Glossary

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Nipoppy is undergoing a major refactor to move from scripts to a command-line interface (CLI) and Python API. The new documentation website (work in progress) can be found at https://nipoppy.readthedocs.io/.

If you are using the (soon-to-be legacy) scripts from Nipoppy 0.1.0, this is still the correct place to be. But we encourage you to check out the new website!

Glossary

This page lists some definitions for important/recurring terms used in the Nipoppy framework.

participant_id

Appears in: manifest.csv, doughnut.csv

Unique identifier for the participant (i.e., subject ID), as provided by the study.

datatype

Appears in: manifest.csv

A BIDS-compliant "data type" value (see the BIDS specification website for a comprehensive list). The most common data types for magnetic resonance imaging (MRI) data are "anat", "func", and "dwi".

visit

Appears in: manifest.csv

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

See also: session vs visit

session

Appears in: manifest.csv, doughnut.csv

A BIDS-compliant session identifier. Consists of the "ses-" prefix followed by the session_id.

session vs visit

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

participant_dicom_dir

Appears in: doughnut.csv

The name of the directory in which the raw DICOM data (before the DICOM organization step) are found. Usually, this is the same as participant_id, but depending on the study it could be different.

dicom_id

Appears in: doughnut.csv

The participant_id, stripped of any non-alphanumerical character. For studies that do not use non-alphanumerical characters in their participant IDs, this is exactly the same as participant_id.

bids_id

Appears in: doughnut.csv

A BIDS-compliant participant identifier. Obtained by adding the "sub-" prefix to the dicom_id, which itself is derived from the participant_id. A participant's raw BIDS data and derived imaging data are stored in directories named after their bids_id.