Entities

This section compiles the entities (key-value pairs within filenames) described throughout this specification, and describes each.

A general introduction to entities is given in the section on filename structure.

The ordering of entities, and whether each is OPTIONAL, REQUIRED, or MUST NOT be specified for a given file type, is specified in the Entity Table.

sub

Full name: Subject

Format: sub-<label>

Definition: A person or animal participating in the study.

ses

Full name: Session

Format: ses-<label>

Definition: 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).

sample

Full name: Sample

Format: sample-<label>

Definition: A sample pertaining to a subject such as tissue, primary cell or cell-free sample. The sample-<label> entity 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.

task

Full name: Task

Format: task-<label>

Definition: A set of structured activities performed by the participant. Tasks are usually accompanied by stimuli and responses, and can greatly vary in complexity.

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.

While tasks may be repeated across multiple acquisitions, a given task may have different sets of stimuli (for example, randomized order) and participant responses across subjects, sessions, and runs.

The task-<label> MUST be consistent across subjects and sessions.

Files with the task-<label> entity SHOULD have an associated events file, as well as certain metadata fields in the associated JSON file.

For the purpose of this specification we consider the so-called "resting state" a task, although events files are not expected for resting state data. Additionally, a common convention in the specification is to include the word "rest" in the task label for resting state files (for example, task-rest).

tracksys

Full name: Tracking system

Format: tracksys-<label>

Definition: The tracksys-<label> entity can be used as a key-value pair to label _motion.tsv and _motion.json files. It can also be used to label _channel.tsv or _events.tsv files when they belong to a specific tracking system.

This entity corresponds to the "TrackingSystemName" metadata field in a *_motion.json file. tracksys-<label> entity is a concise string whereas "TrackingSystemName" may be longer and more human readable.

acq

Full name: Acquisition

Format: acq-<label>

Definition: The acq-<label> entity corresponds to a custom label the user MAY use to distinguish a different set of parameters used for acquiring the same modality.

For example, this should be used when a study includes two T1w images - one full brain low resolution and one restricted field of view but high resolution. In such case two files could have the following names: sub-01_acq-highres_T1w.nii.gz and sub-01_acq-lowres_T1w.nii.gz; however, the user is free to choose any other label than highres and lowres as long as they are consistent across subjects and sessions.

In case different sequences are used to record the same modality (for example, RARE and FLASH for T1w) this field can also be used to make that distinction. The level of detail at which the distinction is made (for example, just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled) remains at the discretion of the researcher.

ce

Full name: Contrast Enhancing Agent

Format: ce-<label>

Definition: The ce-<label> entity can be used to distinguish sequences using different contrast enhanced images. The label is the name of the contrast agent.

This entity represents the "ContrastBolusIngredient" metadata field. Therefore, if the ce-<label> entity is present in a filename, "ContrastBolusIngredient" MAY also be added in the JSON file, with the same label.

trc

Full name: Tracer

Format: trc-<label>

Definition: The trc-<label> entity can be used to distinguish sequences using different tracers.

This entity represents the "TracerName" metadata field. Therefore, if the trc-<label> entity is present in a filename, "TracerName" MUST be defined in the associated metadata. Please note that the <label> does not need to match the actual value of the field.

stain

Full name: Stain

Format: stain-<label>

Definition: The stain-<label> key/pair values can be used to distinguish image files from the same sample using different stains or antibodies for contrast enhancement.

This entity represents the "SampleStaining" metadata field. Therefore, if the stain-<label> entity is present in a filename, "SampleStaining" SHOULD be defined in the associated metadata, although the label may be different.

Descriptions of antibodies SHOULD also be indicated in the "SamplePrimaryAntibodies" and/or "SampleSecondaryAntibodies" metadata fields, as appropriate.

rec

Full name: Reconstruction

Format: rec-<label>

Definition: The rec-<label> entity can be used to distinguish different reconstruction algorithms (for example, MoCo for the ones using motion correction).

dir

Full name: Phase-Encoding Direction

Format: dir-<label>

Definition: The dir-<label> entity can be set to an arbitrary alphanumeric label (for example, dir-LR or dir-AP) to distinguish different phase-encoding directions.

This entity represents the "PhaseEncodingDirection" metadata field. Therefore, if the dir-<label> entity is present in a filename, "PhaseEncodingDirection" MUST be defined in the associated metadata. Please note that the <label> does not need to match the actual value of the field.

run

Full name: Run

Format: run-<index>

Definition: The run-<index> entity is used to distinguish separate data acquisitions with the same acquisition parameters and (other) entities.

If several data acquisitions (for example, MRI scans or EEG recordings) with the same acquisition parameters are acquired in the same session, they MUST be indexed with the run-<index> entity: _run-1, _run-2, _run-3, and so on (only nonnegative integers are allowed as run indices).

If different entities apply, such as a different session indicated by [ses-<label>][../appendices/entities.md#ses), or different acquisition parameters indicated by acq-<label>, then run is not needed to distinguish the scans and MAY be omitted.

mod

Full name: Corresponding Modality

Format: mod-<label>

Definition: The mod-<label> entity corresponds to modality label for defacing masks, for example, T1w, inplaneT1, referenced by a defacemask image. For example, sub-01_mod-T1w_defacemask.nii.gz.

echo

Full name: Echo

Format: echo-<index>

Definition: If files belonging to an entity-linked file collection are acquired at different echo times, the echo-<index> entity MUST be used to distinguish individual files.

This entity represents the "EchoTime" metadata field. Therefore, if the echo-<index> entity is present in a filename, "EchoTime" MUST be defined in the associated metadata. Please note that the <index> denotes the number/index (in the form of a nonnegative integer), not the "EchoTime" value of the separate JSON file.

flip

Full name: Flip Angle

Format: flip-<index>

Definition: If files belonging to an entity-linked file collection are acquired at different flip angles, the _flip-<index> entity pair MUST be used to distinguish individual files.

This entity represents the "FlipAngle" metadata field. Therefore, if the flip-<index> entity is present in a filename, "FlipAngle" MUST be defined in the associated metadata. Please note that the <index> denotes the number/index (in the form of a nonnegative integer), not the "FlipAngle" value of the separate JSON file.

inv

Full name: Inversion Time

Format: inv-<index>

Definition: If files belonging to an entity-linked file collection are acquired at different inversion times, the inv-<index> entity MUST be used to distinguish individual files.

This entity represents the "InversionTime metadata field. Therefore, if the inv-<index> entity is present in a filename, "InversionTime" MUST be defined in the associated metadata. Please note that the <index> denotes the number/index (in the form of a nonnegative integer), not the "InversionTime" value of the separate JSON file.

mt

Full name: Magnetization Transfer

Format: mt-<label>

Allowed values: on, off

Definition: If files belonging to an entity-linked file collection are acquired at different magnetization transfer (MT) states, the _mt-<label> entity MUST be used to distinguish individual files.

This entity represents the "MTState" metadata field. Therefore, if the mt-<label> entity is present in a filename, "MTState" MUST be defined in the associated metadata. Allowed label values for this entity are on and off, for images acquired in presence and absence of an MT pulse, respectively.

part

Full name: Part

Format: part-<label>

Allowed values: mag, phase, real, imag

Definition: This entity is used to indicate which component of the complex representation of the MRI signal is represented in voxel data. The part-<label> entity is associated with the DICOM Tag 0008, 9208. Allowed label values for this entity are phase, mag, real and imag, which are typically used in part-mag/part-phase or part-real/part-imag pairs of files.

Phase images MAY be in radians or in arbitrary units. The sidecar JSON file MUST include the "Units" of the phase image. The possible options are "rad" or "arbitrary".

When there is only a magnitude image of a given type, the part entity MAY be omitted.

proc

Full name: Processed (on device)

Format: proc-<label>

Definition: The proc label is analogous to rec for MR and denotes a variant of a file that was a result of particular processing performed on the device.

This is useful for files produced in particular by Neuromag/Elekta/MEGIN's MaxFilter (for example, sss, tsss, trans, quat or mc), which some installations impose to be run on raw data because of active shielding software corrections before the MEG data can actually be exploited.

hemi

Full name: Hemisphere

Format: hemi-<label>

Allowed values: L, R

Definition: The hemi-<label> entity indicates which hemibrain is described by the file. Allowed label values for this entity are L and R, for the left and right hemibrains, respectively.

space

Full name: Space

Format: space-<label>

Definition: The space-<label> entity can be used to indicate the way in which electrode positions are interpreted (for EEG/MEG/iEEG data) or the spatial reference to which a file has been aligned (for MRI data). The <label> MUST be taken from one of the modality specific lists in the Coordinate Systems Appendix. For example, for iEEG data, the restricted keywords listed under iEEG Specific Coordinate Systems are acceptable for <label>.

For EEG/MEG/iEEG data, this entity can be applied to raw data, but for other data types, it is restricted to derivative data.

split

Full name: Split

Format: split-<index>

Definition: In the case of long data recordings that exceed a file size of 2Gb, .fif files are conventionally split into multiple parts. Each of these files has an internal pointer to the next file. This is important when renaming these split recordings to the BIDS convention.

Instead of a simple renaming, files should be read in and saved under their new names with dedicated tools like MNE-Python, which will ensure that not only the filenames, but also the internal file pointers, will be updated.

It is RECOMMENDED that .fif files with multiple parts use the split-<index> entity to indicate each part. If there are multiple parts of a recording and the optional scans.tsv is provided, all files MUST be listed separately in scans.tsv and the entries for the acq_time column in scans.tsv MUST all be identical, as described in Scans file.

recording

Full name: Recording

Format: recording-<label>

Definition: The recording-<label> entity can be used to distinguish continuous recording files.

This entity is commonly applied when continuous recordings have different sampling frequencies or start times. For example, physiological recordings with different sampling frequencies may be distinguished using labels like recording-100Hz and recording-500Hz.

chunk

Full name: Chunk

Format: chunk-<index>

Definition: The chunk-<index> key/value pair is used to distinguish between images of the same physical sample with different fields of view acquired in the same imaging experiment. This entity applies to collections of 2D images, 3D volumes or 4D volume series (for example, diffusion weighted images), and may be used to indicate different anatomical structures or regions of the same structure.

seg

Full name: Segmentation

Format: seg-<label>

Definition: The seg-<label> key/value pair corresponds to a custom label the user MAY use to distinguish different segmentations.