This document provides an intuitive introduction and guide to the NIDASH Data Model for neuroimaging data sharing. NIDASH defines a core vocabulary that extends the PROV Data Model for provenance with terms that capture information about neuroimaging research, from data acquisition to analysis and results. This primer explains the fundamental NIDASH concepts and provides examples of its use. The primer is intended as a starting point for neuroimaging scientists or developers interested in using or creating apps with NIDM.

Overview

This section provides an overview of the NIDASH Family of Documents and suggestions to the neuroimaging community for implementing these standards to support data sharing activities, as well as in reporting issues or comments.

NIDASH Family of Documents

This document is part of the NIDASH Family of Documents, a set of documents defining various aspects of neuroimaging research that are necessary to achieve the vision of inter-operable interchange of information in heterogeneous environments such as the Web, research consortia, and laboratories. A list of current NIDASH documents and the latest revision of this specification can be found in the NIDM specification index. These documents are listed below.

Implementations Encouraged

The NIDASH Working Group encourages implementation of the specifications overviewed in this document. Work on this document by the NIDASH Working Group is ongoing, errors and suggestions may be reported in the issue tracker and these may be addressed in future revisions.

Please Send Comments

This document was published by the NIDASH Working Group as a Working Draft. If you wish to make comments regarding this document, please report using the NIDM issue tracker. You can also ask questions at Neurostars Q&A. All comments are welcome.

Introduction

This primer document provides ...

Overview of the NIDM Experiment Component

This section provides an explanation of ...

NIDM-experiment UML chart

NIDM-Experiment: Types and relations

Investigation

Table 3:NIDM-Experiment Investigation Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:InvestigationProcess prov:Activity nidm:InvestigationProcess
nidm:ModelSpecification nidm:ModelSpecification
nidm:InvestigationCollection prov:Entity nidm:InvestigationCollection
nidm:Model nidm:Model
nidm:Group nidm:Group
nidm:Contrast nidm:Contrast
nidm:Task nidm:Task
nidm:Condition nidm:Condition

nidm:InvestigationProcess

nidm:ModelSpecification

nidm:InvestigationCollection

nidm:Model

nidm:Model:

nidm:Model is a prov:Entity.

nidm:Group

nidm:Group:

nidm:Group is a prov:Entity.

nidm:Contrast

nidm:Contrast:

nidm:Contrast is a prov:Entity.

nidm:Task

nidm:Task:

nidm:Task is a prov:Entity.

nidm:Condition

nidm:Condition:

nidm:Condition is a prov:Entity.

Session

Table 4:NIDM-Experiment Session Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:SessionAcquisition prov:Activity nidm:SessionAcquisition
nidm:DataCollection prov:Entity nidm:DataCollection

nidm:SessionAcquisition

nidm:DataCollection

Serie

Table 5:NIDM-Experiment Serie Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:AnatomyImagingAcquisition prov:Activity nidm:AnatomyImagingAcquisition
nidm:TaskBasedImagingAcquisition nidm:TaskBasedImagingAcquisition
nidm:AnatomicalScan prov:Entity nidm:AnatomicalScan
nidm:FunctionalScan nidm:FunctionalScan
nidm:BehaviorAndConditionOnsets nidm:BehaviorAndConditionOnsets
nidm:MRScanner prov:Agent nidm:MRScanner
nidm:PresentationSoftware nidm:PresentationSoftware

nidm:AnatomyImagingAcquisition

nidm:TaskBasedImagingAcquisition

nidm:AnatomicalScan

nidm:FunctionalScan

nidm:BehaviorAndConditionOnsets

nidm:MRScanner

nidm:MRScanner:

nidm:MRScanner is a prov:Agent.

nidm:PresentationSoftware

Project

Table 6:NIDM-Experiment Project Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Project Object' prov:Entity nidm:ProjectObject

nidm:'Project Object'

nidm:'Project Object': A project object is an entity that represents administrative information about one or more studies.

nidm:'Project Object' is a prov:Entity.

A nidm:'Project Object' has attributes:

Study

Table 7:NIDM-Experiment Study Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Study Object' prov:Entity nidm:StudyObject

nidm:'Study Object'

nidm:'Study Object': A study object is an entity that represents one or more acquisitions that take place during the same temporal epoch.

nidm:'Study Object' is a prov:Entity.

A nidm:'Study Object' has attributes:

Acquisition

Table 8:NIDM-Experiment Acquisition Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Acquisition Object' prov:Entity nidm:AcquisitionObject

nidm:'Acquisition Object'

nidm:'Acquisition Object': An acquisition object is an entity that represents a single stream of data, where multiple acquisitions in the same study take place simultaneously. For example, fMRI and physiological recordings.

nidm:'Acquisition Object' is a prov:Entity and has the following children: nidm:'Demographics Acquisition Object', nidm:'MRI Acquisition Object'.

A nidm:'Acquisition Object' has attributes:

Other

Table 9:NIDM-Experiment Other Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Baseline Protocol' prov:Entity nidm:BaselineProtocol
nidm:'Demographics Acquisition Object' nidm:DemographicsAcquisitionObject
nidm:'MRI Acquisition Object' nidm:MRIAcquisitionObject
nidm:'fMRI Design Type' nidm:NIDM_0000155

nidm:'Baseline Protocol'

nidm:'Baseline Protocol': A baseline protocol is a plan that represents the study design for a given project.

nidm:'Baseline Protocol' is a prov:Entity.

nidm:'Demographics Acquisition Object'

nidm:'Demographics Acquisition Object': A demographics acquisition object is an entity that represents the demographics information acquired from a person in the participant role.

nidm:'Demographics Acquisition Object' is a nidm:'Acquisition Object'.

A nidm:'Demographics Acquisition Object' has attributes:

nidm:'MRI Acquisition Object'

nidm:'MRI Acquisition Object': An MRI acquisition object represents a specific series or scan during an MRI study.

nidm:'MRI Acquisition Object' is a nidm:'Acquisition Object'.

A nidm:'MRI Acquisition Object' has attributes:

nidm:'fMRI Design Type'

nidm:'fMRI Design Type': The type of stimulus presentation used in the data acquisition, one of block-based design, event-related design or mixed design.

nidm:'fMRI Design Type' is a prov:Entity.

Examples of nidm:'fMRI Design Type' includes

Summary

TBD

Additional Information

TBD

Acknowledgements

This document has been produced by the NIDASH Working Group, and its contents reflect extensive discussion within the Working Group as a whole.

Members of the NIDASH Working Group at the time of publication of this document were: