Glossary

Nipoppy terms

Doughnut file

A tabular file at <DATASET_ROOT>/sourcedata/imaging/doughnut.tsv that keeps track of the status of raw imaging data (i.e., whether it is available and/or has been reorganized and/or has been converted to BIDS). This file is automatically generated/updated by Nipoppy workflows, though it can safely be deleted manually (if e.g. it contains outdated information), in which case it will be regenerated automatically when needed. The doughnut file can also be created/updated with the nipoppy doughnut command if needed.

See here for more information about the columns in the file.

Session ID

A BIDS-compliant session identifier, without the "ses-" prefix.

Visit ID

An identifier for a data collection event, not restricted to imaging data.

Session IDs vs visit IDs

Nipoppy uses the term “session ID” for imaging data, following the convention established by BIDS. The term “visit ID”, on the other hand, is used to refer to any data collection event (not necessarily imaging-related), and is more common in clinical contexts. In most cases, session_id and visit_id will be identical (or session_ids will be a subset of visit_ids). However, having two descriptors becomes particularly useful when imaging and non-imaging assessments do not use the same naming conventions.

Neuroimaging/software terms

API

Application Programming Interface, how software interacts with other software.

BIDS

The Brain Imaging Data Structure, a community standard for organizing neuroimaging (and other) data. See the BIDS website for more information.

Boutiques

A flexible framework for describing and executing command-line tools. Boutiques is based on JSON descriptor files that list tool inputs, outputs, error codes, and more. JSON invocation files are used to specify runtime parameters. See the website for more information.

CLI

Command-line interface, i.e. software that can be run in the Terminal.

conda

An package and environment manager for Python (and other) environments. See the conda website for more information.

HPC

High-perfomance computing system, i.e. a compute cluster or supercomputer.

JSON

JavaScript Object Notation, a file format for storing and sharing data. JSON structures are combinations of objects (key-value pairs) and arrays (ordered lists). See the website for more information.

MRI

Magnetic resonance imaging, the most widely used neuroimaging modality.

PyPI

The Python Package Index, a repository of Python packages that are pip-installable.

venv

A Python built-in library for creating Python virtual environments. See the Python documentation for more information.