Class: Preprocessing

An ordered preprocessing pipeline applied to acquired data before or as part of statistical modeling. This can be expanded with COBIDAS.

URI: neurostudy_ex:Preprocessing

 classDiagram
    class Preprocessing
    click Preprocessing href "../Preprocessing/"
      Preprocessing : description





        Preprocessing --> "0..1" ExtractedString : description
        click ExtractedString href "../ExtractedString/"



      Preprocessing : local_id

      Preprocessing : smoothing_fwhm_mm





        Preprocessing --> "0..1" ExtractedNumberList : smoothing_fwhm_mm
        click ExtractedNumberList href "../ExtractedNumberList/"



      Preprocessing : software





        Preprocessing --> "0..1" ExtractedStringList : software
        click ExtractedStringList href "../ExtractedStringList/"



      Preprocessing : stable_id

      Preprocessing : steps





        Preprocessing --> "0..1" ExtractedStringList : steps
        click ExtractedStringList href "../ExtractedStringList/"

Slots

Name	Cardinality and Range	Description	Inheritance
stable_id	0..1 String	UUID minted by the store the first time this entity appears, never by an extr...	direct
local_id	1 String	Stable identifier used by Analysis foreign-key references	direct
description	0..1 ExtractedString	Narrative overview of the pipeline, its inputs, outputs, and intended purpose	direct
software	0..1 ExtractedStringList	Software packages or methods used, including version and revision identifiers	direct
steps	0..1 ExtractedStringList	Ordered free-text preprocessing operation names, listed in execution order; e...	direct
smoothing_fwhm_mm	0..1 ExtractedNumberList	Full width at half maximum of the applied spatial smoothing kernel, in millim...	direct

Usages

used by	used in	type	used
ModelEstimation	preprocessing	range	Preprocessing
Study	preprocessings	range	Preprocessing

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Preprocessing
description: An ordered preprocessing pipeline applied to acquired data before or
  as part of statistical modeling. This can be expanded with COBIDAS.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
attributes:
  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/analysis
    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
    description: Stable identifier used by Analysis foreign-key references.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    identifier: true
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  description:
    name: description
    description: Narrative overview of the pipeline, its inputs, outputs, and intended
      purpose.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - Table
    - CoordinateSet
    - Study
    range: ExtractedString
  software:
    name: software
    description: Software packages or methods used, including version and revision
      identifiers.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - Preprocessing
    - ModelEstimation
    range: ExtractedStringList
  steps:
    name: steps
    description: Ordered free-text preprocessing operation names, listed in execution
      order; examples include slice-timing correction, motion correction, distortion
      correction, spatial normalization, and smoothing. The smoothing kernel itself
      is `smoothing_fwhm_mm` rather than a phrase in this list, because it is the
      one preprocessing parameter a synthesis filters on.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - Preprocessing
    range: ExtractedStringList
  smoothing_fwhm_mm:
    name: smoothing_fwhm_mm
    description: 'Full width at half maximum of the applied spatial smoothing kernel,
      in millimetres: a list of one value for an isotropic kernel and of three for
      an anisotropic [x, y, z] one. Record 0 when the source states that no smoothing
      was applied.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - Preprocessing
    range: ExtractedNumberList

Induced

name: Preprocessing
description: An ordered preprocessing pipeline applied to acquired data before or
  as part of statistical modeling. This can be expanded with COBIDAS.
from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction
rank: 1000
attributes:
  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/analysis
    owner: Preprocessing
    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
    description: Stable identifier used by Analysis foreign-key references.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    identifier: true
    owner: Preprocessing
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  description:
    name: description
    description: Narrative overview of the pipeline, its inputs, outputs, and intended
      purpose.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    owner: Preprocessing
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - Table
    - CoordinateSet
    - Study
    range: ExtractedString
  software:
    name: software
    description: Software packages or methods used, including version and revision
      identifiers.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: Preprocessing
    domain_of:
    - Preprocessing
    - ModelEstimation
    range: ExtractedStringList
  steps:
    name: steps
    description: Ordered free-text preprocessing operation names, listed in execution
      order; examples include slice-timing correction, motion correction, distortion
      correction, spatial normalization, and smoothing. The smoothing kernel itself
      is `smoothing_fwhm_mm` rather than a phrase in this list, because it is the
      one preprocessing parameter a synthesis filters on.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: Preprocessing
    domain_of:
    - Preprocessing
    range: ExtractedStringList
  smoothing_fwhm_mm:
    name: smoothing_fwhm_mm
    description: 'Full width at half maximum of the applied spatial smoothing kernel,
      in millimetres: a list of one value for an isotropic kernel and of three for
      an anisotropic [x, y, z] one. Record 0 when the source states that no smoothing
      was applied.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: Preprocessing
    domain_of:
    - Preprocessing
    range: ExtractedNumberList