Class: Acquisition

A modality-agnostic protocol used to acquire neuroimaging or associated physiological data, holding only what every modality has in common. One Acquisition carries one modality: simultaneous recordings such as EEG+fMRI are separate Acquisition records that a Task lists together. Everything modality-specific lives in the class the Modality value instantiates -- MRI, EEG, FNIRS, PET, or OtherModality.

• NOTE: this is an abstract class and should not be instantiated directly

URI: neurostudy_ex:Acquisition

 classDiagram
    class Acquisition
    click Acquisition href "../Acquisition/"
      Acquisition <|-- MRI
        click MRI href "../MRI/"
      Acquisition <|-- EEG
        click EEG href "../EEG/"
      Acquisition <|-- FNIRS
        click FNIRS href "../FNIRS/"
      Acquisition <|-- PET
        click PET href "../PET/"
      Acquisition <|-- OtherModality
        click OtherModality href "../OtherModality/"

      Acquisition : acquisition_duration_seconds





        Acquisition --> "0..1" ExtractedNumber : acquisition_duration_seconds
        click ExtractedNumber href "../ExtractedNumber/"



      Acquisition : acquisition_type

      Acquisition : brain_coverage





        Acquisition --> "0..1" ExtractedBrainCoverage : brain_coverage
        click ExtractedBrainCoverage href "../ExtractedBrainCoverage/"



      Acquisition : device





        Acquisition --> "0..1" Device : device
        click Device href "../Device/"



      Acquisition : local_id

      Acquisition : modality





        Acquisition --> "1" ExtractedModality : modality
        click ExtractedModality href "../ExtractedModality/"



      Acquisition : stable_id

Inheritance

• Acquisition
  • MRI
  • EEG
  • FNIRS
  • PET
  • OtherModality

Slots

Name	Cardinality and Range	Description	Inheritance
stable_id	0..1 String	UUID minted by the store the first time this entity appears, never by an extr...	direct
local_id	1 String		direct
acquisition_type	1 String	The concrete subclass this record instantiates	direct
modality	1 ExtractedModality	Imaging or recording modality	direct
acquisition_duration_seconds	0..1 ExtractedNumber	Total usable acquisition or recording duration in seconds	direct
device	0..1 Device	The scanner, amplifier, or recording system this acquisition was made on, by ...	direct
brain_coverage	0..1 ExtractedBrainCoverage	How much of the brain the acquired volume contained	direct

Usages

used by	used in	type	used
Task	acquisitions	range	Acquisition
Analysis	acquisitions	range	Acquisition
Study	acquisitions	range	Acquisition

Identifier and Mapping Information

Schema Source

• from schema: https://neurostuff.org/schemas/neuroimaging-study-extraction

Mappings

Mapping Type	Mapped Value
self	neurostudy_ex:Acquisition
native	neurostudy_ex:Acquisition

LinkML Source

Direct

name: Acquisition
description: 'A modality-agnostic protocol used to acquire neuroimaging or associated
  physiological data, holding only what every modality has in common. One Acquisition
  carries one modality: simultaneous recordings such as EEG+fMRI are separate Acquisition
  records that a Task lists together. Everything modality-specific lives in the class
  the Modality value instantiates -- MRI, EEG, FNIRS, PET, or OtherModality.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
abstract: true
attributes:
  stable_id:
    name: stable_id
    description: UUID minted by the store the first time this entity appears, never
      by an extractor, and kept across re-runs so a later extraction matches the same
      entity.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
  local_id:
    name: local_id
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    identifier: true
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  acquisition_type:
    name: acquisition_type
    description: The concrete subclass this record instantiates. Derived by the mapper
      from the modality value's `instantiates`, never extracted.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    designates_type: true
    domain_of:
    - Acquisition
    range: string
    required: true
  modality:
    name: modality
    description: 'Imaging or recording modality. A value in the Modality vocabulary
      also names the class holding this acquisition''s modality-specific parameters,
      through that value''s `instantiates`.

      Open vocabulary: write the source''s own wording in the field when nothing here
      fits, because the value is required and a closed range would discard the whole
      acquisition over one unrecognised word. Only a vocabulary value carries an `instantiates`,
      so an acquisition outside it resolves to the base class until normalization
      maps the wording back on -- which is why `acquisition_type` is derived rather
      than extracted, and why an unmapped modality is worth reporting.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - Acquisition
    range: ExtractedModality
    required: true
  acquisition_duration_seconds:
    name: acquisition_duration_seconds
    description: Total usable acquisition or recording duration in seconds. Useful
      for filtering studies by the amount of data contributing to an analysis, especially
      resting-state and continuous recordings.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - Acquisition
    range: ExtractedNumber
  device:
    name: device
    description: The scanner, amplifier, or recording system this acquisition was
      made on, by identifier. Acquisitions made on one machine reference one record;
      a second record asserts the study used a second machine.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - Acquisition
    range: Device
    inlined: false
  brain_coverage:
    name: brain_coverage
    description: 'How much of the brain the acquired volume contained. This is the
      extent the SCANNER sampled, and it is a third axis distinct from the two the
      schema already carries: `Analysis.spatial_scope` is what the analysis tested,
      and `InferenceSettings.correction_scope` with `search_volume` is where multiple
      comparisons were controlled. A voxelwise analysis over a volume that clipped
      the cerebellum is `whole_brain` in scope and `partial` here, and an ROI analysis
      of a whole-head acquisition is the reverse. Never infer this from either of
      those.

      It describes the volume behind the REPORTED results. A scan that clipped a structure
      in participants who were then excluded is `whole_brain`, because the analysed
      volume was not clipped; calling it `partial` would say the opposite of what
      the results rest on.

      A field of view or slice prescription in millimetres is not by itself a statement
      of coverage. Where only the geometry is given, the value is an inference and
      `value_source` records it as one. Which structure a partial volume missed is
      not a field of its own -- the evidence span carries that detail.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - Acquisition
    range: ExtractedBrainCoverage

Induced

name: Acquisition
description: 'A modality-agnostic protocol used to acquire neuroimaging or associated
  physiological data, holding only what every modality has in common. One Acquisition
  carries one modality: simultaneous recordings such as EEG+fMRI are separate Acquisition
  records that a Task lists together. Everything modality-specific lives in the class
  the Modality value instantiates -- MRI, EEG, FNIRS, PET, or OtherModality.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
abstract: true
attributes:
  stable_id:
    name: stable_id
    description: UUID minted by the store the first time this entity appears, never
      by an extractor, and kept across re-runs so a later extraction matches the same
      entity.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    owner: Acquisition
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    pattern: ^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$
  local_id:
    name: local_id
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    identifier: true
    owner: Acquisition
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  acquisition_type:
    name: acquisition_type
    description: The concrete subclass this record instantiates. Derived by the mapper
      from the modality value's `instantiates`, never extracted.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    designates_type: true
    owner: Acquisition
    domain_of:
    - Acquisition
    range: string
    required: true
  modality:
    name: modality
    description: 'Imaging or recording modality. A value in the Modality vocabulary
      also names the class holding this acquisition''s modality-specific parameters,
      through that value''s `instantiates`.

      Open vocabulary: write the source''s own wording in the field when nothing here
      fits, because the value is required and a closed range would discard the whole
      acquisition over one unrecognised word. Only a vocabulary value carries an `instantiates`,
      so an acquisition outside it resolves to the base class until normalization
      maps the wording back on -- which is why `acquisition_type` is derived rather
      than extracted, and why an unmapped modality is worth reporting.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: Acquisition
    domain_of:
    - Acquisition
    range: ExtractedModality
    required: true
  acquisition_duration_seconds:
    name: acquisition_duration_seconds
    description: Total usable acquisition or recording duration in seconds. Useful
      for filtering studies by the amount of data contributing to an analysis, especially
      resting-state and continuous recordings.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: Acquisition
    domain_of:
    - Acquisition
    range: ExtractedNumber
  device:
    name: device
    description: The scanner, amplifier, or recording system this acquisition was
      made on, by identifier. Acquisitions made on one machine reference one record;
      a second record asserts the study used a second machine.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: Acquisition
    domain_of:
    - Acquisition
    range: Device
    inlined: false
  brain_coverage:
    name: brain_coverage
    description: 'How much of the brain the acquired volume contained. This is the
      extent the SCANNER sampled, and it is a third axis distinct from the two the
      schema already carries: `Analysis.spatial_scope` is what the analysis tested,
      and `InferenceSettings.correction_scope` with `search_volume` is where multiple
      comparisons were controlled. A voxelwise analysis over a volume that clipped
      the cerebellum is `whole_brain` in scope and `partial` here, and an ROI analysis
      of a whole-head acquisition is the reverse. Never infer this from either of
      those.

      It describes the volume behind the REPORTED results. A scan that clipped a structure
      in participants who were then excluded is `whole_brain`, because the analysed
      volume was not clipped; calling it `partial` would say the opposite of what
      the results rest on.

      A field of view or slice prescription in millimetres is not by itself a statement
      of coverage. Where only the geometry is given, the value is an inference and
      `value_source` records it as one. Which structure a partial volume missed is
      not a field of its own -- the evidence span carries that detail.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: Acquisition
    domain_of:
    - Acquisition
    range: ExtractedBrainCoverage