Class: OtherModality

An acquisition whose modality has no class of its own: MEG, SPECT, and other. Nothing here is normalized, so this is where a modality the schema does not name keeps its parameters. A parameter that MRI, EEG, FNIRS, or PET has no field for belongs on that sibling class instead.

URI: neurostudy_ex:OtherModality

 classDiagram
    class OtherModality
    click OtherModality href "../OtherModality/"
      Acquisition <|-- OtherModality
        click Acquisition href "../Acquisition/"

      OtherModality : acquisition_duration_seconds





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



      OtherModality : acquisition_type

      OtherModality : brain_coverage





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



      OtherModality : device





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



      OtherModality : local_id

      OtherModality : modality





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



      OtherModality : modality_label





        OtherModality --> "1" ExtractedString : modality_label
        click ExtractedString href "../ExtractedString/"



      OtherModality : reason_no_modality_class_used





        OtherModality --> "0..1" ExtractedString : reason_no_modality_class_used
        click ExtractedString href "../ExtractedString/"



      OtherModality : stable_id

Inheritance

• Acquisition
  • OtherModality

Slots

Name	Cardinality and Range	Description	Inheritance
modality_label	1 ExtractedString	The source's own name for the modality or recording technique, verbatim	direct
reason_no_modality_class_used	0..1 ExtractedString	Why this is not an MRI, EEG, FNIRS, or PET record	direct
stable_id	0..1 String	UUID minted by the store the first time this entity appears, never by an extr...	Acquisition
local_id	1 String		Acquisition
acquisition_type	1 String	The concrete subclass this record instantiates	Acquisition
modality	1 ExtractedModality	Imaging or recording modality	Acquisition
acquisition_duration_seconds	0..1 ExtractedNumber	Total usable acquisition or recording duration in seconds	Acquisition
device	0..1 Device	The scanner, amplifier, or recording system this acquisition was made on, by ...	Acquisition
brain_coverage	0..1 ExtractedBrainCoverage	How much of the brain the acquired volume contained	Acquisition

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: OtherModality
description: 'An acquisition whose modality has no class of its own: MEG, SPECT, and
  `other`. Nothing here is normalized, so this is where a modality the schema does
  not name keeps its parameters. A parameter that MRI, EEG, FNIRS, or PET has no field
  for belongs on that sibling class instead.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
is_a: Acquisition
attributes:
  modality_label:
    name: modality_label
    description: The source's own name for the modality or recording technique, verbatim.
      Always populated, since the Modality vocabulary is coarser than what a source
      reports.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - OtherModality
    range: ExtractedString
    required: true
  reason_no_modality_class_used:
    name: reason_no_modality_class_used
    description: Why this is not an MRI, EEG, FNIRS, or PET record.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - OtherModality
    range: ExtractedString

Induced

name: OtherModality
description: 'An acquisition whose modality has no class of its own: MEG, SPECT, and
  `other`. Nothing here is normalized, so this is where a modality the schema does
  not name keeps its parameters. A parameter that MRI, EEG, FNIRS, or PET has no field
  for belongs on that sibling class instead.'
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
is_a: Acquisition
attributes:
  modality_label:
    name: modality_label
    description: The source's own name for the modality or recording technique, verbatim.
      Always populated, since the Modality vocabulary is coarser than what a source
      reports.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: OtherModality
    domain_of:
    - OtherModality
    range: ExtractedString
    required: true
  reason_no_modality_class_used:
    name: reason_no_modality_class_used
    description: Why this is not an MRI, EEG, FNIRS, or PET record.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: OtherModality
    domain_of:
    - OtherModality
    range: ExtractedString
  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: OtherModality
    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: OtherModality
    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: OtherModality
    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: OtherModality
    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: OtherModality
    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: OtherModality
    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: OtherModality
    domain_of:
    - Acquisition
    range: ExtractedBrainCoverage