Glossary

B0FieldIdentifier: A sidecar field that names a fieldmap acquisition; the runs it corrects name it in their B0FieldSource. The newer way to link fieldmaps and runs. More
BIDS: The Brain Imaging Data Structure, a standard for naming and describing neuroimaging and electrophysiology data in folders, files, JSON sidecars and tables. More
BIDS preview: The third view of the panel beside the Converter's table, which lists every file a conversion will write and predicts the content of each. More
BIDS URI: A reference to a file inside a dataset written as bids::sub-01/func/..., used by IntendedFor and similar fields.
classifier: The part of the scan that decides what each MRI series is, from its acquisition parameters, the series name and the series around it. More
companion file: A file that belongs with a recording but is not its data, such as events.tsv, channels.tsv or a physiological recording.
confidence: How sure the classifier is of the name it proposed for a series, from 0 to 1. Rows below the threshold are marked to check.
datatype: The folder a recording lands in inside a session, such as anat, func, dwi, fmap, eeg, meg, pet, mrs or beh. More
deep checks: A slower validation that also reads the image headers and file contents, and finds a header that disagrees with its sidecar.
defacing: Removing the face from an anatomical image so the participant cannot be recognised from a rendering of it. More
derivatives: The folder of a dataset for data computed from the raw data, such as skull-stripped images or quality-check results.
DICOM: The file format scanners write: one file per slice or frame, each with a header describing the acquisition and the patient.
empty-room recording: An MEG recording made with nobody in the scanner, to measure the noise of the room and the sensors.
entity: A key-value pair in a BIDS file name, such as sub-001, ses-01, task-rest or run-1. The standard says which entities a file may have and in which order. More
fieldmap: An acquisition that measures distortions of the magnetic field, used to correct the functional and diffusion images taken in the same session. More
finding: One thing validation reports about a file: an error, which breaks the standard, or a warning, which is worth fixing.
index: An entity whose value is a number, such as run or echo.
inheritance: The BIDS rule that a sidecar higher in the folder tree applies to every matching file below it, unless a closer sidecar says otherwise. More
IntendedFor: A fieldmap's sidecar field listing the runs it corrects. More
label: An entity whose value is a word made of letters and digits, such as task-rest or acq-highres.
modality: How data was acquired: MRI, PET, EEG, MEG. Not the same as the datatype (the folder) or the suffix (what the recording is). More
NIfTI: The image format BIDS uses for MRI and PET, one file per series (.nii or .nii.gz), with the voxel sizes and orientation in its header.
participants.tsv: The dataset's table of participants, one row per subject, with columns such as age, sex and handedness, described in participants.json.
physiological recording: A recording taken alongside another one, such as heart rate, breathing or a trigger during an MRI run, stored as _physio.tsv.gz with a sidecar.
placeholder: The value BIDS Manager writes into a field the standard asks for and no file answered, so the field is easy to find and fill: TODO, or n/a where the field accepts it. More
project: A BIDS dataset folder that BIDS Manager keeps a history in, in its .bidsmgr/ folder, so scans and edits can be resumed and undone. More
raw folder: The folder of recordings as they came from the scanner or the recording system, before conversion. BIDS Manager reads it and never writes into it.
requirement level: Whether the standard calls a field required, recommended or optional for a given file. More
residual: A secondary file dcm2niix writes beside the real image of a series, such as a single-volume duplicate. Skipped by default.
scan: Reading a raw folder and listing what is in it, one row per recording, without converting anything. More
scan rules: Your own rules applied at every scan, to leave out series by name or to give your own names to series.
scan table: The table a scan produces: one row per recording found in the raw folder, with its properties and proposed BIDS name, and every edit made to it. The Converter shows it in the Table view; the file is inventory.tsv. A project can hold several. More
scans table: The _scans.tsv file of a session (or subject) that lists each recording with its acquisition time.
schema: The machine-readable form of the BIDS standard, from which BIDS Manager reads which names, entities and fields are allowed.
series: One acquisition on an MRI or PET scanner, such as a T1w or a BOLD run: a set of DICOM files sharing a series identifier.
session: One visit of a participant, written as the ses entity and a ses- folder. A dataset where everyone came once may have no sessions.
sidecar: A JSON file beside a data file that holds its metadata, named like the data file with the extension .json.
skull stripping: Keeping only the brain of an anatomical image. The result is a derivative, not raw data.
sourcedata: The folder of a dataset for the data before conversion, such as the DICOM files. Optional, and not to be shared when it holds identifiers.
subject: One participant of a study, written as the sub entity and a sub- folder.
suffix: The last part of a BIDS file name before the extension, saying what the recording is, such as T1w, bold, dwi, eeg or physio. More
TODO: The placeholder value BIDS Manager writes into a field the standard asks for and no file answered. More
validation: Checking a dataset against the BIDS standard. BIDS Manager validates after each conversion in the GUI (a setting, on by default) and on request in the Editor. More