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:Region

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

      Region : definition_method

      Region : description

      Region : id

      Region : name

      Region : region_type

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 String	Stable identifier	direct
name	1 String	The region as the source names it -- aSCC, left dlPFC parcel, salience networ...	direct
definition_method	1 String or  RegionDefinition	How the region was delimited, which is a statement about independence: one dr...	direct
region_type	0..1 String or  RegionType	What kind of thing the region is, which definition_method does not settle: ...	direct
atlas	0..1 String	The atlas, parcellation or template it came from, as named -- AAL, WFU_Pickat...	direct
description	0..1 String	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

Rules

Rule Applied	Preconditions	Postconditions	Elseconditions
slot_conditions

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	neurostudy:Region
native	neurostudy: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-storage
rank: 1000
attributes:
  id:
    name: id
    description: Stable identifier.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    identifier: true
    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
  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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Analysis
    - ModelTerm
    - ExternalDataset
    - PerformanceMetric
    range: string
    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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    rank: 1000
    domain_of:
    - Region
    required: true
    any_of:
    - range: RegionDefinition
    - range: string
  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.'
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    rank: 1000
    domain_of:
    - Region
    any_of:
    - range: RegionType
    - range: string
  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.'
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    rank: 1000
    domain_of:
    - Region
    range: string
  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.'
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - StatisticalMap
    - Table
    - CoordinateSet
    - Study
    range: string
rules:
- preconditions:
    slot_conditions:
      name:
        name: name
        pattern: (?i)^\s*(bi|bi-)?(lateral\s+)?(whole\s+)?(gr[ae]y|white)[\s-]*matter\s*(mask|volume|density|concentration|images?|regions?)?\s*$
  postconditions:
    slot_conditions:
      name:
        name: name
        value_presence: ABSENT
  description: A bare tissue class is not a region. Record the mask as InferenceSettings.search_volume
    and leave the analysis whole-brain.

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-storage
rank: 1000
attributes:
  id:
    name: id
    description: Stable identifier.
    in_subset:
    - mvp
    - deterministic
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    identifier: true
    owner: Region
    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
  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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    owner: Region
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Analysis
    - ModelTerm
    - ExternalDataset
    - PerformanceMetric
    range: string
    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.'
    in_subset:
    - mvp
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    rank: 1000
    owner: Region
    domain_of:
    - Region
    range: string
    required: true
    any_of:
    - range: RegionDefinition
    - range: string
  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.'
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    rank: 1000
    owner: Region
    domain_of:
    - Region
    range: string
    any_of:
    - range: RegionType
    - range: string
  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.'
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    rank: 1000
    owner: Region
    domain_of:
    - Region
    range: string
  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.'
    in_subset:
    - model_extracted
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-storage/region
    owner: Region
    domain_of:
    - StudyDesign
    - Arm
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Preprocessing
    - StatisticalMap
    - Table
    - CoordinateSet
    - Study
    range: string
rules:
- preconditions:
    slot_conditions:
      name:
        name: name
        pattern: (?i)^\s*(bi|bi-)?(lateral\s+)?(whole\s+)?(gr[ae]y|white)[\s-]*matter\s*(mask|volume|density|concentration|images?|regions?)?\s*$
  postconditions:
    slot_conditions:
      name:
        name: name
        value_presence: ABSENT
  description: A bare tissue class is not a region. Record the mask as InferenceSettings.search_volume
    and leave the analysis whole-brain.