Vocabulary

Imaging modality, as a DICOM Modality code (MR, CT, PT, ...) or a local id where DICOM has none (DOT).

Image contrast. MR sequences use BIDS suffixes (T1w, T2w, FLAIR, dwi, ...). CT phases, stains and ultrasound modes have their own terms. Counts mean subjects that have at least this contrast.

The exact set of contrasts a subject has, joined with `+` in alphabetical order, e.g. `FLAIR+T1w+T2w`. Each subject belongs to exactly one set. This is what allows exact answers to "how many subjects have both T1w and FLAIR".

Radiotracer used for PET or SPECT.

Body region or organ that was imaged. Mapped to UBERON.

Disease, finding or group (including healthy controls). Mapped to MONDO, or to HPO for findings. A subject can have several conditions.

Sex as reported by the dataset. Values follow the BIDS participants.tsv levels.

Age bin in completed years. `60-69` covers everyone aged 60 up to their 70th birthday, `90+` everyone aged 90 or older. Decimal bounds are allowed for children, e.g. `0-0.5`.

Scanner manufacturer. Raw DICOM Manufacturer strings are listed as synonyms.

MR field strength in tesla, e.g. `1.5`, `3`, `7`.

Country of the acquisition site, as an ISO 3166-1 alpha-2 code (US, DE, CN, ...).

Official data split.

Projection or view for radiographs and mammograms.

Distinct people (or animals). Use this whenever the source reports patients, participants or cases that are people.

Imaging sessions, exams or visits. A longitudinal subject has several.

3D volumes or series, e.g. one T1w volume.

2D images, e.g. radiographs, fundus photos or ultrasound frames.

Whole-slide images in digital pathology.

Magnetic resonance imaging

Computed tomography

Positron emission tomography

Nuclear medicine including SPECT

Projection radiography (DICOM DX). Filtering for it also finds computed radiography.

Computed radiography with imaging plates

Slide microscopy, including whole-slide images

Ophthalmic photography

Ophthalmic optical coherence tomography

External camera photography, e.g. dermatology

Near-infrared light imaging of tissue absorption, e.g. brain hemodynamics. DICOM has no Modality code for it.

Gadolinium-enhanced T1w. BIDS writes this as a T1w with the ce- entity.

Fluid-attenuated inversion recovery

Short tau inversion recovery (fat-suppressed)

Inversion-recovery T1-weighted image with the inversion time set to null white matter, giving high contrast between deep gray matter nuclei such as the thalamic nuclei

Chemical-shift imaging that gives in-phase, opposed-phase, fat and water images from one acquisition. BIDS has no suffix for it.

Susceptibility-weighted imaging built from magnitude and phase of a gradient echo. BIDS has no suffix for it.

Multi-echo gradient-echo magnitude and phase images, e.g. for QSM or R2* mapping

Multi-echo spin-echo images, e.g. for T2 mapping

Quantitative T2* relaxation time map

Paired images acquired with and without a magnetization transfer pulse (mt-on, mt-off), used for magnetization transfer ratio maps.

Gradient echo images with single- and dual-frequency magnetization transfer saturation, used for myelin-sensitive ihMT ratio maps.

Spoiled gradient echo and/or balanced SSFP images at several flip angles for T1, T2 or myelin water mapping.

Apparent diffusion coefficient map

Dynamic contrast-enhanced MRI

Dynamic susceptibility contrast MRI

Cardiac cine imaging, e.g. balanced SSFP

Cine imaging with a saturation grid or lines laid on the myocardium to track its deformation

Displacement encoding with stimulated echoes, cine phase images that encode myocardial displacement

Proton or other nuclear magnetic resonance spectra from a single voxel (SVS, e.g. PRESS, STEAM, MEGA-PRESS) or a spectroscopic imaging grid (MRSI). BIDS stores these with the svs and mrsi suffixes.

Contrast-enhanced CT where the phase is not specified

Immunofluorescence imaging of many protein markers on one tissue section, e.g. by cyclic staining rounds

Velocity-encoded phase-contrast imaging of blood flow

Amyloid tracer

Amyloid tracer

Amyloid tracer

Amyloid tracer

Amyloid tracer

Tau tracer

Tau tracer

Amyloid tracer

Tau tracer

Tau tracer

Tau tracer

Prostate-specific membrane antigen tracers

SPECT dopamine transporter tracer

PET tracer for the vesicular monoamine transporter type 2 (VMAT2)

TSPO tracer for microglial activation

TSPO tracer for glial and immune cell activation

Cerebral blood flow tracer

Amino acid tracer

No known condition of interest

No MONDO term exists. Closest HPO term is the broader Cognitive impairment (HP:0100543).

Focal dystonia of the arm or hand. Closest MONDO term is focal hand dystonia (MONDO:0000482).

Also used for corticobasal syndrome, the clinical presentation, when the pathology is not confirmed.

Stroke of any or unspecified type. Use ischemic_stroke when the dataset is limited to ischemic stroke.

Impaired production or comprehension of language, a finding often caused by stroke.

Loss of part of the visual field, such as hemianopia after a lesion of the visual pathway.

Reduced, absent or distorted sense of smell (hyposmia, anosmia, parosmia).

A stimulus in one sense or concept reliably triggers an additional experience, such as letters evoking colours.

Focal dilatation of a cerebral artery, saccular or fusiform. No MONDO term covers both shapes; the closest is intracranial berry aneurysm (MONDO:0016483), which covers the saccular type only.

Small hemosiderin deposits seen as hypointense foci on T2*-weighted or susceptibility-weighted MRI. No MONDO or HPO term exists.

ARIA-E (edema, effusion) and ARIA-H (microbleeds, superficial siderosis), mostly seen under anti-amyloid antibody treatment. No MONDO or HPO term exists.

Fluid-filled spaces around small brain vessels that are large enough to be seen on MRI. A marker of cerebral small vessel disease.

Small fluid-filled cavities in deep grey or white matter, the imaging trace of a past small subcortical infarct or hemorrhage. A marker of cerebral small vessel disease. HP:0032325 (Lacunar stroke) names the clinical event, not the imaging finding, so no mapping is given.

Disease of the small arteries, arterioles, capillaries and venules of the brain, seen on MRI as white matter hyperintensities, lacunes, microbleeds and enlarged perivascular spaces. MONDO has only monogenic forms (brain small vessel disease 1 to 6, HTRA1-related), so no mapping is given.

Brain injury from reduced oxygen supply and blood flow, most often around birth in term neonates. MONDO and HPO have no matching term, so the NCIt code is given.

Tissue necrosis caused by radiotherapy, e.g. temporal lobe necrosis after radiotherapy for nasopharyngeal carcinoma. MONDO and HPO have no matching term, so the NCIt code is given.

Bleeding from the germinal matrix of the preterm brain, with or without extension into the ventricles, usually graded I to IV after Papile.

Birth before 37 completed weeks of gestation.

Attenuated or brief psychotic symptoms, or genetic risk with functional decline, that meet psychosis-risk syndrome criteria without a psychotic disorder. No MONDO or HPO term exists.

Persistent difficulty learning and using language in childhood without a known biomedical cause. MONDO lists the synonym only under familial developmental dysphasia (MONDO:0010821), a narrower FOXP2-related form.

Exposure to abuse or interpersonal violence in childhood. An exposure, not a diagnosis. No MONDO or HPO term exists.

Avoidant, dependent or obsessive-compulsive personality disorder (DSM cluster C). No MONDO term exists for the cluster.

DSM-5 childhood disorder of severe chronic irritability with temper outbursts. No MONDO term exists.

No MONDO term exists. Mapped to the broader HPO term Addictive non-substance behaviors.

Malignant neoplasm of any type or site

Astrocytoma other than glioblastoma, including IDH-mutant astrocytoma of grade 2 and 3.

High-grade glioma in children, including diffuse midline glioma and diffuse intrinsic pontine glioma (DIPG).

Benign nerve sheath tumor of the vestibular nerve. MONDO places it under peripheral nervous system neoplasms, not under brain neoplasms.

Any pancreatic tumour or cystic neoplasm, e.g. IPMN, neuroendocrine tumour or PDAC

Hernia of any kind, e.g. hiatus hernia seen on a chest radiograph

Image or study in which none of the dataset's target findings were reported. Not the same as a healthy control: other abnormalities may be present.

Enlarged right ventricle or reduced right ventricular ejection fraction. No single upstream term; closest HPO terms are Abnormal right ventricle morphology (HP:0001707) and Abnormal right ventricular function (HP:0033118).

Partial or complete tear of the anterior cruciate ligament of the knee. No human term in MONDO or HPO.

Acquired loss of part or all of an arm or hand through surgery or trauma, e.g. transradial or transhumeral amputation. MONDO and HPO only have terms for congenital or spontaneous limb loss.

Learning disability with impaired written language, such as spelling, handwriting or composition. Includes isolated spelling deficits without a reading deficit.

Perception of sound without an external source

Person living with a transplanted liver, usually under long-term immunosuppression. A post-procedure state, not a disease, so MONDO and HPO have no term for it.

Height well below the norm for age and sex, e.g. a height-for-age z-score below -2 (stunting).

Maker of the Artemis fusion biopsy system

Maker of the Swoop 64 mT portable MRI system

Bounding boxes or points

e.g. brain age or clinical scores

Landmarks or paired scans for alignment

Images paired with free-text reports

Raw k-space or sinogram data

Paired modalities for translation

Repeated scans of the same subjects

Mostly healthy subjects for reference ranges

NIfTI files in the Brain Imaging Data Structure

Aperio whole-slide format

Hamamatsu NanoZoomer whole-slide format

Download without an account

Create an account and accept terms online

Sign a data use agreement, often reviewed by the provider

Identity check and ethics training (e.g. CITI) plus an agreement

A research proposal is reviewed and approved

Access costs money

Ask the authors or the data holder. No published process or terms, and access is at their discretion

The data are not available outside the institution or study that holds them

Mammography

Mammography