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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:FNIRS

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

      FNIRS : acquisition_duration_seconds

      FNIRS : acquisition_type

      FNIRS : brain_coverage





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



      FNIRS : device





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



      FNIRS : id

      FNIRS : modality

      FNIRS : nirs_channel_count

      FNIRS : nirs_placement_scheme

      FNIRS : nirs_system_type

      FNIRS : recorded_signal_types

      FNIRS : sampling_frequency_hz

      FNIRS : short_channel_count

      FNIRS : source_detector_distances_mm

      FNIRS : wavelengths_nm

Inheritance

Slots

Name Cardinality and Range Description Inheritance
sampling_frequency_hz 0..1
Float		 Sampling frequency of the fNIRS data in hertz direct
nirs_system_type 0..1
String		 Instrument principle, such as continuous-wave, frequency-domain, or time-doma... direct
nirs_channel_count 0..1
Integer		 Total number of NIRS channels, including short-separation channels direct
wavelengths_nm *
Float		 Nominal emitted wavelengths in nanometers direct
short_channel_count 0..1
Integer		 Number of short-separation channels; zero indicates none direct
source_detector_distances_mm *
Float		 Reported source-detector separations in millimeters direct
nirs_placement_scheme *
String		 Standard placement system or listed optode positions, such as 10-20, Cz, or P... direct
recorded_signal_types *
String		 Raw or derived channel signal types, such as continuous-wave amplitude, optic... direct
id 1
String		 Acquisition
acquisition_type 1
String		 The concrete subclass this record instantiates Acquisition
modality 1
String or 
Modality		 Imaging or recording modality Acquisition
acquisition_duration_seconds 0..1
Float		 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
BrainCoverage		 How much of the brain the acquired volume contained Acquisition

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self neurostudy:FNIRS
native neurostudy: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-storage
rank: 1000
is_a: Acquisition
attributes:
  sampling_frequency_hz:
    name: sampling_frequency_hz
    description: Sampling frequency of the fNIRS data in hertz.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    domain_of:
    - EEG
    - FNIRS
    range: float
    minimum_value: 0
  nirs_system_type:
    name: nirs_system_type
    description: Instrument principle, such as continuous-wave, frequency-domain,
      or time-domain NIRS.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: string
  nirs_channel_count:
    name: nirs_channel_count
    description: Total number of NIRS channels, including short-separation channels.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: integer
    minimum_value: 0
  wavelengths_nm:
    name: wavelengths_nm
    description: Nominal emitted wavelengths in nanometers.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: float
    multivalued: true
    minimum_value: 0
  short_channel_count:
    name: short_channel_count
    description: Number of short-separation channels; zero indicates none.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: integer
    minimum_value: 0
  source_detector_distances_mm:
    name: source_detector_distances_mm
    description: Reported source-detector separations in millimeters.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: float
    multivalued: true
    minimum_value: 0
  nirs_placement_scheme:
    name: nirs_placement_scheme
    description: Standard placement system or listed optode positions, such as 10-20,
      Cz, or Pz.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: string
    multivalued: true
  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.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    domain_of:
    - FNIRS
    range: string
    multivalued: true

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-storage
rank: 1000
is_a: Acquisition
attributes:
  sampling_frequency_hz:
    name: sampling_frequency_hz
    description: Sampling frequency of the fNIRS data in hertz.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    owner: FNIRS
    domain_of:
    - EEG
    - FNIRS
    range: float
    minimum_value: 0
  nirs_system_type:
    name: nirs_system_type
    description: Instrument principle, such as continuous-wave, frequency-domain,
      or time-domain NIRS.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: string
  nirs_channel_count:
    name: nirs_channel_count
    description: Total number of NIRS channels, including short-separation channels.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: integer
    minimum_value: 0
  wavelengths_nm:
    name: wavelengths_nm
    description: Nominal emitted wavelengths in nanometers.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: float
    multivalued: true
    minimum_value: 0
  short_channel_count:
    name: short_channel_count
    description: Number of short-separation channels; zero indicates none.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: integer
    minimum_value: 0
  source_detector_distances_mm:
    name: source_detector_distances_mm
    description: Reported source-detector separations in millimeters.
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: float
    multivalued: true
    minimum_value: 0
  nirs_placement_scheme:
    name: nirs_placement_scheme
    description: Standard placement system or listed optode positions, such as 10-20,
      Cz, or Pz.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: string
    multivalued: true
  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.
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - FNIRS
    range: string
    multivalued: true
  id:
    name: id
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    identifier: true
    owner: FNIRS
    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: 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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    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: FNIRS
    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: 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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/acquisition
    rank: 1000
    owner: FNIRS
    domain_of:
    - Acquisition
    range: BrainCoverage