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Class: MRI

An MRI acquisition of any kind -- functional, structural, or diffusion, as modality records. Its own attributes are the ones commonly useful for study selection, subgrouping, or sensitivity analyses in coordinate- or image-based meta-analysis.

URI: neurostudy_ex:MRI

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

      MRI : acquisition_duration_seconds





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



      MRI : acquisition_type

      MRI : acquisition_voxel_size_mm





        MRI --> "0..1" ExtractedNumberList : acquisition_voxel_size_mm
        click ExtractedNumberList href "../ExtractedNumberList/"



      MRI : brain_coverage





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



      MRI : device





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



      MRI : echo_time_seconds





        MRI --> "0..1" ExtractedNumberList : echo_time_seconds
        click ExtractedNumberList href "../ExtractedNumberList/"



      MRI : local_id

      MRI : magnetic_field_strength_tesla





        MRI --> "0..1" ExtractedNumber : magnetic_field_strength_tesla
        click ExtractedNumber href "../ExtractedNumber/"



      MRI : modality





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



      MRI : mr_acquisition_type





        MRI --> "0..1" ExtractedString : mr_acquisition_type
        click ExtractedString href "../ExtractedString/"



      MRI : number_of_volumes





        MRI --> "0..1" ExtractedInteger : number_of_volumes
        click ExtractedInteger href "../ExtractedInteger/"



      MRI : pulse_sequence_type





        MRI --> "0..1" ExtractedString : pulse_sequence_type
        click ExtractedString href "../ExtractedString/"



      MRI : repetition_time_seconds





        MRI --> "0..1" ExtractedNumber : repetition_time_seconds
        click ExtractedNumber href "../ExtractedNumber/"



      MRI : stable_id

Inheritance

Slots

Name Cardinality and Range Description Inheritance
magnetic_field_strength_tesla 0..1
ExtractedNumber		 Nominal static magnetic field strength in tesla direct
pulse_sequence_type 0..1
ExtractedString		 General pulse sequence family, such as EPI, MPRAGE, SPGR, or spin echo direct
mr_acquisition_type 0..1
ExtractedString		 Acquisition dimensionality, such as 2D or 3D; useful for distinguishing proto... direct
repetition_time_seconds 0..1
ExtractedNumber		 Time between the start of successive acquired volumes, in seconds direct
echo_time_seconds 0..1
ExtractedNumberList		 Echo time in seconds, as a list of one value per echo direct
acquisition_voxel_size_mm 0..1
ExtractedNumberList		 Original acquisition voxel size [x, y, z] in millimeters, before interpolatio... direct
number_of_volumes 0..1
ExtractedInteger		 Number of acquired volumes contributing to the recording, when reported; a pr... 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:MRI
native neurostudy_ex:MRI

LinkML Source

Direct

name: MRI
description: An MRI acquisition of any kind -- functional, structural, or diffusion,
  as modality records. Its own attributes are the ones commonly useful for study selection,
  subgrouping, or sensitivity analyses in coordinate- or image-based meta-analysis.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
is_a: Acquisition
attributes:
  magnetic_field_strength_tesla:
    name: magnetic_field_strength_tesla
    description: Nominal static magnetic field strength in tesla.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - MRI
    range: ExtractedNumber
  pulse_sequence_type:
    name: pulse_sequence_type
    description: General pulse sequence family, such as EPI, MPRAGE, SPGR, or spin
      echo.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - MRI
    range: ExtractedString
  mr_acquisition_type:
    name: mr_acquisition_type
    description: Acquisition dimensionality, such as 2D or 3D; useful for distinguishing
      protocols with materially different spatial sampling.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - MRI
    range: ExtractedString
  repetition_time_seconds:
    name: repetition_time_seconds
    description: Time between the start of successive acquired volumes, in seconds.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - MRI
    range: ExtractedNumber
  echo_time_seconds:
    name: echo_time_seconds
    description: Echo time in seconds, as a list of one value per echo. A multi-echo
      sequence has several; a single-echo one has a list of length one.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - MRI
    range: ExtractedNumberList
  acquisition_voxel_size_mm:
    name: acquisition_voxel_size_mm
    description: Original acquisition voxel size [x, y, z] in millimeters, before
      interpolation or resampling.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - MRI
    range: ExtractedNumberList
  number_of_volumes:
    name: number_of_volumes
    description: Number of acquired volumes contributing to the recording, when reported;
      a proxy for scan length and temporal sampling in functional acquisitions.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    domain_of:
    - MRI
    range: ExtractedInteger

Induced

name: MRI
description: An MRI acquisition of any kind -- functional, structural, or diffusion,
  as modality records. Its own attributes are the ones commonly useful for study selection,
  subgrouping, or sensitivity analyses in coordinate- or image-based meta-analysis.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
is_a: Acquisition
attributes:
  magnetic_field_strength_tesla:
    name: magnetic_field_strength_tesla
    description: Nominal static magnetic field strength in tesla.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: MRI
    domain_of:
    - MRI
    range: ExtractedNumber
  pulse_sequence_type:
    name: pulse_sequence_type
    description: General pulse sequence family, such as EPI, MPRAGE, SPGR, or spin
      echo.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: MRI
    domain_of:
    - MRI
    range: ExtractedString
  mr_acquisition_type:
    name: mr_acquisition_type
    description: Acquisition dimensionality, such as 2D or 3D; useful for distinguishing
      protocols with materially different spatial sampling.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: MRI
    domain_of:
    - MRI
    range: ExtractedString
  repetition_time_seconds:
    name: repetition_time_seconds
    description: Time between the start of successive acquired volumes, in seconds.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: MRI
    domain_of:
    - MRI
    range: ExtractedNumber
  echo_time_seconds:
    name: echo_time_seconds
    description: Echo time in seconds, as a list of one value per echo. A multi-echo
      sequence has several; a single-echo one has a list of length one.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: MRI
    domain_of:
    - MRI
    range: ExtractedNumberList
  acquisition_voxel_size_mm:
    name: acquisition_voxel_size_mm
    description: Original acquisition voxel size [x, y, z] in millimeters, before
      interpolation or resampling.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: MRI
    domain_of:
    - MRI
    range: ExtractedNumberList
  number_of_volumes:
    name: number_of_volumes
    description: Number of acquired volumes contributing to the recording, when reported;
      a proxy for scan length and temporal sampling in functional acquisitions.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/acquisition
    rank: 1000
    owner: MRI
    domain_of:
    - MRI
    range: ExtractedInteger
  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: MRI
    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: MRI
    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: MRI
    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: MRI
    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: MRI
    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: MRI
    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: MRI
    domain_of:
    - Acquisition
    range: ExtractedBrainCoverage