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: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 : acquisition_type

      Acquisition : brain_coverage





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



      Acquisition : device





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



      Acquisition : id

      Acquisition : modality

Inheritance

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

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 String		direct
acquisition_type	1 String	The concrete subclass this record instantiates	direct
modality	1 String or  Modality	Imaging or recording modality	direct
acquisition_duration_seconds	0..1 Float	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 BrainCoverage	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-storage

Mappings

Mapping Type	Mapped Value
self	neurostudy:Acquisition
native	neurostudy: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-storage
rank: 1000
abstract: true
attributes:
  id:
    name: id
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    identifier: true
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - StatisticalMap
    - 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.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - Acquisition
    required: true
    any_of:
    - range: Modality
    - range: string
  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.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - Acquisition
    range: float
    minimum_value: 0
  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.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - Acquisition
    range: BrainCoverage

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-storage
rank: 1000
abstract: true
attributes:
  id:
    name: id
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    identifier: true
    owner: Acquisition
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - StatisticalMap
    - 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.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: Acquisition
    domain_of:
    - Acquisition
    range: string
    required: true
    any_of:
    - range: Modality
    - range: string
  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.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: Acquisition
    domain_of:
    - Acquisition
    range: float
    minimum_value: 0
  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.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: Acquisition
    domain_of:
    - Acquisition
    range: BrainCoverage