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common_principles.yaml
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common_principles.yaml
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---
# This file describes terms defined in the specification as "Common Principles".
# WARNING: The terms are presented here in alphabetical order!
# The order in which these terms are presented in the specification is defined in `rules/common_principles.yaml`,
# rather than this file (`objects/common_principles.yaml`).
data_acquisition:
display_name: Data acquisition
description: |
A continuous uninterrupted block of time during which a brain scanning instrument was acquiring data according to
particular scanning sequence/protocol.
data_type:
display_name: Data type
description: |
A functional group of different types of data.
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.
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)
12. `nirs` (near infrared spectroscopy)
13. `motion` (motion)
14. `mrs` (magnetic resonance spectroscopy)
dataset:
display_name: Dataset
description: |
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.
deprecated:
display_name: DEPRECATED
description: |
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.
event:
display_name: Event
description: |
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").
extension:
display_name: File extension
description: |
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.
index:
display_name: index
description: |
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.
label:
display_name: label
description: |
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](SPEC_ROOT/common-principles.md#case-collision-intolerance)).
modality:
display_name: Modality
description: |
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**.
run:
display_name: Run
description: |
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](SPEC_ROOT/modality-specific-files/magnetic-resonance-imaging-data.md)
or [MEG](SPEC_ROOT/modality-specific-files/magnetoencephalography.md),
if a subject leaves the scanner, the acquisition must be restarted.
For some types of [PET](SPEC_ROOT/modality-specific-files/positron-emission-tomography.md) acquisitions,
a subject may leave and re-enter the scanner without interrupting the scan.
sample:
display_name: Sample
description: |
A sample pertaining to a subject such as tissue, primary cell or cell-free sample.
Sample labels MUST be unique within a subject and it is RECOMMENDED
that they be unique throughout the dataset.
session:
display_name: Session
description: |
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](SPEC_ROOT/modality-specific-files/positron-emission-tomography.md) context,
a session may also indicate a group of related scans, taken in one or more visits.
suffix:
display_name: suffix
description: |
An alphanumeric string that forms part of a filename, located after all
[entities](SPEC_ROOT/common-principles.md#entities) and
following a final `_`, right before the **file extension**;
for example, it is `eeg` in `sub-05_task-matchingpennies_eeg.vhdr`.
subject:
display_name: Subject
description: |
A person or animal participating in the study.
Used interchangeably with term **Participant**.
task:
display_name: Task
description: |
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.