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Class: Region

A brain region the study delimited and used: a connectivity seed or target, the search space an analysis was restricted to, a level of a factor comparing regions, or the signal a model term carries. Declared once and referenced from each, because the same seed written separately in each place is three spellings nothing can join.

URI: neurostudy_ex:Region

 classDiagram
    class Region
    click Region href "../Region/"
      Region : atlas





        Region --> "0..1" ExtractedString : atlas
        click ExtractedString href "../ExtractedString/"



      Region : definition_method





        Region --> "1" ExtractedRegionDefinition : definition_method
        click ExtractedRegionDefinition href "../ExtractedRegionDefinition/"



      Region : description





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



      Region : local_id

      Region : name





        Region --> "1" ExtractedString : name
        click ExtractedString href "../ExtractedString/"



      Region : region_type





        Region --> "0..1" ExtractedRegionType : region_type
        click ExtractedRegionType href "../ExtractedRegionType/"



      Region : stable_id

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 direct
name 1
ExtractedString		 The region as the source names it -- aSCC, left dlPFC parcel, salience networ... direct
definition_method 1
ExtractedRegionDefinition		 How the region was delimited, which is a statement about independence: one dr... direct
region_type 0..1
ExtractedRegionType		 What kind of thing the region is, which definition_method does not settle: ... direct
atlas 0..1
ExtractedString		 The atlas, parcellation or template it came from, as named -- AAL, WFU_Pickat... direct
description 0..1
ExtractedString		 How the source defines the region, including any geometry it states: "8 mm sp... direct

Usages

used by used in type used
Analysis regions range Region
Analysis defines_regions range Region
ModelTerm region range Region
FactorLevel regions range Region
InferenceSettings correction_regions range Region
CoordinateSet regions range Region
Study regions range Region
ConnectivityDetails seed_regions range Region
ConnectivityDetails target_regions range Region
ConnectivityEdge source_region range Region
ConnectivityEdge target_region range Region

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Region
description: 'A brain region the study delimited and used: a connectivity seed or
  target, the search space an analysis was restricted to, a level of a factor comparing
  regions, or the signal a model term carries. Declared once and referenced from each,
  because the same seed written separately in each place is three spellings nothing
  can join.'
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/region
    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.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    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
  name:
    name: name
    description: 'The region as the source names it -- aSCC, left dlPFC parcel, salience
      network. Its own words: normalization to an anatomical vocabulary happens downstream
      and needs the original to map from.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Analysis
    - ModelTerm
    - ExternalDataset
    - PerformanceMetric
    range: ExtractedString
    required: true
  definition_method:
    name: definition_method
    description: 'How the region was delimited, which is a statement about independence:
      one drawn from the study''s own prior contrast is not independent of an effect
      tested inside it. Per region, since one analysis may use an atlas mask and a
      functional ROI at once. Required, so a source that does not say still carries
      the slot, as `extraction_status: not_reported`. Open vocabulary: write the source''s
      own wording in the field when nothing here fits, because the value is required
      and a closed range discards the whole region rather than the one unrecognised
      word.


      Two values are routinely confused and the difference is the entire point of
      the field. `functional_localizer` means a *separate* acquisition or run whose
      only purpose was to locate the region, independent of the effect later tested
      in it. A region that is a peak, a cluster, or a component of one of *this paper''s
      own* analyses is `same_study_analysis` however functionally it was defined --
      and that value is what makes the circularity visible, which is why `Analysis.defines_regions`
      exists to name the analysis it came from. Reaching for `functional_localizer`
      because the region is functional, rather than because a localizer was run, is
      the mistake to avoid.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    rank: 1000
    domain_of:
    - Region
    range: ExtractedRegionDefinition
    required: true
  region_type:
    name: region_type
    description: 'What kind of thing the region is, which `definition_method` does
      not settle: an atlas parcel and an anatomical structure can both come from an
      atlas, and a network is neither.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    rank: 1000
    domain_of:
    - Region
    range: ExtractedRegionType
  atlas:
    name: atlas
    description: 'The atlas, parcellation or template it came from, as named -- AAL,
      WFU_Pickatlas, Schaefer 400 -- with version or parcel index when given. `definition_method:
      atlas` records that one was used, not which, which is not enough to pool two
      studies.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    rank: 1000
    domain_of:
    - Region
    range: ExtractedString
  description:
    name: description
    description: 'How the source defines the region, including any geometry it states:
      "8 mm spheres centered at [0 36 -6]". Definitional coordinates have no structured
      slot and belong here, where the evidence span makes them checkable; result coordinates
      reach the record through the table parser instead.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - Table
    - CoordinateSet
    - Study
    range: ExtractedString

Induced

name: Region
description: 'A brain region the study delimited and used: a connectivity seed or
  target, the search space an analysis was restricted to, a level of a factor comparing
  regions, or the signal a model term carries. Declared once and referenced from each,
  because the same seed written separately in each place is three spellings nothing
  can join.'
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/region
    owner: Region
    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.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    identifier: true
    owner: Region
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  name:
    name: name
    description: 'The region as the source names it -- aSCC, left dlPFC parcel, salience
      network. Its own words: normalization to an anatomical vocabulary happens downstream
      and needs the original to map from.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    owner: Region
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Analysis
    - ModelTerm
    - ExternalDataset
    - PerformanceMetric
    range: ExtractedString
    required: true
  definition_method:
    name: definition_method
    description: 'How the region was delimited, which is a statement about independence:
      one drawn from the study''s own prior contrast is not independent of an effect
      tested inside it. Per region, since one analysis may use an atlas mask and a
      functional ROI at once. Required, so a source that does not say still carries
      the slot, as `extraction_status: not_reported`. Open vocabulary: write the source''s
      own wording in the field when nothing here fits, because the value is required
      and a closed range discards the whole region rather than the one unrecognised
      word.


      Two values are routinely confused and the difference is the entire point of
      the field. `functional_localizer` means a *separate* acquisition or run whose
      only purpose was to locate the region, independent of the effect later tested
      in it. A region that is a peak, a cluster, or a component of one of *this paper''s
      own* analyses is `same_study_analysis` however functionally it was defined --
      and that value is what makes the circularity visible, which is why `Analysis.defines_regions`
      exists to name the analysis it came from. Reaching for `functional_localizer`
      because the region is functional, rather than because a localizer was run, is
      the mistake to avoid.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    rank: 1000
    owner: Region
    domain_of:
    - Region
    range: ExtractedRegionDefinition
    required: true
  region_type:
    name: region_type
    description: 'What kind of thing the region is, which `definition_method` does
      not settle: an atlas parcel and an anatomical structure can both come from an
      atlas, and a network is neither.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    rank: 1000
    owner: Region
    domain_of:
    - Region
    range: ExtractedRegionType
  atlas:
    name: atlas
    description: 'The atlas, parcellation or template it came from, as named -- AAL,
      WFU_Pickatlas, Schaefer 400 -- with version or parcel index when given. `definition_method:
      atlas` records that one was used, not which, which is not enough to pool two
      studies.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    rank: 1000
    owner: Region
    domain_of:
    - Region
    range: ExtractedString
  description:
    name: description
    description: 'How the source defines the region, including any geometry it states:
      "8 mm spheres centered at [0 36 -6]". Definitional coordinates have no structured
      slot and belong here, where the evidence span makes them checkable; result coordinates
      reach the record through the table parser instead.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/region
    owner: Region
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - Table
    - CoordinateSet
    - Study
    range: ExtractedString