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:'Common Data Element' prov:'Entity' nidm:CommonDataElement
nidm:'Data Element' nidm:DataElement
nidm:'Gender' nidm:Gender
nidm:'Group' nidm:Group
nidm:'Personal Data Element' nidm:PersonalDataElement
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'

sio:'clinical trial':

sio:'clinical trial' is a nidm:'Project'.

nidm:'Common Data Element'

nidm:'Common Data Element': A common data element is a data element that is part of a collection of data elements, curated or not, which are available for reuse.

nidm:'Common Data Element' is a nidm:'Data Element'.

nidm:'Data Element'

nidm:'Data Element': A data element is a variable, used in a scientific study, used to store either information regarding the acquisition, processing, or analysis of the acquisition object that resulted from the study activity.

nidm:'Data Element' is a prov:'Entity' and has the following children: nidm:'Common Data Element', nidm:'Personal Data Element'.

nidm:'Gender'

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

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

nidm:'Group'

nidm:'Group': A group is a collection of agents or entities 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:'Personal Data Element'

nidm:'Personal Data Element': A personal data element is a data element that is part of a collection of data elements that have been defined locally, e.g., used to single study, lab, or project, but that are not meant for adoption by a wider community.

nidm:'Personal Data Element' is a nidm:'Data Element'.

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:'Series' nidm:Series
nidm:'Session' nidm:Session
nidm:'Task' nidm:Task
nidm:'Resting' nidm:Resting
nidm:'Acquisition Method' prov:'Entity' nidm:AcquisitionMethod
nidm:'Acquisition Modality' nidm:AcquisitionModality
nidm:'Acquisition Object' nidm:AcquisitionObject
nidm:'Acquisition Object Quality' nidm:AcquisitionObjectQuality
nidm:'Acquisition Usage Type' nidm:AcquisitionUsageType
nidm:'AuxiliaryFile' nidm:AuxiliaryFile
nidm:'Auxiliary File Collection' nidm:AuxiliaryFileCollection
nidm:'Calculated Parameter' nidm:CalculatedParameter
nidm:'Ex Vivo' nidm:ExVivo
nidm:'In Vitro' nidm:InVitro
nidm:'In Vivo' nidm:InVivo
nidm:'Magnitude' nidm:Magnitude
nidm:'Performed Plan' nidm:PerformedPlan
nidm:'Phase' nidm:Phase
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 study participant is gathered.

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

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:behavioural-test:

onli:behavioural-test is a prov:Activity.

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:experimental-psychology-test:

onli:experimental-psychology-test is and has the following child: onli:psychophysical-test.

onli:psychophysical-test

onli:psychophysical-test:

onli:psychophysical-test is.

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:coded-variable-assessment:

onli:coded-variable-assessment is a prov:Activity.

onli:numerical-variable-assessment

onli:numerical-variable-assessment:

onli:numerical-variable-assessment is a prov:Activity.

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'.

nidm:'Session'

nidm:'Session': A session is an activity during which data, potentially of different types, is acquired from a study participant 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 study Participant to elucidate some aspect of human behavior or underlying process.

nidm:'Task' is a prov:Activity.

nidm:'Resting'

nidm:'Resting': Resting is an activity in which the study participant does not perform a specific task.

nidm:'Resting' is a prov:Activity.

nidm:'Acquisition Method'

nidm:'Acquisition Method': An acquisition method is a specific form of a procedure that was used to gather data from a study participant.

nidm:'Acquisition Method' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Amperometry', nidm:'Angiography', nidm:'Arterial Spin Labeling', nidm:'Current Clamp', nidm:'Dynamic Contrast Enhanced', nidm:'Dynamic Susceptibility Contrast', nidm:'Electrocardiography', nidm:'Electrocorticography', nidm:'Electroencephalography', nidm:'Electromyography', nidm:'Electrooculography', nidm:'Fast Field Echo', nidm:'Field Potential', nidm:'Fluid Attenuated Inversion Recovery', nidm:'Gradient Recalled Echo', nidm:'Intracranial Electroencephalography', nidm:'Multi-unit Recording', nidm:'Parallel Imaging', nidm:'Patch Clamp', nidm:'Sharp Electrode', nidm:'Simultaneous Multislice', nidm:'Single-unit Recording', nidm:'Spin Echo', nidm:'Steady State Free Precession', nidm:'Stereoelectroencephalography', nidm:'Voltage Clamp', nidm:'X-ray Computed Tomography'.

nidm:'Acquisition Modality'

nidm:'Acquisition Modality': An acquisition modality is a description of the general type of experiment that was used to gather data from a study participant.

nidm:'Acquisition Modality' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Electroencephalography', nidm:'Electrophysiology Recording', nidm:'Magnetic Resonance Imaging', nidm:'Magnetoencephalography', nidm:'Nuclear Magnetic Resonance Spectroscopic Imaging', nidm:'Nuclear Magnetic Resonance Spectroscopy', nidm:'Positron Emission Tomography', nidm:'Single Photon Emission Computed Tomography', nidm:'X-ray'.

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 study participant during an acquisition activity.

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

nidm:'Acquisition Usage Type'

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

nidm:'Acquisition Usage Type' is a nidm:'Acquisition Object Quality' and has the following children: nidm:'Image Usage Type', nidm:'Noise Measurement'.

nidm:'AuxiliaryFile'

nidm:'AuxiliaryFile': 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:'AuxiliaryFile' 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:'Calculated Parameter'

nidm:'Calculated Parameter': A Calculated Parameter is a variable that is the result of the processing of a set of measurements.

nidm:'Calculated Parameter' is a prov:'Entity' and has the following children: nidm:'Cerebral Blood Flow', nidm:'Cerebral Blood Volume', nidm:'Magnitude', nidm:'Phase'.

nidm:'Ex Vivo'

nidm:'Ex Vivo': Ex vivo is a organismal quality, usually used as an attribute of an Agent, that indicates that the Agent it describes was once part of a living organism, but has been removed.

nidm:'Ex Vivo' is.

nidm:'In Vitro'

nidm:'In Vitro': In vitro is a organismal quality, usually used as an attribute of an Agent, that indicates that the Agent it describes is outside of a living organism.

nidm:'In Vitro' is.

nidm:'In Vivo'

nidm:'In Vivo': In vivo is a organismal quality, usually used as an attribute of an Agent, that indicates that the Agent it describes is a living organism.

nidm:'In Vivo' is.

nidm:'Magnitude'

nidm:'Magnitude': Magnitude is a calculated parameter that measures the number of periods accumulated by a variable during an evolution duration.

nidm:'Magnitude' is a nidm:'Calculated Parameter'.

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:'Phase'

nidm:'Phase': Phase is a calculated parameter that measures the number of periods accumulated by a variable during an evolution duration.

nidm:'Phase' is a nidm:'Calculated Parameter'.

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 study participant in a task-based assessment activity.

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

nidm:'Stimulus Response File'

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

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

nidm:'Presentation Software'

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

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

Assessment Instrument

Table 5:NIDM-Experiment Assessment Instrument Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Behavioral Instrument' prov:'Entity' nidm:BehavioralInstrument
nidm:'Demographics Instrument' nidm:DemographicsInstrument
nidm:'Informed Consent Instrument' nidm:InformedConsentInstrument
nidm:'Instrument Usage Type' nidm:InstrumentUsageType

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:'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:'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:'Demographics Instrument', nidm:'Informed Consent Instrument'.

Magnetic Resonance Imaging

Table 6: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:'Angiography' nidm:Angiography
nidm:'Arterial Spin Labeling' nidm:ArterialSpinLabeling
nidm:'Blood Oxygen Level Dependent Weighted' nidm:BloodOxygenLevelDependentWeighted
nidm:'Cartesian' nidm:Cartesian
nidm:'Cerebral Blood Flow' nidm:CerebralBloodFlow
nidm:'Cerebral Blood Volume' nidm:CerebralBloodVolume
nidm:'Continuous Arterial Spin Labeling' nidm:ContinuousArterialSpinLabeling
nidm:'DICOM Tag Collection' nidm:DICOMTagCollection
nidm:'Diffusion Tensor' nidm:DiffusionTensor
nidm:'Diffusion Weighted' nidm:DiffusionWeighted
nidm:'DistortionCorrection' nidm:DistortionCorrection
nidm:'Dynamic Contrast Enhanced' nidm:DynamicContrastEnhanced
nidm:'Dynamic Susceptibility Contrast' nidm:DynamicSusceptibilityContrast
nidm:'Echo Planar' nidm:EchoPlanar
nidm:'Fast Field Echo' nidm:FastFieldEcho
nidm:'Fast Imaging Employing Steady State Acquisition' nidm:FastImagingEmployingSteadyStateAcquisition
nidm:'Fast Imaging With Steady State' nidm:FastImagingWithSteadyStatePrecession
nidm:'Fast Low Angle Shot' nidm:FastLowAngleShot
nidm:'Fast Spin Echo' nidm:FastSpinEcho
nidm:'Flow Weighted' nidm:FlowWeighted
nidm:'Fluid Attenuated Inversion Recovery' nidm:FluidAttenuatedInversionRecovery
nidm:'Functional' nidm:Functional
nidm:'Gradient Recalled Acquisition in Steady State' nidm:GradientRecalledAcquisitionInSteadyState
nidm:'Gradient Recalled Echo' nidm:GradientRecalledEcho
nidm:'Image Contrast Type' nidm:ImageContrastType
nidm:'Image Usage Type' nidm:ImageUsageType
nidm:'Inside-out Spiral' nidm:Inside-outSpiral
nidm:'Localization' nidm:Localization
nidm:'Magnetic Resonance Imaging' nidm:MagneticResonanceImaging
nidm:'Magnetic Resonance Imaging Scanner' nidm:MagneticResonanceImagingScanner
nidm:'Multiple Spin Echo' nidm:MultipleSpinEcho
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:'Pseudo Continuous Arterial Spin Labeling' nidm:PseudoContinuousArterialSpinLabeling
nidm:'Pulsed Arterial Spin Labeling' nidm:PulsedArterialSpinLabeling
nidm:'Quantitative Susceptibility Mapping' nidm:QuantitativeSusceptibilityMapping
nidm:'Rectilinear' nidm:Rectilinear
nidm:'Resting State' nidm:RestingState
nidm:'Simultaneous Multislice' nidm:SimultaneousMultislice
nidm:'Spin Echo' nidm:SpinEcho
nidm:'Spoiled Gradient Recalled Echo' nidm:SpoiledGradientRecalledEcho
nidm:'Steady State Free Precession' nidm:SteadyStateFreePrecession
nidm:'Structural' nidm:Structural
nidm:'Susceptibility Weighted' nidm:SusceptibilityWeighted
nidm:'Susceptibility Weighted Imaging' nidm:SusceptibilityWeightedImaging
nidm:'T1 Fast Field Echo' nidm:T1FastFieldEcho
nidm:'T1 Weighted' nidm:T1Weighted
nidm:'T2 Star Weighted' nidm:T2StarWeighted
nidm:'T2 Weighted' nidm:T2Weighted
nidm:'Task Based' nidm:TaskBased
nidm:'True Fast Imaging With Steady State' nidm:TrueFastImagingWithSteadyStatePrecession
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:'Pulse Sequence' prov:Agent nidm:PulseSequence

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:'Angiography'

nidm:'Angiography': Angiography is an acquisition method that visualizes the venus and arterial systems of the body.

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

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' and has the following children: nidm:'Continuous Arterial Spin Labeling', nidm:'Pseudo Continuous Arterial Spin Labeling', nidm:'Pulsed Arterial Spin Labeling'.

nidm:'Blood Oxygen Level Dependent Weighted'

nidm:'Blood Oxygen Level Dependent Weighted': Blood Oxygen Level Dependent Weighted is an image contrast type in which differences in voxel intensity are based on magnetic susceptibility differences between oxygenated and de-oxygenated blood.

nidm:'Blood Oxygen Level Dependent Weighted' is a nidm:'Image Contrast Type'.

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:'Cerebral Blood Flow'

nidm:'Cerebral Blood Flow': Cerebral Blood Flow (CBF) is a calculated parameter that characterizes the blood volume in the brain.

nidm:'Cerebral Blood Flow' is a nidm:'Calculated Parameter'.

nidm:'Cerebral Blood Volume'

nidm:'Cerebral Blood Volume': Cerebral Blood Volume (CBV) is a calculated parameter that characterizes the blood volume in the brain.

nidm:'Cerebral Blood Volume' is a nidm:'Calculated Parameter'.

nidm:'Continuous Arterial Spin Labeling'

nidm:'Continuous Arterial Spin Labeling': Continuous arterial spin labeling is a magnetic resonance imaging acquisition method that uses continuous irradiation to invert the magnetization of flowing spins to measure perfusion.

nidm:'Continuous Arterial Spin Labeling' is a nidm:'Arterial Spin Labeling'.

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 used 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:'DistortionCorrection'

nidm:'DistortionCorrection': Distortion correction is a description of the usage of a given acquisition object, indicating that the purpose of the object is to provide information used to correct distortions in a set of images.

nidm:'DistortionCorrection' is a nidm:'Image Usage 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:'Fast Field Echo'

nidm:'Fast Field Echo': Fast Field Echo is a magnetic resonance imaging acquisition method that employs a gradient to dephase and rephase the signal to create an echo, a gradient-recalled echo, which is then measured.

nidm:'Fast Field Echo' is a nidm:'Acquisition Method'.

nidm:'Fast Imaging Employing Steady State Acquisition'

nidm:'Fast Imaging Employing Steady State Acquisition': Fast imaging employing steady state acquisition (FIESTA) is a gradient recalled echo based magnetic resonance imaging acquisition method in which a series of phase-alternating radiofrequency pulses are applied, in conjunction with a balanced set of gradients, generating free induction decays and a steady-state transverse magnetization, the signal from which is collected.

nidm:'Fast Imaging Employing Steady State Acquisition' is a nidm:'Steady State Free Precession'.

nidm:'Fast Imaging With Steady State'

nidm:'Fast Imaging With Steady State': Fast imaging with steady state precession (FISP) is a gradient recalled echo based magnetic resonance imaging acquisition method in which a series of phase-alternating radiofrequency pulses are applied, in conjunction with spoiler and rewinder gradients, generating free induction decays and a steady-state transverse magnetization, the signal from which is collected.

nidm:'Fast Imaging With Steady State' is a nidm:'Steady State Free Precession'.

nidm:'Fast Low Angle Shot'

nidm:'Fast Low Angle Shot': Fast Low Angle Shot is a magnetic resonance imaging acquisition method that employs a gradient to dephase and rephase the signal to create an echo, which is then measured, and an additional gradient to destroy any residual magnetization at the end of the pulse sequence.

nidm:'Fast Low Angle Shot' is a nidm:'Spoiled Gradient Recalled Echo'.

nidm:'Fast Spin Echo'

nidm:'Fast Spin Echo': Fast spin echo is a magnetic resonance imaging acquisition method in which the echo used in the measurement is generated by application of an initial radiofrequency 90 degree pulse and multiple subsequent 180 degree pulses, the latter in conjunction with a different phase-encoding gradient at each refocussed echo.

nidm:'Fast Spin Echo' is a nidm:'Spin Echo'.

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:'Fluid Attenuated Inversion Recovery'

nidm:'Fluid Attenuated Inversion Recovery': Fluid Attenuated Inversion Recovery, which is often known by its acronym, FLAIR, is a magnetic resonance imaging acquisition method in which images are acquired after an initial magnetization inversion pulse is applied and a delay duration that is selected such that the signal from bulk fluid such as cerebral spinal fluid or fluid in lesions is nulled.

nidm:'Fluid Attenuated Inversion Recovery' is a nidm:'Acquisition Method'.

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' and has the following children: nidm:'Resting State', nidm:'Task Based'.

nidm:'Gradient Recalled Acquisition in Steady State'

nidm:'Gradient Recalled Acquisition in Steady State': Gradient recalled acquisition in steady state (GRASS) is a gradient recalled echo based magnetic resonance imaging acquisition method in which a series of phase-alternating radiofrequency pulses are applied, generating free induction decays and a steady-state transverse magnetization, the signal from which is collected.

nidm:'Gradient Recalled Acquisition in Steady State' is a nidm:'Steady State Free Precession'.

nidm:'Gradient Recalled Echo'

nidm:'Gradient Recalled Echo': Gradient recalled echo is a magnetic resonance imaging acquisition method in which the echo used in the measurement is generated by application and subsequent reversal of the frequency-encoding gradient and is characterized by flip angles of less than 90 degrees and the evolution being governed by T2star decay.

nidm:'Gradient Recalled Echo' is a nidm:'Acquisition Method' and has the following children: nidm:'Magnetization Prepared Rapid Gradient Echo', nidm:'Spoiled Gradient Recalled Echo'.

nidm:'Magnetization Prepared Rapid Gradient Echo'

nidm:'Magnetization Prepared Rapid Gradient Echo': Magnetization Prepared Rapid Gradient Echo is a magnetic resonance imaging acquisition method in which the echoes used in the measurement is generated by application of an initial radiofrequency 180 degree pulse followed by multiple subsequent small flip angle pulses separated by short echo times.

nidm:'Magnetization Prepared Rapid Gradient Echo' is a nidm:'Gradient Recalled Echo'.

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:'Blood Oxygen Level Dependent Weighted', nidm:'Diffusion Weighted', nidm:'Flow Weighted', nidm:'Linear Attenuation Coefficient', nidm:'Maximum Intensity Projection', nidm:'Proton Density Weighted', nidm:'Susceptibility Weighted', nidm:'T1 Rho Weighted', nidm:'T1 Weighted', nidm:'T2 Star Weighted', nidm:'T2 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 Usage Type' and has the following children: nidm:'Anatomical', nidm:'Diffusion Tensor', nidm:'DistortionCorrection', nidm:'Functional', nidm:'Localization', nidm:'Perfusion', nidm:'Quantitative Susceptibility Mapping', nidm:'Structural', nidm:'Susceptibility Weighted Imaging'.

nidm:'Perfusion'

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

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

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:'Localization'

nidm:'Localization': Localization is a description of the usage of a given acquisition object, indicating that the purpose of the object is to provide information on the placement and orientation of the imaged object in space.

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

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 study participant and the characteristics of the detected signal are used to generate intensity contrast between different tissue types or structures.

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

nidm:'Magnetic Resonance Imaging Scanner'

nidm:'Magnetic Resonance Imaging Scanner': A magnetic resonance imaging scanner is a data acquisition device that uses radiofrequency electromagnetic radiation to excite nuclei of a study participant and uses the characteristics of the detected signal are used to generate intensity contrast between different tissue types or structures.

nidm:'Magnetic Resonance Imaging Scanner' is a nidm:'Image Acquisition Device'.

nidm:'Multiple Spin Echo'

nidm:'Multiple Spin Echo': Multiple spin echo is a magnetic resonance imaging acquisition method in which the echoes used in the measurement are generated by application of an initial radiofrequency 90 degree pulse and multiple subsequent 180 degree pulses,and each succeeding echo is used as a k-space line in an image with a longer echo time.

nidm:'Multiple Spin Echo' is a nidm:'Spin Echo'.

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 study participant, 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 study participant, 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:'Pseudo Continuous Arterial Spin Labeling'

nidm:'Pseudo Continuous Arterial Spin Labeling': Pseudo-continuous arterial spin labeling (pCASL)is a magnetic resonance imaging acquisition method that uses a long series of short RF-pulses and strong slice-selection gradients to invert the magnetization of flowing spins from a thin slice to measure perfusion.

nidm:'Pseudo Continuous Arterial Spin Labeling' is a nidm:'Arterial Spin Labeling'.

nidm:'Pulsed Arterial Spin Labeling'

nidm:'Pulsed Arterial Spin Labeling': Pulsed arterial spin labeling (pCASL)is a magnetic resonance imaging acquisition method that inverts the magnetization of flowing spins in a slab of tissue below the imaging slice to measure perfusion.

nidm:'Pulsed Arterial Spin Labeling' is a nidm:'Arterial Spin Labeling'.

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:'Resting State'

nidm:'Resting State': Resting state is an image usage type that indicates that no specific task was performed during the data acquisition.

nidm:'Resting State' is a nidm:'Functional'.

nidm:'Simultaneous Multislice'

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

nidm:'Spin Echo'

nidm:'Spin Echo': Spin echo is a magnetic resonance imaging acquisition method in which the echo used in the measurement is generated by application of an initial radiofrequency pulse and a subsequent pulse, generally, though not necessarily, with flip angles of 90 and 180 degrees respectively.

nidm:'Spin Echo' is a nidm:'Acquisition Method' and has the following children: nidm:'Fast Spin Echo', nidm:'Multiple Spin Echo'.

nidm:'Spoiled Gradient Recalled Echo'

nidm:'Spoiled Gradient Recalled Echo': Spoiled Gradient Recalled Echo (SPGR), is a magnetic resonance imaging acquisition method that employs gradient echoes and a low-flip angle radio-frequency excitation of the sample magnetization along with a short repetition time.

nidm:'Spoiled Gradient Recalled Echo' is a nidm:'Gradient Recalled Echo' and has the following children: nidm:'Fast Low Angle Shot', nidm:'T1 Fast Field Echo'.

nidm:'Steady State Free Precession'

nidm:'Steady State Free Precession': Steady State Free Precession is a magnetic resonance imaging acquisition method that uses the steady state magnetization, formed by a series of phase-alternated radiofrequency pulses, spoiler gradients in the slice-selection direction, rewinder gradients in the phase-encoding direction to form images.

nidm:'Steady State Free Precession' is a nidm:'Acquisition Method' and has the following children: nidm:'Fast Imaging Employing Steady State Acquisition', nidm:'Fast Imaging With Steady State', nidm:'Gradient Recalled Acquisition in Steady State', nidm:'True Fast Imaging With Steady State'.

nidm:'Structural'

nidm:'Structural': A stimulus response file is an auxiliary file that contains the recorded response of the study participant 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 Fast Field Echo'

nidm:'T1 Fast Field Echo': T1 Fast Field Echo, is a magnetic resonance imaging acquisition method that employs a gradient to dephase and rephase the signal to create an echo, which is then measured and an additional gradient to destroy any residual magnetization at the end of the pulse sequence.

nidm:'T1 Fast Field Echo' is a nidm:'Spoiled Gradient Recalled Echo'.

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:'Task Based'

nidm:'Task Based': Task based is an image usage type indicating that a specific task was performed during the data acquisition.

nidm:'Task Based' is a nidm:'Functional'.

nidm:'True Fast Imaging With Steady State'

nidm:'True Fast Imaging With Steady State': True fast imaging with steady state precession (TrueFISP) is a gradient recalled echo based magnetic resonance imaging acquisition method in which a series of phase-alternating radiofrequency pulses are applied, in conjunction with a balanced set of gradients, generating free induction decays and a steady-state transverse magnetization, the signal from which is collected.

nidm:'True Fast Imaging With Steady State' is a nidm:'Steady State Free Precession'.

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:'AuxiliaryFile'.

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:'AuxiliaryFile'.

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'.

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 study participant and the acquisition of data.

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

Electrophysiology

Table 7:NIDM-Experiment Electrophysiology Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Amperometry' prov:'Entity' nidm:Amperometry
nidm:'Current Clamp' nidm:CurrentClamp
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:'Multi-unit Recording' nidm:MultiUnitRecording
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:'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:'Multi-unit Recording'

nidm:'Multi-unit Recording': Multi-unit 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 the study participant 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'.

Devices

Table 8:NIDM-Experiment Devices Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Attenuator' prov:'Entity' nidm:Attenuator
nidm:'Bandpass Filter' nidm:BandpassFilter
nidm:'Current Amplifier' nidm:CurrentAmplifier
nidm:'Data Acquisition Device' nidm:DataAcquisitionDevice
nidm:'Data Processing Device' nidm:DataProcessingDevice
nidm:'Electrode' nidm:Electrode
nidm:'Electroencephalography Acquisition Device' nidm:ElectroencephalographyAcquisitionDevice
nidm:'Eye Tracking Device' nidm:EyeTrackingDevice
nidm:'Heart Rate Monitor' nidm:HeartRateMonitor
nidm:'High-Pass Filter' nidm:HighPassFilter
nidm:'Image Acquisition Device' nidm:ImageAcquisitionDevice
nidm:'Low-Pass Filter' nidm:LowPassFilter
nidm:'Multi-electrode Array' nidm:MultielectrodeArray
nidm:'Receive Coil' nidm:ReceiveCoil
nidm:'Respiration Rate Monitor' nidm:RespirationRateMonitor
nidm:'Signal Filter' nidm:SignalFilter
nidm:'Signal Generator' nidm:SignalGenerator
nidm:'Stimulus Generator' nidm:StimulusGenerator
nidm:'Stimulus Isolator' nidm:StimulusIsolator
nidm:'Transmit Coil' nidm:TransmitCoil
nidm:'Voltage Amplifier' nidm:VoltageAmplifier

nidm:'Attenuator'

nidm:'Attenuator': An attenuator is a device that reduces the amplitude of an input signal by a fixed amount while keeping the timecourse of the signal essentially unchanged.

nidm:'Attenuator' is a nidm:'Data Processing Device'.

nidm:'Bandpass Filter'

nidm:'Bandpass Filter': A bandpass filter is a device that modifies or removes certain signal components outside a selected frequency range from an electrical signal.

nidm:'Bandpass Filter' is a nidm:'Signal Filter'.

nidm:'Current Amplifier'

nidm:'Current Amplifier': A current amplifier is a device that increases the electrical current amplitude of an input electrical signal by a fixed amount, while keeping the voltage constant.

nidm:'Current Amplifier' is a nidm:'Data Processing Device'.

nidm:'Data Acquisition Device'

nidm:'Data Acquisition Device': A data acquisition device is a device that collects a packet or stream of analog or digital information from an entity.

nidm:'Data Acquisition Device' is a prov:'Entity' and has the following children: nidm:'Electrode', nidm:'Electroencephalography Acquisition Device', nidm:'Eye Tracking Device', nidm:'Heart Rate Monitor', nidm:'Image Acquisition Device', nidm:'Magnetoencephalography Acquisition Device', nidm:'Multi-electrode Array', nidm:'Nuclear Magnetic Resonance Device', nidm:'Receive Coil', nidm:'Respiration Rate Monitor'.

nidm:'Data Processing Device'

nidm:'Data Processing Device': A data processing device is a device that manipulates a data packet, stream, or file by performing an operation on the data.

nidm:'Data Processing Device' is a prov:'Entity' and has the following children: nidm:'Attenuator', nidm:'Current Amplifier', nidm:'Voltage Amplifier'.

nidm:'Electrode'

nidm:'Electrode': An electrode is a data acquisition device that consists of a conductor that is used to record an electrical signal from a study participant.

nidm:'Electrode' is a nidm:'Data Acquisition Device'.

nidm:'Electroencephalography Acquisition Device'

nidm:'Electroencephalography Acquisition Device': An electroencephalography (EEG) acquisition device is a device that measures the electrical activity of the brain and consists of a set of electrodes placed on the surface of the head and a recording device that collects the signal from each electrode.

nidm:'Electroencephalography Acquisition Device' is a nidm:'Data Acquisition Device'.

nidm:'Eye Tracking Device'

nidm:'Eye Tracking Device': An eye tracking device is a device that consists of hardware that follows the motion of one or both eyes of the study participant, which allows the determination of either the gaze location or of relative eye motion.

nidm:'Eye Tracking Device' is a nidm:'Data Acquisition Device'.

nidm:'Heart Rate Monitor'

nidm:'Heart Rate Monitor': A heart rate monitor is a data acquisition device that records the number of heart beats in a given period of time of a subject.

nidm:'Heart Rate Monitor' is a nidm:'Data Acquisition Device'.

nidm:'High-Pass Filter'

nidm:'High-Pass Filter': A high-pass filter is a device that removes or attenuates signal components below a selected frequency value from an electrical signal.

nidm:'High-Pass Filter' is a nidm:'Signal Filter'.

nidm:'Image Acquisition Device'

nidm:'Image Acquisition Device': An image acquisition device is a data acquisition device that has an image as its primary output.

nidm:'Image Acquisition Device' is a nidm:'Data Acquisition Device' and has the following children: nidm:'Magnetic Resonance Imaging Scanner', nidm:'Positron Emission Tomography Scanner', nidm:'Single Photon Emission Computed Tomography Scanner', nidm:'X-ray Computed Tomography Acquisition Device'.

nidm:'Positron Emission Tomography Scanner'

nidm:'Positron Emission Tomography Scanner': A positron emission tomography scanner is a data-acquisition device that collects gamma rays emitted by a study participant who is administered a positron-emitting radioactive substance and creates an image by calculating the originating position of the gamma rays.

nidm:'Positron Emission Tomography Scanner' is a nidm:'Image Acquisition Device'.

nidm:'Single Photon Emission Computed Tomography Scanner'

nidm:'Single Photon Emission Computed Tomography Scanner': A single-photon emission computed tomography (SPECT)scanner is an acquisition device that collects gamma-rays emitted by a study participant in a series of cross-sectional views, acquired in detectors encircling the study participant, enabling a three-dimensional volume to be reconstructed using a tomographic reconstruction method.

nidm:'Single Photon Emission Computed Tomography Scanner' is a nidm:'Image Acquisition Device'.

nidm:'X-ray Computed Tomography Acquisition Device'

nidm:'X-ray Computed Tomography Acquisition Device': X-ray Computed tomography is an acquisition modality in which an x-ray beam is scanned across a study participant 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 Acquisition Device' is a nidm:'Image Acquisition Device'.

nidm:'Low-Pass Filter'

nidm:'Low-Pass Filter': A low-pass filter is a device that removes or attenuates signal components above a selected frequency value from an electrical signal.

nidm:'Low-Pass Filter' is a nidm:'Signal Filter'.

nidm:'Multi-electrode Array'

nidm:'Multi-electrode Array': A multi-electrode array is a data acquisition device that records more than one concurrent electrical signal from study participant or sample.

nidm:'Multi-electrode Array' is a nidm:'Data Acquisition Device'.

nidm:'Receive Coil'

nidm:'Receive Coil': A receive coil is a data acquisition device used in nuclear magnetic resonance and magnetic resonance imaging to receive the signal from the sample. .

nidm:'Receive Coil' is a nidm:'Data Acquisition Device'.

nidm:'Respiration Rate Monitor'

nidm:'Respiration Rate Monitor': A respiration rate monitor is a data acquisition device that records the number of breaths taken by a study participant in a given period of time.

nidm:'Respiration Rate Monitor' is a nidm:'Data Acquisition Device'.

nidm:'Signal Filter'

nidm:'Signal Filter': A signal filter is a device that modifies or removes certain components of an electrical signal.

nidm:'Signal Filter' is a prov:'Entity' and has the following children: nidm:'Bandpass Filter', nidm:'High-Pass Filter', nidm:'Low-Pass Filter'.

nidm:'Signal Generator'

nidm:'Signal Generator': A signal generator is a device that supplies an electrical voltage signal of a specified amplitude and shape.

nidm:'Signal Generator' is a prov:'Entity'.

nidm:'Stimulus Generator'

nidm:'Stimulus Generator': A stimulus generator is a device that can deliver a current or voltage waveform that is used to stimulate a sample, cell, or body part.

nidm:'Stimulus Generator' is a prov:'Entity'.

nidm:'Stimulus Isolator'

nidm:'Stimulus Isolator': A stimulus isolatator is a device that can deliver a current or voltage waveform that is used to stimulate a sample, cell, or body part, but is isolated from electrical ground, which both decreases the stimulus artifact in the acquired signal and increases the safety for the user.

nidm:'Stimulus Isolator' is a prov:'Entity'.

nidm:'Transmit Coil'

nidm:'Transmit Coil': A transmit coil is a data device used in nuclear magnetic resonance and magnetic resonance imaging to apply the stimulating energy to the sample. .

nidm:'Transmit Coil' is a prov:'Entity'.

nidm:'Voltage Amplifier'

nidm:'Voltage Amplifier': Voltage amplifier is an device that produces a higher output voltage than was input into the device.

nidm:'Voltage Amplifier' is a nidm:'Data Processing Device'.

Positron Emission Tomography

Table 9:NIDM-Experiment Positron Emission Tomography Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Positron Emission Tomography' prov:'Entity' nidm:PositronEmissionTomography
nidm:'Positron Emission Tomography Scanner' nidm:PositronEmissionTomographyScanner

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 study participant 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'.

nidm:'Positron Emission Tomography Scanner'

nidm:'Positron Emission Tomography Scanner': A positron emission tomography scanner is a data-acquisition device that collects gamma rays emitted by a study participant who is administered a positron-emitting radioactive substance and creates an image by calculating the originating position of the gamma rays.

nidm:'Positron Emission Tomography Scanner' is a nidm:'Image Acquisition Device'.

X-ray Computed Tomography

Table 10: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 Acquisition Device' nidm:X-rayComputedTomographyAcquisitionDevice

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 study participant 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 Method'.

nidm:'X-ray Computed Tomography Acquisition Device'

nidm:'X-ray Computed Tomography Acquisition Device': X-ray Computed tomography is an acquisition modality in which an x-ray beam is scanned across a study participant 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 Acquisition Device' is a nidm:'Image Acquisition Device'.

Magnetoencephalography

Table 11:NIDM-Experiment Magnetoencephalography Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Magnetoencephalography' prov:'Entity' nidm:Magnetoencephalography
nidm:'Magnetoencephalography Acquisition Device' nidm:MagnetoencephalographyAcquisitionDevice
nidm:'Noise Measurement' nidm:NoiseMeasurement

nidm:'Magnetoencephalography'

nidm:'Magnetoencephalography': Magnetoencephalography (MEG) 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:'Magnetoencephalography Acquisition Device'

nidm:'Magnetoencephalography Acquisition Device': An magnetoencephalography (MEG) acquisition device is a device that measures magnetic signals generated by the electrical activity of the brain and consists of a set of magnetometers placed near the surface of the head and a recording device that collects the signal from each electrode.

nidm:'Magnetoencephalography Acquisition Device' is a nidm:'Data Acquisition Device'.

nidm:'Noise Measurement'

nidm:'Noise Measurement': Noise measurement is an acquisition usage type that denotes that the acquisition object collected has been used to measure the intrinsic noise level of the acquisition hardware.

nidm:'Noise Measurement' is a nidm:'Acquisition Usage Type'.

Electroencephalography

Table 12:NIDM-Experiment Electroencephalography Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Electroencephalography' prov:'Entity' nidm:Electroencephalography
nidm:'Electroencephalography Acquisition Device' nidm:ElectroencephalographyAcquisitionDevice

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:'Electroencephalography Acquisition Device'

nidm:'Electroencephalography Acquisition Device': An electroencephalography (EEG) acquisition device is a device that measures the electrical activity of the brain and consists of a set of electrodes placed on the surface of the head and a recording device that collects the signal from each electrode.

nidm:'Electroencephalography Acquisition Device' is a nidm:'Data Acquisition Device'.

SinglePhotonEmissionComputedTomography

Table 13:NIDM-Experiment SinglePhotonEmissionComputedTomography Concepts
NIDM-Experiment Concept PROV type Identifier
nidm:'Single Photon Emission Computed Tomography' prov:'Entity' nidm:SinglePhotonEmissionComputedTomography
nidm:'Single Photon Emission Computed Tomography Scanner' nidm:SinglePhotonEmissionComputedTomographyScanner

nidm:'Single Photon Emission Computed Tomography'

nidm:'Single Photon Emission Computed Tomography': Single-photon emission computed tomography (SPECT)is an acquisition modality in which a gamma-ray-emitting radioisotope is introduced into the study participant and the emitted gamma rays are detected in a series of cross-sectional views, acquired in detectors encircling the study participant, enabling a three-dimensional volume to be reconstructed using a tomographic reconstruction method.

nidm:'Single Photon Emission Computed Tomography' is a nidm:'Acquisition Modality'.

nidm:'Single Photon Emission Computed Tomography Scanner'

nidm:'Single Photon Emission Computed Tomography Scanner': A single-photon emission computed tomography (SPECT)scanner is an acquisition device that collects gamma-rays emitted by a study participant in a series of cross-sectional views, acquired in detectors encircling the study participant, enabling a three-dimensional volume to be reconstructed using a tomographic reconstruction method.

nidm:'Single Photon Emission Computed Tomography Scanner' is a nidm:'Image Acquisition Device'.

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: