Glossary

AMP

Automatic Mixed Precision — a training technique that combines 16- and 32-bit floating-point operations to speed up computation and reduce memory usage. See torch.amp.

BIDS

Brain Imaging Data Structure — a community standard for naming and organising neuroimaging files on disk (source).

BIDS derivative

A dataset derived from a raw BIDS dataset (e.g. example preprocessed images) that follows the BIDS derivatives convention.

CAPS

ClinicA Processed Data Structure — the output format of Clinica’s preprocessing pipelines, organised as a BIDS derivative (source).

data leakage

A flaw in the evaluation of a model where information from the test data leaks into training, leading to over-optimistic performance estimates. In neuroimaging, it typically happens when different sessions of the same participant are split across the training and test sets.

MAPS

Model Analysis and Processing Structure — the single directory in which ClinicaDL gathers all the outputs and hyperparameters of an experiment. See Section 3.2 of the User Guide.

NIfTI

Neuroimaging Informatics Technology Initiative - the standard format for storing volumetric data in neuroimaging. You will recognise these files with the extensions .nii or .nii.gz (compressed). Neuroimaging data must be stored in the NIfTI file format in a BIDS.

RAS+

A standard anatomical orientation convention for neuroimaging. The axes are respectively: left to Right, posterior to Anterior, and inferior to Superior (source).