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Class: FNIRS

An fNIRS acquisition. Its own attributes are the ones affecting cortical sensitivity, spatial sampling, or comparability, and so can support study filtering or moderator analyses.

URI: neurostudy_ex:FNIRS

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

      FNIRS : acquisition_duration_seconds





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



      FNIRS : acquisition_type

      FNIRS : brain_coverage





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



      FNIRS : device





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



      FNIRS : local_id

      FNIRS : modality





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



      FNIRS : nirs_channel_count





        FNIRS --> "0..1" ExtractedInteger : nirs_channel_count
        click ExtractedInteger href "../ExtractedInteger/"



      FNIRS : nirs_placement_scheme





        FNIRS --> "0..1" ExtractedStringList : nirs_placement_scheme
        click ExtractedStringList href "../ExtractedStringList/"



      FNIRS : nirs_system_type





        FNIRS --> "0..1" ExtractedString : nirs_system_type
        click ExtractedString href "../ExtractedString/"



      FNIRS : recorded_signal_types





        FNIRS --> "0..1" ExtractedStringList : recorded_signal_types
        click ExtractedStringList href "../ExtractedStringList/"



      FNIRS : sampling_frequency_hz





        FNIRS --> "0..1" ExtractedNumber : sampling_frequency_hz
        click ExtractedNumber href "../ExtractedNumber/"



      FNIRS : short_channel_count





        FNIRS --> "0..1" ExtractedInteger : short_channel_count
        click ExtractedInteger href "../ExtractedInteger/"



      FNIRS : source_detector_distances_mm





        FNIRS --> "0..1" ExtractedNumberList : source_detector_distances_mm
        click ExtractedNumberList href "../ExtractedNumberList/"



      FNIRS : stable_id

      FNIRS : wavelengths_nm





        FNIRS --> "0..1" ExtractedNumberList : wavelengths_nm
        click ExtractedNumberList href "../ExtractedNumberList/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sampling_frequency_hz 0..1
ExtractedNumber		 Sampling frequency of the fNIRS data in hertz direct
nirs_system_type 0..1
ExtractedString		 Instrument principle, such as continuous-wave, frequency-domain, or time-doma... direct
nirs_channel_count 0..1
ExtractedInteger		 Total number of NIRS channels, including short-separation channels direct
wavelengths_nm 0..1
ExtractedNumberList		 Nominal emitted wavelengths in nanometers direct
short_channel_count 0..1
ExtractedInteger		 Number of short-separation channels; zero indicates none direct
source_detector_distances_mm 0..1
ExtractedNumberList		 Reported source-detector separations in millimeters direct
nirs_placement_scheme 0..1
ExtractedStringList		 Standard placement system or listed optode positions, such as 10-20, Cz, or P... direct
recorded_signal_types 0..1
ExtractedStringList		 Raw or derived channel signal types, such as continuous-wave amplitude, optic... 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:FNIRS
native neurostudy_ex:FNIRS

LinkML Source

Direct

name: FNIRS
description: An fNIRS acquisition. Its own attributes are the ones affecting cortical
  sensitivity, spatial sampling, or comparability, and so can support study filtering
  or moderator analyses.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
is_a: Acquisition
attributes:
  sampling_frequency_hz:
    name: sampling_frequency_hz
    description: Sampling frequency of the fNIRS data in hertz.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    domain_of:
    - EEG
    - FNIRS
    range: ExtractedNumber
  nirs_system_type:
    name: nirs_system_type
    description: Instrument principle, such as continuous-wave, frequency-domain,
      or time-domain NIRS.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: ExtractedString
  nirs_channel_count:
    name: nirs_channel_count
    description: Total number of NIRS channels, including short-separation channels.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: ExtractedInteger
  wavelengths_nm:
    name: wavelengths_nm
    description: Nominal emitted wavelengths in nanometers.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: ExtractedNumberList
  short_channel_count:
    name: short_channel_count
    description: Number of short-separation channels; zero indicates none.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: ExtractedInteger
  source_detector_distances_mm:
    name: source_detector_distances_mm
    description: Reported source-detector separations in millimeters.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: ExtractedNumberList
  nirs_placement_scheme:
    name: nirs_placement_scheme
    description: Standard placement system or listed optode positions, such as 10-20,
      Cz, or Pz.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: ExtractedStringList
  recorded_signal_types:
    name: recorded_signal_types
    description: Raw or derived channel signal types, such as continuous-wave amplitude,
      optical density, oxygenated hemoglobin, or deoxygenated hemoglobin.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: ExtractedStringList

Induced

name: FNIRS
description: An fNIRS acquisition. Its own attributes are the ones affecting cortical
  sensitivity, spatial sampling, or comparability, and so can support study filtering
  or moderator analyses.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
is_a: Acquisition
attributes:
  sampling_frequency_hz:
    name: sampling_frequency_hz
    description: Sampling frequency of the fNIRS data in hertz.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    owner: FNIRS
    domain_of:
    - EEG
    - FNIRS
    range: ExtractedNumber
  nirs_system_type:
    name: nirs_system_type
    description: Instrument principle, such as continuous-wave, frequency-domain,
      or time-domain NIRS.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: ExtractedString
  nirs_channel_count:
    name: nirs_channel_count
    description: Total number of NIRS channels, including short-separation channels.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: ExtractedInteger
  wavelengths_nm:
    name: wavelengths_nm
    description: Nominal emitted wavelengths in nanometers.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: ExtractedNumberList
  short_channel_count:
    name: short_channel_count
    description: Number of short-separation channels; zero indicates none.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: ExtractedInteger
  source_detector_distances_mm:
    name: source_detector_distances_mm
    description: Reported source-detector separations in millimeters.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: ExtractedNumberList
  nirs_placement_scheme:
    name: nirs_placement_scheme
    description: Standard placement system or listed optode positions, such as 10-20,
      Cz, or Pz.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: ExtractedStringList
  recorded_signal_types:
    name: recorded_signal_types
    description: Raw or derived channel signal types, such as continuous-wave amplitude,
      optical density, oxygenated hemoglobin, or deoxygenated hemoglobin.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: ExtractedStringList
  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: FNIRS
    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: FNIRS
    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: FNIRS
    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: FNIRS
    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: FNIRS
    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: FNIRS
    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: FNIRS
    domain_of:
    - Acquisition
    range: ExtractedBrainCoverage