPREP Outputs",
"BIDSVersion": "1.6.0",
"DatasetType": "derivative",
"GeneratedBy": [
{
"Name": "fmriprep",
"Version": "1.4.1",
"Container": {
"Type": "docker",
"Tag": "poldracklab/fmriprep:1.4.1"
}
},
{
"Name": "Manual",
"Description": "Re-added RepetitionTime metadata to bold.json files"
}
],
"SourceDatasets": [
{
"DOI": "doi:10.18112/openneuro.ds000114.v1.0.1",
"URL": "https://openneuro.org/datasets/ds000114/versions/1.0.1",
"Version": "1.0.1"
}
]
}A REQUIRED text file, README, SHOULD describe the dataset in more detail.
The README file MUST be either in ASCII or UTF-8 encoding and MAY have one of the extensions:
.md (Markdown),
.rst (reStructuredText),
or .txt.
A BIDS dataset MUST NOT contain more than one README file (with or without extension)
at its root directory.
BIDS does not make any recommendations with regards to the
Markdown flavor
and does not validate the syntax of Markdown and reStructuredText.
The README file SHOULD be structured such that its contents can be easily understood
even if the used format is not rendered.
A guideline for creating a good README file can be found in the
bids-starter-kit.
Version history of the dataset (describing changes, updates and corrections) MAY
be provided in the form of a CHANGES text file. This file MUST follow the
CPAN Changelog convention.
The CHANGES file MUST be either in ASCII or UTF-8 encoding.
Example:
1.0.1 2015-08-27
- Fixed slice timing information.
1.0.0 2015-08-17
- Initial release.
A LICENSE file MAY be provided in addition to the short specification of the
used license in the dataset_description.json "License" field.
The "License" field and LICENSE file MUST correspond.
The LICENSE file MUST be either in ASCII or UTF-8 encoding.
Template:
participants.tsv
participants.json
The purpose of this RECOMMENDED file is to describe properties of participants
such as age, sex, handedness, species and strain.
If this file exists, it MUST contain the column participant_id,
which MUST consist of sub-<label> values identifying one row for each participant,
followed by a list of optional columns describing participants.
Each participant MUST be described by one and only one row.
The RECOMMENDED species column SHOULD be a binomial species name from the
NCBI Taxonomy
(for examples homo sapiens, mus musculus, rattus norvegicus).
For backwards compatibility, if species is absent, the participant is assumed to be
homo sapiens.
Commonly used optional columns in participants.tsv files are age, sex,
handedness, strain, and strain_rrid. We RECOMMEND to make use
of these columns, and in case that you do use them, we RECOMMEND to use the
following values for them:
{{ MACROS___make_columns_table("modality_agnostic.Participants") }}
Throughout BIDS you can indicate missing values with n/a (for "not
available").
participants.tsv example:
participant_id age sex handedness group
sub-01 34 M right read
sub-02 12 F right write
sub-03 33 F n/a read
It is RECOMMENDED to accompany each participants.tsv file with a sidecar
participants.json file to describe the TSV column names and properties of their values (see also
the section on tabular files).
Such sidecar files are needed to interpret the data, especially so when
optional columns are defined beyond age, sex, handedness, species, strain,
and strain_rrid, such as group in this example, or when a different
age unit is needed (for example, gestational weeks).
If no units is provided for age, it will be assumed to be in years relative
to date of birth.
participants.json example:
{
"age": {
"Description": "age of the participant",
"Units": "years"
},
"sex": {
"Description": "sex of the participant as reported by the participant",
"Levels": {
"M": "male",
"F": "female"
}
},
"handedness": {
"Description": "handedness of the participant as reported by the participant",
"Levels": {
"left": "left",
"right": "right"
}
},
"group": {
"Description": "experimental group the participant belonged to",
"Levels": {
"read": "participants who read an inspirational text before the experiment",
"write": "participants who wrote an inspirational text before the experiment"
}
}
}Template:
samples.tsv
samples.json
The purpose of this file is to describe properties of samples, indicated by the sample entity.
This file is REQUIRED if sample-<label> is present in any filename within the dataset.
Each sample MUST be described by one and only one row.
{{ MACROS___make_columns_table("modality_agnostic.Samples") }}
samples.tsv example:
sample_id participant_id sample_type derived_from
sample-01 sub-01 tissue n/a
sample-02 sub-01 tissue sample-01
sample-03 sub-01 tissue sample-01
sample-04 sub-02 tissue n/a
sample-05 sub-02 tissue n/a
It is RECOMMENDED to accompany each samples.tsv file with a sidecar
samples.json file to describe the TSV column names and properties of their values
(see also the section on tabular files).
samples.json example:
{
"sample_type": {
"Description": "type of sample from ENCODE Biosample Type (https://www.encodeproject.org/profiles/biosample_type)",
},
"derived_from": {
"Description": "sample_id from which the sample is derived"
}
}Template:
phenotype/
<measurement_tool_name>.tsv
<measurement_tool_name>.json
Optional: Yes
If the dataset includes multiple sets of participant level measurements (for
example responses from multiple questionnaires) they can be split into
individual files separate from participants.tsv.
Each of the measurement files MUST be kept in a /phenotype directory placed
at the root of the BIDS dataset and MUST end with the .tsv extension.
File names SHOULD be chosen to reflect the contents of the file.
For example, the "Adult ADHD Clinical Diagnostic Scale" could be saved in a file
called /phenotype/acds_adult.tsv.
The files can include an arbitrary set of columns, but one of them MUST be
participant_id and the entries of that column MUST correspond to the subjects
in the BIDS dataset and participants.tsv file.
As with all other tabular data, the additional phenotypic information files MAY be accompanied by a JSON file describing the columns in detail (see Tabular files).
In addition to the column descriptions, the JSON file MAY contain the following fields:
{{ MACROS___make_metadata_table( { "MeasurementToolMetadata": "OPTIONAL", "Derivative": "OPTIONAL", } ) }}
As an example, consider the contents of a file called
phenotype/acds_adult.json:
{
"MeasurementToolMetadata": {
"Description": "Adult ADHD Clinical Diagnostic Scale V1.2",
"TermURL": "https://www.cognitiveatlas.org/task/id/trm_5586ff878155d"
},
"adhd_b": {
"Description": "B. CHILDHOOD ONSET OF ADHD (PRIOR TO AGE 7)",
"Levels": {
"1": "YES",
"2": "NO"
}
},
"adhd_c_dx": {
"Description": "As child met A, B, C, D, E and F diagnostic criteria",
"Levels": {
"1": "YES",
"2": "NO"
}
}
}Please note that in this example MeasurementToolMetadata includes information
about the questionnaire and adhd_b and adhd_c_dx correspond to individual
columns.
In addition to the keys available to describe columns in all tabular files
(LongName, Description, Levels, Units, and TermURL) the
participants.json file as well as phenotypic files can also include column
descriptions with a Derivative field that, when set to true, indicates that
values in the corresponding column is a transformation of values from other
columns (for example a summary score based on a subset of items in a
questionnaire).
Template:
sub-<label>/
[ses-<label>/]
sub-<label>[_ses-<label>]_scans.tsv
sub-<label>[_ses-<label>]_scans.json
Optional: Yes
The purpose of this file is to describe timing and other properties of each neural recording file within one session. In general, each of these files SHOULD be described by exactly one row.
For file formats that are based on several files of different extensions,
or a directory of files with different extensions (multi-file file formats),
only that file SHOULD be listed that would also be passed to analysis software for reading the data.
For example for BrainVision data (.vhdr, .vmrk, .eeg),
only the .vhdr SHOULD be listed;
for EEGLAB data (.set, .fdt),
only the .set file SHOULD be listed;
and for CTF data (.ds),
the whole .ds directory SHOULD be listed,
and not the individual files in that directory.
Some neural recordings consist of multiple parts,
that span several files,
but that share the same extension.
For example in entity-linked file collections,
commonly used for qMRI,
where recordings may be linked through entities such as echo and part
(using .nii or .nii.gz extensions).
For another example consider the case of large files in .fif format that are linked through the split entity
(see Split files).
Such recordings MUST be documented with one row per file
(unlike the case of multi-file file formats described above).
{{ MACROS___make_columns_table("modality_agnostic.Scans") }}
Additional fields can include external behavioral measures relevant to the
scan.
For example vigilance questionnaire score administered after a resting
state scan.
All such included additional fields SHOULD be documented in an accompanying
_scans.json file that describes these fields in detail
(see Tabular files).
Example _scans.tsv:
filename acq_time
func/sub-control01_task-nback_bold.nii.gz 1877-06-15T13:45:30
func/sub-control01_task-motor_bold.nii.gz 1877-06-15T13:55:33
meg/sub-control01_task-rest_split-01_meg.nii.gz 1877-06-15T12:15:27
meg/sub-control01_task-rest_split-02_meg.nii.gz 1877-06-15T12:15:27
Template:
sub-<label>/
sub-<label>_sessions.tsv
Optional: Yes
In case of multiple sessions there is an option of adding additional
sessions.tsv files describing variables changing between sessions.
In such case one file per participant SHOULD be added.
These files MUST include a session_id column and describe each session by one and only one row.
Column names in sessions.tsv files MUST be different from group level participant key column names in the
participants.tsv file.
{{ MACROS___make_columns_table("modality_agnostic.Sessions") }}
_sessions.tsv example:
session_id acq_time systolic_blood_pressure
ses-predrug 2009-06-15T13:45:30 120
ses-postdrug 2009-06-16T13:45:30 100
ses-followup 2009-06-17T13:45:30 110
Template: code/*
Source code of scripts that were used to prepare the dataset MAY be stored here. Examples include anonymization or defacing of the data, or the conversion from the format of the source data to the BIDS format (see source vs. raw vs. derived data). Extra care should be taken to avoid including original IDs or any identifiable information with the source code. There are no limitations or recommendations on the language and/or code organization of these scripts at the moment.