This document provides an intuitive introduction 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 presented in this document. Work on this document by the NIDASH Working Group is active and 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 and questions are welcome.

Introduction

This primer document provides information on the NIDM-Experiment specification. The goal of NIDM-Experiment is to provide terms that describe entities and activities for general scientific experiments with a focus on those specific to neuroscience. It is meant to work with NIDM-Workflow, which describes the processing and analysis of data and NIDM-Results that describes the results of workflows in the fMRI domain. It also provides terms used in PyNIDM, which can be used to annotate data.

Overview of the NIDM Experiment Component

This section provides an explanation of NIDM-Experiment, which is based on the W3C PROV ontology (Prov-O) that has as it basic elements Entities, Activities, and Agents. In constructing NIDM-Experiment, we have reused terms from existing terminologies and ontologies where possible. Terms that are reused from other ontologies are imported into the main NIDM-Experiment OWL file and can be found in the /imports directory. The most extensive modality coverage is for MRI, but there are also terms useful for electrophysiology experiments. Extensions to other modalities and expansions of existing modalities are ongoing and requests for the inclusion of terms for specific experiments are encouraged.

A MR imaging experiment modeled using NIDM-experiment.

NIDM-Experiment will be integrated into PyNIDM PyNIDMin the future. PyNIDM will include a mechanism by which users can search for terms necessary to annotate their specific dataset. It will also provide a mechanism by which users can request needed missing terms to be included in future NIDM-Experiment releases.

NIDM-Experiment: Types and relations

Project

Table 3:NIDM-Experiment Project Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Model Specification' prov:Activity nidm:ModelSpecification
nidm:'Project' nidm:Project
nidm:'Gender' prov:'Entity' nidm:Gender
nidm:'Group' nidm:Group
nidm:'Protocol' nidm:Protocol
nidm:'Specified Plan' nidm:SpecifiedPlan

nidm:'Model Specification'

nidm:'Model Specification': Model specification is an activity in which the model designer creates the model that describes an experiment.

nidm:'Model Specification' is a prov:Activity.

nidm:'Project'

nidm:'Project': A project is a coordinated set of activities designed to generate data acquisition objects, with the ultimate goal of discovery or hypothesis testing.

nidm:'Project' is a prov:Activity and has the following child: sio:'clinical trial'.

sio:'clinical trial'

nidm:'Gender'

nidm:'Gender': Gender is a social entity that identifies which of either male or female that a person identifies as, which may be different from biological sex.

nidm:'Gender' is a prov:'Entity'.

nidm:'Group'

nidm:'Group': A group is a collection of subjects or objects formed by the assignment of membership through the selection of one or more common characteristics.

nidm:'Group' is a prov:'Entity' and has the following children: sio:'control group', sio:'intervention group'.

nidm:'Protocol'

nidm:'Protocol': An protocol is a specified plan that contains information necessary to acquire the desired data during a session and the acquisition device parameters that are to be used in that acquisition.

nidm:'Protocol' is a nidm:'Specified Plan'.

nidm:'Specified Plan'

nidm:'Specified Plan': A specified plan is a plan that describes how the acquisition activity is to be carried out.

nidm:'Specified Plan' is a prov:'Entity' and has the following child: nidm:'Protocol'.

Acquisition

Table 4:NIDM-Experiment Acquisition Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Acquisition' prov:Activity nidm:Acquisition
nidm:'Image Data Reconstruction' nidm:ImageDataReconstruction
nidm:'Session' nidm:Session
nidm:'Task' nidm:Task
nidm:'Acquisition Method' prov:'Entity' nidm:AcquisitionMethod
nidm:'Acquisition Modality' nidm:AcquisitionModality
nidm:'Acquisition Object' nidm:AcquisitionObject
nidm:'Acquisition Object Quality' nidm:AcquisitionObjectQuality
nidm:'Behavioral Instrument' nidm:BehavioralInstrument
nidm:'Auxiliary File' nidm:AuxiliaryFile
nidm:'Auxiliary File Collection' nidm:AuxiliaryFileCollection
nidm:'Clinical Instrument' nidm:ClinicalInstrument
nidm:'Demographics Instrument' nidm:DemographicsInstrument
nidm:'Image Contrast Type' nidm:ImageContrastType
nidm:'Image Usage Type' nidm:ImageUsageType
nidm:'Informed Consent Instrument' nidm:InformedConsentInstrument
nidm:'Instrument Usage Type' nidm:InstrumentUsageType
nidm:'Performed Plan' nidm:PerformedPlan
nidm:'Processed Acquisition Object' nidm:ProcessedAcquisitionObject
nidm:'Raw Acquisition Object' nidm:RawAcquisitionObject
nidm:'Reconstructed Acquisition Object' nidm:ReconstructedAcquisitionObject
nidm:'Session Object' nidm:SessionObject
nidm:'Stimulus Presentation File' nidm:StimulusPresentationFile
nidm:'Stimulus Response File' nidm:StimulusResponseFile
nidm:'Presentation Software' prov:Agent nidm:PresentationSoftware

nidm:'Acquisition'

nidm:'Acquisition': An acquisition is an activty in which data about a subject is gathered.

nidm:'Acquisition' is a prov:Activity and has the following children: nidm:'Series', onli:instrument-based-assessment, onli:variable-assessment.

nidm:'Series'

nidm:'Series': A series is an activity in which data of a single type is acquired such that one acquisition takes place during the same temporal epoch.

nidm:'Series' is a nidm:'Acquisition'.

onli:instrument-based-assessment

onli:instrument-based-assessment: An INSTRUMENT-BASED ASSESSMENT is a SUBJECT DATA ACQUISITION that captures some required information concerning the subject and involves the integration of data from instruments: TEST(-INSTRUMENTS) and/or QUESTIONNAIRES. When the purpose of the patient's examination is the assessment of her/his behavior, the examiner uses questionnaires rather than tests to rate the level of intensity/severity of a behavioral trait. Then, the appropriate action is a BEHAVIOURAL INTERVIEW rather than a BEHAVIOURAL TEST which is less adapted. INSTRUMENT-BASED ASSESSMENTS are divided among TEST-BASED ASSESSMENTS and QUESTIONNAIRE-BASED ASSESSMENTS according to the kind of instrument which is administrated and therefore to the specific roles played by the subject and the healthcare professional in the assessment.

onli:instrument-based-assessment is a nidm:'Acquisition' and has the following children: onli:questionnaire-based-assessment, onli:test-based-assessment.

onli:questionnaire-based-assessment

onli:questionnaire-based-assessment: A Questionnaire-based assessment is an Instrument-based assessment which involves the integration of data from questionnaires. A questionnaire-based assessment involves sets of questions (items), carried out in a structured way (known as structured interview) or semi-structured way, to provide normative data. Interview-based measures and rating scales are designed to be completed by clinicians, subjects, parents, caregivers. The scoring of each item contributes to the measure of the explored domain (e.g. Depression). “A directed conversation with the subject aimed at eliciting information for psychiatric diagnosis, evaluation, treatment planning, etc. The interview may be conducted by a social worker or psychologist.” (Source: MSH/MH). (Concept: [CUI C0021819] Interview, Psychological, Semantic Type: Diagnostic Procedure). QUESTIONNAIRE-BASED ASSESSMENTS are divided among PSYCHOLOGICAL INTERVIEWS, BEHAVIOURAL INTERVIEWS, and NEUROCLINICAL INTERVIEWS according to the kind of questionnaire that is used.

onli:questionnaire-based-assessment is a prov:Activity and has the following children: onli:behavioural-interview, onli:neuroclinical-interview, onli:psychological-interview.

onli:behavioural-interview

onli:behavioural-interview: A behavioural interview is a Questionnaire-based assessment carried out during a behavioral examination.

onli:behavioural-interview is a prov:Activity.

onli:neuroclinical-interview

onli:neuroclinical-interview: A neuroclinical interview is a Questionnaire-based assessment carried out during a neurological examination.

onli:neuroclinical-interview is a prov:Activity.

onli:psychological-interview

onli:psychological-interview: A psychological interview is a Questionnaire-based assessment carried out during a psychological examination.

onli:psychological-interview is a prov:Activity.

onli:test-based-assessment

onli:test-based-assessment: A Test-based assessment is an Instrument-based assessment which involves the integration of data from tests. A Test-based assessment is conducted as a formal testing session to provide normative data. TEST-BASED ASSESSMENTS are divided among PSYCHOLOGICAL TESTS, BEHAVIOURAL TESTS and NEUROCLINICAL TESTS according to the kind of instrument that is used.

onli:test-based-assessment is a prov:Activity and has the following children: onli:behavioural-test, onli:neuroclinical-test, onli:psychological-test.

onli:behavioural-test

onli:neuroclinical-test

onli:neuroclinical-test: “The Neuroclinical examination (Neurological test) is the usual clinical approach to the study of the brain functions. The Neurological test includes extensive study of the brain's chief product-behavior. [...] The neurologist examines the strength, efficiency, reactivity, and appropriateness of the patient's responses to commands, questions, discrete stimulation of particular neural subsystems, and challenges to specific muscle groups and motor patterns. […] In the neurological examination of behavior, the clinician reviews behavior patterns generated by neuroanatomical subsystems, measuring patients' responses in relatively coarse graduations or nothing their absence" (Lezak et al., 2004).

onli:neuroclinical-test is a prov:Activity.

onli:psychological-test

onli:psychological-test: "[…] psychological assessment […] involves the intensive study of behavior by means of interviews and standardized scaled tests and questionnaires that provide relatively precise and sensitive indices of behaviour." (Lezak et al., 2004). PSYCHOLOGICAL TESTS are divided among NEUROPSYCHOLOGICAL TESTS and EXPERIMENTAL PSYCHOLOGY TESTS according to the kind of instrument that is used.

onli:psychological-test is a prov:Activity and has the following children: onli:experimental-psychology-test, onli:neuropsychological-test.

onli:experimental-psychology-test

onli:psychophysical-test

onli:neuropsychological-test

onli:neuropsychological-test: "Neuropsychological assessment is a method of examining the brain by studying its behavioural product. Since the subject matter of neuropsychological assessment is behavior, it relies on many of the same techniques, assumptions, and theories as does psychological assessment. The distinctive character of neuropsychological assessment lies in a conceptual frame of reference that takes brain function as its point of departure. Regardless of whether a behavioral study is undertaken for clinical or research purposes, it is neuropsychological so long as the questions that prompted it, the central issues, the findings, or the inferences drawn from them ultimately relate to brain function" (Lezak et al., 2004).

onli:neuropsychological-test is.

onli:variable-assessment

onli:variable-assessment: A variable assessment is an activity that results in a value assigned to a specific item on an assessment instrument question or test.

onli:variable-assessment is a nidm:'Acquisition' and has the following children: onli:coded-variable-assessment, onli:numerical-variable-assessment.

onli:coded-variable-assessment

onli:numerical-variable-assessment

nidm:'Image Data Reconstruction'

nidm:'Image Data Reconstruction': Image data reconstruction is an activity in which raw data is transformed into a matrix of values that represent the spatial distribution of intensity based on some image contrast type.

nidm:'Image Data Reconstruction' is a prov:Activity.

nidm:'Session'

nidm:'Session': A session is an activity during which data, potentially of different types, is acquired from a subject by an experimenter during a single unbroken time period.

nidm:'Session' is a prov:Activity.

nidm:'Task'

nidm:'Task': A task is an activity that is performed by a subject to elucidate some aspect of human behavior or underlying process.

nidm:'Task' is a prov:Activity.

nidm:'Acquisition Method'

nidm:'Acquisition Modality'

nidm:'Acquisition Object'

nidm:'Acquisition Object': An acquisition object is an entity that is gathered from a subject during an acquisition activity.

nidm:'Acquisition Object' is a prov:'Entity' and has the following children: nidm:'Processed Acquisition Object', nidm:'Raw Acquisition Object', nidm:'Reconstructed Acquisition Object', onli:assessment-instrument, onli:instrument-variable.

nidm:'Acquisition Object Quality'

nidm:'Acquisition Object Quality': An acquisition object quality is an quality that describes an essential feature of an object that is gathered from a subject during an acquisition activity.

nidm:'Acquisition Object Quality' is a prov:'Entity' and has the following children: nidm:'Acquisition Method', nidm:'Acquisition Modality', nidm:'Image Contrast Type', nidm:'Image Usage Type', nidm:'Instrument Usage Type', nidm:'fMRI Design Type', nidm:'k-space Traversal Scheme'.

nidm:'Behavioral Instrument'

nidm:'Behavioral Instrument': A behavioral instrument is a instrument usage type that signifies that the type of data to be collected by the instrument is behaviorally-related data.

nidm:'Behavioral Instrument' is a nidm:'Instrument Usage Type'.

nidm:'Auxiliary File'

nidm:'Auxiliary File': An auxiliary file is an information-bearing object that is either used to inform the execution of an experiment or that is generated during the execution of the experiment.

nidm:'Auxiliary File' is a prov:'Entity' and has the following children: nidm:'Stimulus Presentation File', nidm:'Stimulus Response File', nidm:'b-value File', nidm:'b-vector File'.

nidm:'Auxiliary File Collection'

nidm:'Auxiliary File Collection': An auxiliary file collection is a grouping that contains the URI's of files that are necessary for the execution of the experiment or the processing of the data.

nidm:'Auxiliary File Collection' is a prov:'Entity'.

nidm:'Clinical Instrument'

nidm:'Clinical Instrument': A clinical instrument is a instrument usage type that signifies that the type of data to be collected by the instrument is clinically-related data.

nidm:'Clinical Instrument' is a nidm:'Instrument Usage Type'.

nidm:'Demographics Instrument'

nidm:'Demographics Instrument': A demographics instrument is a instrument usage type that signifies that the type of data to be collected by the instrument is demographics-related data.

nidm:'Demographics Instrument' is a nidm:'Instrument Usage Type'.

nidm:'Image Contrast Type'

nidm:'Image Contrast Type': Image Contrast Type is an acquisition object quality that denotes the physical properties on which differences in image intensity, in an image, are based.

nidm:'Image Contrast Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Diffusion Weighted', nidm:'Flow Weighted', nidm:'Proton Density Weighted', nidm:'Susceptibility Weighted', nidm:'T1 Weighted', nidm:'T2 Weighted', nidm:'T2-Star Weighted'.

nidm:'Image Usage Type'

nidm:'Image Usage Type': Image Usage Type is an acquisition object quality that denotes to what purpose the acquired object will be employed.

nidm:'Image Usage Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Anatomical', nidm:'Diffusion Tensor', nidm:'Functional', nidm:'Quantitative Susceptibility Mapping', nidm:'Structural', nidm:'Susceptibility Weighted Imaging'.

nidm:'Instrument Usage Type'

nidm:'Instrument Usage Type': Instrument Usage Type is an acquisition object quality that denotes to what purpose the acquired object will be employed.

nidm:'Instrument Usage Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Behavioral Instrument', nidm:'Clinical Instrument', nidm:'Demographics Instrument', nidm:'Informed Consent Instrument'.

nidm:'Performed Plan'

nidm:'Performed Plan': A performed plan is a plan that is actually implemented during an acquisition activity.

nidm:'Performed Plan' is a prov:'Entity'.

nidm:'Processed Acquisition Object'

nidm:'Processed Acquisition Object': A processeded acquisition object is an acquisition object that has undergone an image reconstruction activity resulting in a matrix of values that when viewed form an image.

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

nidm:'Raw Acquisition Object'

nidm:'Raw Acquisition Object': A raw acquisition object is an acquisition object that has not yet undergone any further processing steps such asthe image reconstruction process.

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

nidm:'Reconstructed Acquisition Object'

nidm:'Reconstructed Acquisition Object': A reconstructed acquisition object is an acquisition object that has undergone an image reconstruction activity resulting in a matrix of values that when viewed form an image.

nidm:'Reconstructed Acquisition Object' is a nidm:'Acquisition Object' and has the following child: dctype:Image.

nidm:'Session Object'

nidm:'Session Object': A session object is an entity that represents one or more acquisitions that take place during the same temporal epoch (session).

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

A nidm:'Session Object' has attributes:

nidm:'Stimulus Presentation File'

nidm:'Stimulus Presentation File': A stimulus presentation file is an auxiliary files that contains the presentation timing and/or location of the experimental stimulus (e.g., words, pictures) that are shown to the subject in a task-based assessment activity.

nidm:'Stimulus Presentation File' is a nidm:'Auxiliary File'.

nidm:'Stimulus Response File'

nidm:'Stimulus Response File': A stimulus response file is an auxiliary file that contains the recorded response of the subject to an experimental stimulus the course of a task-based assessment activity.

nidm:'Stimulus Response File' is a nidm:'Auxiliary File'.

nidm:'Presentation Software'

nidm:'Presentation Software': Presentation software is a software agent that provides the stimulus to the subject during a functional imaging (MRI, MEG, EEG) or behavioral data acquisition activity.

nidm:'Presentation Software' is a prov:Agent.

Magnetic Resonance Imaging

Table 5:NIDM-Experiment Magnetic Resonance Imaging Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Image Data Reconstruction' prov:Activity nidm:ImageDataReconstruction
nidm:'Anatomical' prov:'Entity' nidm:Anatomical
nidm:'Arterial Spin Labeling' nidm:ArterialSpinLabeling
nidm:'Cartesian' nidm:Cartesian
nidm:'DICOM Tag Collection' nidm:DICOMTagCollection
nidm:'Diffusion Tensor' nidm:DiffusionTensor
nidm:'Diffusion Weighted' nidm:DiffusionWeighted
nidm:'Dynamic Contrast Enhanced' nidm:DynamicContrastEnhanced
nidm:'Dynamic Susceptibility Contrast' nidm:DynamicSusceptibilityContrast
nidm:'Echo Planar' nidm:EchoPlanar
nidm:'Flow Weighted' nidm:FlowWeighted
nidm:'Functional' nidm:Functional
nidm:'Image Contrast Type' nidm:ImageContrastType
nidm:'Image Usage Type' nidm:ImageUsageType
nidm:'Inside-out Spiral' nidm:Inside-outSpiral
nidm:'Magnetic Resonance Imaging' nidm:MagneticResonanceImaging
nidm:'Nuclear Magnetic Resonance Spectroscopy' nidm:NuclearMagneticResonanceSpectroscopy
nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging' nidm:NuclearMagneticResonanceSpectroscopicImaging
nidm:'Outside-in Spiral' nidm:Outside-inSpiral
nidm:'Parallel Imaging' nidm:ParallelImaging
nidm:'Proton Density Weighted' nidm:ProtonDensityWeighted
nidm:'Pulse Sequence' nidm:PulseSequence
nidm:'Quantitative Susceptibility Mapping' nidm:QuantitativeSusceptibilityMapping
nidm:'Rectilinear' nidm:Rectilinear
nidm:'Simultaneous Multislice Method' nidm:SimultaneousMultisliceMethod
nidm:'Structural' nidm:Structural
nidm:'Susceptibility Weighted' nidm:SusceptibilityWeighted
nidm:'Susceptibility Weighted Imaging' nidm:SusceptibilityWeightedImaging
nidm:'T1 Weighted' nidm:T1Weighted
nidm:'T2-Star Weighted' nidm:T2StarWeighted
nidm:'T2 Weighted' nidm:T2Weighted
nidm:'b-value File' nidm:b-ValueFile
nidm:'b-vector File' nidm:b-VectorFile
nidm:'k-space Traversal Scheme' nidm:k-spaceTraversalScheme
nidm:'Block-Based Design' nidm:NIDM_0000152
nidm:'Event-Related Design' nidm:NIDM_0000153
nidm:'Mixed Design' nidm:NIDM_0000154
nidm:'fMRI Design Type' nidm:NIDM_0000155

nidm:'Image Data Reconstruction'

nidm:'Image Data Reconstruction': Image data reconstruction is an activity in which raw data is transformed into a matrix of values that represent the spatial distribution of intensity based on some image contrast type.

nidm:'Image Data Reconstruction' is a prov:Activity.

nidm:'Anatomical'

nidm:'Anatomical': Anatomical is a description of the usage of a given acquisition object, indicating that the purpose of the object is to provide information on the anatomy of the object on which the acquisition was performed.

nidm:'Anatomical' is a nidm:'Image Usage Type'.

nidm:'Arterial Spin Labeling'

nidm:'Arterial Spin Labeling': Arterial spin labeling is a magnetic resonance imaging acquisition method that measures perfusion using the flow of saturated blood into a predefined area by comparing the image intensity obtained in the slice with and without the saturation pulse.

nidm:'Arterial Spin Labeling' is a nidm:'Acquisition Method'.

nidm:'Cartesian'

nidm:'Cartesian': Cartesian is a k-space traversal scheme in MRI in which the path of the data acquisition follows a straight line parallel to one axis of the defined k-space and perpendicular to the other k=space axis.

nidm:'Cartesian' is a nidm:'k-space Traversal Scheme'.

nidm:'DICOM Tag Collection'

nidm:'DICOM Tag Collection': A DICOM tag collection is a group of identifiers and their values that are stored in the headers of DICOM-formatted acquisition objects and that record the acquisition and reconstruction parameters for that acquisition object.

nidm:'DICOM Tag Collection' is a prov:'Entity'.

nidm:'Diffusion Tensor'

nidm:'Diffusion Tensor': Diffusion tensor is an image usage type that denotes that the acquisition object collected can be use to construct the diffusion tensor of the imaged tissue.

nidm:'Diffusion Tensor' is a nidm:'Image Usage Type'.

nidm:'Diffusion Weighted'

nidm:'Diffusion Weighted': Diffusion weighted is an image contrast type in which differences in voxel intensity are based on the brownian-motion behavior of the species that generates the detected signal from that voxel.

nidm:'Diffusion Weighted' is a nidm:'Image Contrast Type'.

nidm:'Dynamic Contrast Enhanced'

nidm:'Dynamic Contrast Enhanced': Dynamic contrast enhanced is a magnetic resonance imaging acquisition method in which T1-weighted images are acquired both before and then sequentially after a contrast agent has been injected in order to quantify metrics related to the permeability of the blood-brain barrier.

nidm:'Dynamic Contrast Enhanced' is a nidm:'Acquisition Method'.

nidm:'Dynamic Susceptibility Contrast'

nidm:'Dynamic Susceptibility Contrast': Dynamic sysceptibility contrast is a magnetic resonance imaging acquisition method in which T2*-weighted images are acquired sequentially after a contrast agent has been injected in order to quantify metrics related to blood volume and flow.

nidm:'Dynamic Susceptibility Contrast' is a nidm:'Acquisition Method'.

nidm:'Echo Planar'

nidm:'Echo Planar': Echo planar is a k-space traversal scheme used to acquire the k-space data in magnetic resonance imaging in which the entirety of k-space is continuously traversed for each repetition of the pulse sequence.

nidm:'Echo Planar' is a nidm:'k-space Traversal Scheme'.

nidm:'Flow Weighted'

nidm:'Flow Weighted': Flow weighted is an image contrast type in which differences in voxel intensity are based on the bulk motion behavior of the species that generates the detected signal from that voxel.

nidm:'Flow Weighted' is a nidm:'Image Contrast Type'.

nidm:'Functional'

nidm:'Functional': Functional is a description of the usage of a given acquisition object, indicating that the purpose of the object is to provide information on the biological function of some aspect of the object on which the acquisition was performed.

nidm:'Functional' is a nidm:'Image Usage Type'.

nidm:'Image Contrast Type'

nidm:'Image Contrast Type': Image Contrast Type is an acquisition object quality that denotes the physical properties on which differences in image intensity, in an image, are based.

nidm:'Image Contrast Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Diffusion Weighted', nidm:'Flow Weighted', nidm:'Proton Density Weighted', nidm:'Susceptibility Weighted', nidm:'T1 Weighted', nidm:'T2 Weighted', nidm:'T2-Star Weighted'.

nidm:'Image Usage Type'

nidm:'Image Usage Type': Image Usage Type is an acquisition object quality that denotes to what purpose the acquired object will be employed.

nidm:'Image Usage Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Anatomical', nidm:'Diffusion Tensor', nidm:'Functional', nidm:'Quantitative Susceptibility Mapping', nidm:'Structural', nidm:'Susceptibility Weighted Imaging'.

nidm:'Inside-out Spiral'

nidm:'Inside-out Spiral': Inside-out spiral is a k-space traversal scheme in which the path along which magnetic resonance imaging k-space data is acquired is in the shape of a spiral and the data at the center of k-space is acquired first.

nidm:'Inside-out Spiral' is a nidm:'k-space Traversal Scheme'.

nidm:'Magnetic Resonance Imaging'

nidm:'Magnetic Resonance Imaging': Magnetic Resonance Imaging is an acquisition modality in which radiofrequency electromagnetic radiation is used to excite nuclei of the sample or subject and the characteristics of the detected signal are used to generate intensity contrast between different spatial locations.

nidm:'Magnetic Resonance Imaging' is a nidm:'Acquisition Modality'.

nidm:'Nuclear Magnetic Resonance Spectroscopy'

nidm:'Nuclear Magnetic Resonance Spectroscopy': Nuclear magnetic resonance spectroscopy is an acquisition modality in which radiofrequency electromagnetic radiation is used to excite nuclei of the sample or subject, the characteristics of the detected signal are used to generate signal intensity contrast over an entire selected volume, and the resulting signal is displayed as a signal spectrum rather than as matrix meant to be a representation of the underlying object.

nidm:'Nuclear Magnetic Resonance Spectroscopy' is a nidm:'Acquisition Modality'.

nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging'

nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging': Nuclear magnetic resonance spectroscopic imaging is an acquisition modality in which radiofrequency electromagnetic radiation is used to excite nuclei of the sample or subject, the characteristics of the detected signal are used to generate intensity contrast over a restricted (usually grid-like) area, and the resulting signal is displayed as a spectrum for each one of the spatially-resolved areas.

nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging' is a nidm:'Acquisition Modality'.

nidm:'Outside-in Spiral'

nidm:'Outside-in Spiral': Outside-inSpiral is a k-space traversal scheme in which the path, along which magnetic resonance imaging k-space data is acquired, is spiral and the data further away from the center of k-space is acquired first.

nidm:'Outside-in Spiral' is a nidm:'k-space Traversal Scheme'.

nidm:'Parallel Imaging'

nidm:'Parallel Imaging': Parallel imaging is an acquisition method used in magnetic resonance imaging to acquire the k-space data in which multiple coils are employed and the signals from each coil are disambiguated using the coil sensitivity profile.

nidm:'Parallel Imaging' is a nidm:'Acquisition Method'.

nidm:'Proton Density Weighted'

nidm:'Proton Density Weighted': Proton density weighted is a image contrast type in magnetic resonance imaging in which differences in voxel intensity reflect underlying differences in the number of protons in those voxels.

nidm:'Proton Density Weighted' is a nidm:'Image Contrast Type'.

nidm:'Pulse Sequence'

nidm:'Pulse Sequence': A pulse sequence is a collection of commands sent to the magnetic resonance imaging or nuclear magnetic resonance hardware to control the excitation of the subject or sample and the acquisition of data.

nidm:'Pulse Sequence' is a prov:'Entity'.

nidm:'Quantitative Susceptibility Mapping'

nidm:'Quantitative Susceptibility Mapping': Quantitative susceptibility mapping is a magentic resonance imaging image-usage type in which differences in voxel intensity reflect quantitative differences magnetic susceptibilty of the underlying sample.

nidm:'Quantitative Susceptibility Mapping' is a nidm:'Image Usage Type'.

nidm:'Rectilinear'

nidm:'Rectilinear': Rectilinear is a k-space traversal scheme in magnetic resonance imaging in which the path in k-space over which the data is acquired is linear and aligned perpendicular to either the phase-encoding or frequency-encoding direction.

nidm:'Rectilinear' is a nidm:'k-space Traversal Scheme'.

nidm:'Simultaneous Multislice Method'

nidm:'Simultaneous Multislice Method': Simultaneous multislice is an acquisition method in magnetic resonance imaging used to acquire the k-space in which data from multiple slices are acquired at the same time and the coil sensitivity profiles are used to separate the data from each slice.

nidm:'Simultaneous Multislice Method' is a nidm:'Acquisition Method'.

nidm:'Structural'

nidm:'Structural': A stimulus response file is an auxiliary file that contains the recorded response of the subject to an experimental stimulus the course of a task-based assessment activity.

nidm:'Structural' is a nidm:'Image Usage Type'.

nidm:'Susceptibility Weighted'

nidm:'Susceptibility Weighted': Susceptibility weighted is a magentic resonance imaging image-contrast type in which differences in voxel intensity reflect differences in magnetic susceptibilty of the underlying sample.

nidm:'Susceptibility Weighted' is a nidm:'Image Contrast Type'.

nidm:'Susceptibility Weighted Imaging'

nidm:'Susceptibility Weighted Imaging': Susceptibility weighted imaging is a magentic resonance imaging image-usage type in which differences in voxel intensity reflect differences in magnetic susceptibilty of the underlying sample, but are not caculated values.

nidm:'Susceptibility Weighted Imaging' is a nidm:'Image Usage Type'.

nidm:'T1 Weighted'

nidm:'T1 Weighted': T1 weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-lattice relaxation time of the probe in the underlying sample.

nidm:'T1 Weighted' is a nidm:'Image Contrast Type'.

nidm:'T2-Star Weighted'

nidm:'T2-Star Weighted': T2-star weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-spin relaxation time of the probe as well as the field inhomogeneities in the underlying sample.

nidm:'T2-Star Weighted' is a nidm:'Image Contrast Type'.

nidm:'T2 Weighted'

nidm:'T2 Weighted': T2 weighted is an image contrast type in which differences in voxel intensity reflect differences in the spin-spin relaxation time of the probe in the underlying sample.

nidm:'T2 Weighted' is a nidm:'Image Contrast Type'.

nidm:'b-value File'

nidm:'b-value File': A b-value file is an auxiliary file, used in a diffusion-weighted magnetic resonance imaging acquisition activity, that contains the b-values used to control the diffusion-sensitization weighting.

nidm:'b-value File' is a nidm:'Auxiliary File'.

nidm:'b-vector File'

nidm:'b-vector File': A b-vector file is an auxiliary file, used in a diffusion-weighted magnetic resonance imaging acquisition activity, that contains the direction vectors used to control the direction of the diffusion-sensitization weighting.

nidm:'b-vector File' is a nidm:'Auxiliary File'.

nidm:'k-space Traversal Scheme'

nidm:'k-space Traversal Scheme': The k-space traversal scheme is an acquisition object quality that describes, in a magnetic resonance imaging acquisition, the path in k-space along which the signal is acquired.

nidm:'k-space Traversal Scheme' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Cartesian', nidm:'Echo Planar', nidm:'Inside-out Spiral', nidm:'Outside-in Spiral', nidm:'Rectilinear'.

nidm:'Block-Based Design'

nidm:'Block-Based Design': A block-based design is a fMRI design comprised of epochs of stimulus and/or behavior.

nidm:'Block-Based Design' is a nidm:'fMRI Design Type'.

nidm:'Mixed Design'

nidm:'Mixed Design': A mixed design is a fMRI design comprised of both epochs & discrete events of stimulus and/or behavior.

nidm:'Mixed Design' is a nidm:'fMRI Design Type'.

nidm:'fMRI Design Type'

nidm:'fMRI Design Type': An fMRI design type is 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 nidm:'Acquisition Object Quality' and has the following children: nidm:'Block-Based Design', nidm:'Event-Related Design', nidm:'Mixed Design'.

Electrophysiology

Table 6:NIDM-Experiment Electrophysiology Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Amperometry' prov:'Entity' nidm:Amperometry
nidm:'Current Clamp' nidm:CurrentClamp
nidm:'Electroencephalography' nidm:Electroencephalography
nidm:'Electrocorticography' nidm:Electrocorticography
nidm:'Electrophysiology Recording' nidm:ElectrophysiologyRecording
nidm:'Extracellular Electrophysiology Recording' nidm:ExtracellularElectrophysiologyRecording
nidm:'Field Potential' nidm:FieldPotential
nidm:'Intracellular Electrophysiology Recording' nidm:IntracellularElectrophysiologyRecording
nidm:'Magnetoencephalography' nidm:Magnetoencephalography
nidm:'Multi-unit Recording' nidm:MultiUnitReccording
nidm:'Sharp Electrode' nidm:SharpElectrode
nidm:'Single-unit Recording' nidm:SingleUnitReccording
nidm:'Patch Clamp' nidm:PatchClamp
nidm:'Voltage Clamp' nidm:VoltageClamp

nidm:'Amperometry'

nidm:'Amperometry': Amperometry is an extracellular acquisition method in electrophysiology in which an electrode is brought near a cell to detect the release of ions by vesicles.

nidm:'Amperometry' is a nidm:'Acquisition Method'.

nidm:'Current Clamp'

nidm:'Current Clamp': A current clamp is an intracellular electrophysiology acquisition method in which current is injected into a cell and the voltage generated by the cell is recorded.

nidm:'Current Clamp' is a nidm:'Acquisition Method'.

nidm:'Electroencephalography'

nidm:'Electroencephalography': Electroencephalography (EEG) is an electrophysiological acquisition method in which the electrical activity of the brain is measured using electrodes that are placed on the surface of the head.

nidm:'Electroencephalography' is a nidm:'Acquisition Method'.

nidm:'Electrocorticography'

nidm:'Electrocorticography': Electrocorticography (ECoG) is an electrophysiological acquisition method in which the electrical activity of the brain is measured using electrodes that are placed directly on the cortical surface of the brain.

nidm:'Electrocorticography' is a nidm:'Acquisition Method'.

nidm:'Electrophysiology Recording'

nidm:'Electrophysiology Recording': Electrophysiology Recording is an acquisition modality in which electrical signals are recorded from one or more electrodes inserted into living tissue.

nidm:'Electrophysiology Recording' is a nidm:'Acquisition Modality' and has the following children: nidm:'Extracellular Electrophysiology Recording', nidm:'Intracellular Electrophysiology Recording'.

nidm:'Extracellular Electrophysiology Recording'

nidm:'Extracellular Electrophysiology Recording': Extracellular Electrophysiology Recording is an acquisition modality in which one or more electrodes are inserted into living tissue and the electrical signals from adjacent cells are recorded.

nidm:'Extracellular Electrophysiology Recording' is a nidm:'Electrophysiology Recording'.

nidm:'Field Potential'

nidm:'Field Potential': The field potential is an extracellular electrophysiology acquisition method in which an electrode is used to measure the voltage that is generated by synaptic activity (in neural tissue).

nidm:'Field Potential' is a nidm:'Acquisition Method'.

nidm:'Intracellular Electrophysiology Recording'

nidm:'Intracellular Electrophysiology Recording': Intracellular Electrophysiology Recording is an activity in which electrical measurements of the interior cell environment are made.

nidm:'Intracellular Electrophysiology Recording' is a nidm:'Electrophysiology Recording'.

nidm:'Magnetoencephalography'

nidm:'Magnetoencephalography': Magnetoencephalography is an acquisition modality in which the magnetic fields, resulting from electrical activity in the brain, are detected and used to elucidate the time course of brain electrical activity.

nidm:'Magnetoencephalography' is a nidm:'Acquisition Modality'.

nidm:'Multi-unit Recording'

nidm:'Multi-unit Recording': Multiunit recording is an extracellular electrophysiological acquisition method in which an acquisition object is gathered using multiple recording devices.

nidm:'Multi-unit Recording' is a nidm:'Acquisition Method'.

nidm:'Sharp Electrode'

nidm:'Sharp Electrode': Sharp electrode is intracellular electrophysiological acquisition method used for measuring the potential of the intracellular environment with minimal disturbance of that environment, in which a pipette, filled with electrolyte and with a very small opening, is inserted into the cell and the potential measured.

nidm:'Sharp Electrode' is a nidm:'Acquisition Method'.

nidm:'Single-unit Recording'

nidm:'Single-unit Recording': Single-unit recording is an extracellular electrophysiological acquisition method, in which a thin electrode is introduced into the extracellular space of a sample or subject and the action potential from a single neuron is recorded.

nidm:'Single-unit Recording' is a nidm:'Acquisition Method'.

nidm:'Patch Clamp'

nidm:'Patch Clamp': Patch clamp is an intracellular electrophysiological acquisiiton method in which a micropipette tip is brought near a cell and scution applied drawing a section of cell membrane into the tip in order that ion movement or the intracellular environment can be studied.

nidm:'Patch Clamp' is a nidm:'Acquisition Method'.

nidm:'Voltage Clamp'

nidm:'Voltage Clamp': Voltage clamp is an intracellular electrophysiological acquisition method in in which the cell membrane potential is fixed to a set value and the ionic current that crosses the cell membrane at that potential is measured.

nidm:'Voltage Clamp' is a nidm:'Acquisition Method'.

Positron Emission Tomography

Table 7:NIDM-Experiment Positron Emission Tomography Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Positron Emission Tomography' prov:'Entity' nidm:PositronEmissionTomography

nidm:'Positron Emission Tomography'

nidm:'Positron Emission Tomography': Positron emission tomography is an acquisition modality in which a positron-emitting radioactive tracer is introduced into the subject and the gamma rays emitted after a positron-electron collision are detected and their originating position calculated.

nidm:'Positron Emission Tomography' is a nidm:'Acquisition Modality'.

X-ray Computed Tomography

Table 8:NIDM-Experiment X-ray Computed Tomography Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'X-ray Computed Tomography' prov:'Entity' nidm:X-rayComputedTomography

nidm:'X-ray Computed Tomography'

nidm:'X-ray Computed Tomography': X-ray Computed tomography is an acquisition modality in which an x-ray beam is scanned across a subject and the resulting data is reconstructed into two-dimensional slices or a three-dimensional volume in which the contrast is generated by the differential absorption of x-rays.

nidm:'X-ray Computed Tomography' is a nidm:'Acquisition Modality'.

Other

Table 9:NIDM-Experiment Other Concepts
NIDM-Experiment Concept PROV type Identifier

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: