Glossary

Nipoppy terms

Manifest file

The manifest file at <DATASET_ROOT>/manifest.tsv contains ground truth information about the participants and visits/sessions available for a dataset.

There must be only one row per unique participant/visit combination.

Global config file

The global configuration file at <DATASET_ROOT>/global_config.json allows for high-level configuration of the Nipoppy software tools (e.g., user-provided paths needed to run pipelines, container runtime arguments).

Tracker config file

The tracker config file lists the expected output files for a given pipeline. Nipoppy checks the presence of these files to mark successful completion of the pipeline. Note that the default tracker configuration files are somewhat minimal and do not check all possible output files generated these pipelines.

Curation status file

Note

In older versions of nipoppy, this file was called the “doughnut file”.

A tabular file at <DATASET_ROOT>/sourcedata/imaging/curation_status.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is automatically generated/updated by Nipoppy workflows, though it can safely be deleted manually (if e.g. it contains outdated information), in which case it will be regenerated automatically when needed.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 curation status file can also be created/updated with the nipoppy track-curation command if needed.

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

Processing status file

Note

In older versions of nipoppy, this file was called the “bagel file”.

A tabular file at <DATASET_ROOT>/derivatives/processing_status.tsv that indicates the completion status of processing pipelines of interest at the participant-session level. The processing status file is created by the nipoppy track command and can be used as input to the Neurobagel CLI.

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.