Class: InferenceSettings

One thresholding and correction procedure. This is the canonical storage home for thresholding, correction, and cluster-inference metadata. The test statistic itself belongs to the tested effect and lives in Effect.statistic.

One record may be referenced by several Analyses, so every field must hold for all of them; an analysis thresholded or corrected differently takes its own record. The test is mechanical: two analyses share a record when the threshold, its type, the correction method, the scope corrected over and the alpha are all the same. A paper that states one correction scheme in Methods and applies it throughout has one record.

Inference attaches to the analysis, not to the fit: one model estimated once is often thresholded several ways -- an ROI test Bonferroni-corrected over four regions and a searchlight over the same fit corrected by FDR. See storage-schema-design-notes.md for the reasoning behind this shape.

URI: neurostudy_ex:InferenceSettings

 classDiagram
    class InferenceSettings
    click InferenceSettings href "../InferenceSettings/"
      InferenceSettings : alpha_level





        InferenceSettings --> "0..1" ExtractedNumber : alpha_level
        click ExtractedNumber href "../ExtractedNumber/"



      InferenceSettings : cluster_extent_threshold





        InferenceSettings --> "0..1" ExtractedInteger : cluster_extent_threshold
        click ExtractedInteger href "../ExtractedInteger/"



      InferenceSettings : clusterwise_threshold_value





        InferenceSettings --> "0..1" ExtractedNumber : clusterwise_threshold_value
        click ExtractedNumber href "../ExtractedNumber/"



      InferenceSettings : correction_regions





        InferenceSettings --> "*" Region : correction_regions
        click Region href "../Region/"



      InferenceSettings : correction_scope





        InferenceSettings --> "0..1" ExtractedSpatialScope : correction_scope
        click ExtractedSpatialScope href "../ExtractedSpatialScope/"



      InferenceSettings : height_threshold_type





        InferenceSettings --> "0..1" ExtractedString : height_threshold_type
        click ExtractedString href "../ExtractedString/"



      InferenceSettings : height_threshold_value





        InferenceSettings --> "0..1" ExtractedNumber : height_threshold_value
        click ExtractedNumber href "../ExtractedNumber/"



      InferenceSettings : inference_level





        InferenceSettings --> "0..1" ExtractedString : inference_level
        click ExtractedString href "../ExtractedString/"



      InferenceSettings : local_id

      InferenceSettings : multiple_comparison_method





        InferenceSettings --> "0..1" ExtractedString : multiple_comparison_method
        click ExtractedString href "../ExtractedString/"



      InferenceSettings : neighborhood_definition





        InferenceSettings --> "0..1" ExtractedString : neighborhood_definition
        click ExtractedString href "../ExtractedString/"



      InferenceSettings : number_of_tests





        InferenceSettings --> "0..1" ExtractedInteger : number_of_tests
        click ExtractedInteger href "../ExtractedInteger/"



      InferenceSettings : permutation_count





        InferenceSettings --> "0..1" ExtractedInteger : permutation_count
        click ExtractedInteger href "../ExtractedInteger/"



      InferenceSettings : search_volume





        InferenceSettings --> "0..1" ExtractedString : search_volume
        click ExtractedString href "../ExtractedString/"



      InferenceSettings : stable_id

      InferenceSettings : tfce_parameters





        InferenceSettings --> "0..1" ExtractedString : tfce_parameters
        click ExtractedString href "../ExtractedString/"



      InferenceSettings : tfce_used





        InferenceSettings --> "0..1" ExtractedBoolean : tfce_used
        click ExtractedBoolean href "../ExtractedBoolean/"

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
inference_level	0..1 ExtractedString	Level at which inference is made, such as voxel, vertex, cluster, region, net...	direct
height_threshold_value	0..1 ExtractedNumber	The threshold applied to each element's statistic, before correction and befo...	direct
height_threshold_type	0..1 ExtractedString	Meaning of height_threshold_value, such as p, q, t, z, or F	direct
cluster_extent_threshold	0..1 ExtractedInteger	Minimum surviving cluster extent in voxels, vertices, or the unit stated in t...	direct
clusterwise_threshold_value	0..1 ExtractedNumber	Numeric cluster-level threshold for retaining clusters	direct
multiple_comparison_method	0..1 ExtractedString	Correction method, such as FWE, FDR, Bonferroni, permutation, Monte Carlo, or...	direct
correction_scope	0..1 ExtractedSpatialScope	Whether the multiple-comparison correction searched the whole acquired volume...	direct
correction_regions	* Region	The regions correction was restricted to -- what correction_scope: roi name...	direct
search_volume	0..1 ExtractedString	Reported search volume, mask size, or number of vertices or voxels used for i...	direct
neighborhood_definition	0..1 ExtractedString	Voxel or vertex adjacency or connectivity rule used for cluster formation	direct
tfce_used	0..1 ExtractedBoolean	Whether threshold-free cluster enhancement was used	direct
tfce_parameters	0..1 ExtractedString	TFCE parameters such as height and extent exponents when reported	direct
permutation_count	0..1 ExtractedInteger	Number of permutations, randomizations, or simulations used for inference	direct
alpha_level	0..1 ExtractedNumber	Family-wise, false-discovery, or nominal alpha threshold when reported	direct
number_of_tests	0..1 ExtractedInteger	Number of statistical tests considered by the multiple-comparison procedure	direct

Usages

used by	used in	type	used
Analysis	inference_settings	range	InferenceSettings
Study	inference_settings	range	InferenceSettings

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: InferenceSettings
description: 'One thresholding and correction procedure. This is the canonical storage
  home for thresholding, correction, and cluster-inference metadata. The test statistic
  itself belongs to the tested effect and lives in Effect.statistic.

  One record may be referenced by several Analyses, so every field must hold for all
  of them; an analysis thresholded or corrected differently takes its own record.
  The test is mechanical: two analyses share a record when the threshold, its type,
  the correction method, the scope corrected over and the alpha are all the same.
  A paper that states one correction scheme in Methods and applies it throughout has
  one record.

  Inference attaches to the analysis, not to the fit: one model estimated once is
  often thresholded several ways -- an ROI test Bonferroni-corrected over four regions
  and a searchlight over the same fit corrected by FDR. See storage-schema-design-notes.md
  for the reasoning behind this shape.'
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
  inference_level:
    name: inference_level
    description: Level at which inference is made, such as voxel, vertex, cluster,
      region, network or other.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedString
  height_threshold_value:
    name: height_threshold_value
    description: 'The threshold applied to each element''s statistic, before correction
      and before any cluster-level test. Papers name it for whichever of its two jobs
      they are describing -- the *voxelwise* (or vertexwise) threshold when elements
      are tested individually, the *cluster-forming* threshold when surviving elements
      are grouped into clusters -- and it is one number either way, applied once to
      the map. Record it once here, whichever word the source uses.

      Not the cluster-level threshold: `clusterwise_threshold_value` is the p or q
      a whole cluster had to beat, and `cluster_extent_threshold` the size it had
      to reach. A paper reporting "p < 0.001 uncorrected, cluster-level p < 0.05 FWE"
      states this field and `clusterwise_threshold_value`, not this field twice.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedNumber
  height_threshold_type:
    name: height_threshold_type
    description: Meaning of height_threshold_value, such as p, q, t, z, or F.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedString
  cluster_extent_threshold:
    name: cluster_extent_threshold
    description: Minimum surviving cluster extent in voxels, vertices, or the unit
      stated in the source.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedInteger
  clusterwise_threshold_value:
    name: clusterwise_threshold_value
    description: Numeric cluster-level threshold for retaining clusters.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedNumber
  multiple_comparison_method:
    name: multiple_comparison_method
    description: Correction method, such as FWE, FDR, Bonferroni, permutation, Monte
      Carlo, or none.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedString
  correction_scope:
    name: correction_scope
    description: 'Whether the multiple-comparison correction searched the whole acquired
      volume or was restricted to regions. The correction''s own domain, not the analysis''s:
      a whole-brain voxelwise model whose significance was corrected inside an anatomical
      mask has `Analysis.spatial_scope: whole_brain` and `correction_scope: roi`,
      and the two differing is the ordinary case rather than a contradiction.

      A domain the enum cannot name is written here as free text. An inference level
      such as "cluster level" is not a scope and belongs in `inference_level`.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedSpatialScope
  correction_regions:
    name: correction_regions
    description: 'The regions correction was restricted to -- what `correction_scope:
      roi` names, as `Analysis.regions` names what `spatial_scope: roi` restricts
      the search space to. Empty for a whole-brain correction.

      Not the analysis''s search space. Naming the correction mask on the analysis
      instead says the model was fitted within it, which is a different claim about
      what the paper did.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: Region
    multivalued: true
    inlined: false
  search_volume:
    name: search_volume
    description: Reported search volume, mask size, or number of vertices or voxels
      used for inference.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedString
  neighborhood_definition:
    name: neighborhood_definition
    description: Voxel or vertex adjacency or connectivity rule used for cluster formation.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedString
  tfce_used:
    name: tfce_used
    description: Whether threshold-free cluster enhancement was used.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedBoolean
  tfce_parameters:
    name: tfce_parameters
    description: TFCE parameters such as height and extent exponents when reported.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedString
  permutation_count:
    name: permutation_count
    description: Number of permutations, randomizations, or simulations used for inference.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedInteger
  alpha_level:
    name: alpha_level
    description: Family-wise, false-discovery, or nominal alpha threshold when reported.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedNumber
  number_of_tests:
    name: number_of_tests
    description: Number of statistical tests considered by the multiple-comparison
      procedure.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    domain_of:
    - InferenceSettings
    range: ExtractedInteger

Induced

name: InferenceSettings
description: 'One thresholding and correction procedure. This is the canonical storage
  home for thresholding, correction, and cluster-inference metadata. The test statistic
  itself belongs to the tested effect and lives in Effect.statistic.

  One record may be referenced by several Analyses, so every field must hold for all
  of them; an analysis thresholded or corrected differently takes its own record.
  The test is mechanical: two analyses share a record when the threshold, its type,
  the correction method, the scope corrected over and the alpha are all the same.
  A paper that states one correction scheme in Methods and applies it throughout has
  one record.

  Inference attaches to the analysis, not to the fit: one model estimated once is
  often thresholded several ways -- an ROI test Bonferroni-corrected over four regions
  and a searchlight over the same fit corrected by FDR. See storage-schema-design-notes.md
  for the reasoning behind this shape.'
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: InferenceSettings
    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: InferenceSettings
    domain_of:
    - Arm
    - Timepoint
    - Group
    - Task
    - Condition
    - Assessment
    - Region
    - Acquisition
    - Device
    - Analysis
    - Measure
    - Preprocessing
    - ModelEstimation
    - ModelTerm
    - InferenceSettings
    - Table
    - CoordinateSet
    - Study
    range: string
    required: true
  inference_level:
    name: inference_level
    description: Level at which inference is made, such as voxel, vertex, cluster,
      region, network or other.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedString
  height_threshold_value:
    name: height_threshold_value
    description: 'The threshold applied to each element''s statistic, before correction
      and before any cluster-level test. Papers name it for whichever of its two jobs
      they are describing -- the *voxelwise* (or vertexwise) threshold when elements
      are tested individually, the *cluster-forming* threshold when surviving elements
      are grouped into clusters -- and it is one number either way, applied once to
      the map. Record it once here, whichever word the source uses.

      Not the cluster-level threshold: `clusterwise_threshold_value` is the p or q
      a whole cluster had to beat, and `cluster_extent_threshold` the size it had
      to reach. A paper reporting "p < 0.001 uncorrected, cluster-level p < 0.05 FWE"
      states this field and `clusterwise_threshold_value`, not this field twice.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedNumber
  height_threshold_type:
    name: height_threshold_type
    description: Meaning of height_threshold_value, such as p, q, t, z, or F.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedString
  cluster_extent_threshold:
    name: cluster_extent_threshold
    description: Minimum surviving cluster extent in voxels, vertices, or the unit
      stated in the source.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedInteger
  clusterwise_threshold_value:
    name: clusterwise_threshold_value
    description: Numeric cluster-level threshold for retaining clusters.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedNumber
  multiple_comparison_method:
    name: multiple_comparison_method
    description: Correction method, such as FWE, FDR, Bonferroni, permutation, Monte
      Carlo, or none.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedString
  correction_scope:
    name: correction_scope
    description: 'Whether the multiple-comparison correction searched the whole acquired
      volume or was restricted to regions. The correction''s own domain, not the analysis''s:
      a whole-brain voxelwise model whose significance was corrected inside an anatomical
      mask has `Analysis.spatial_scope: whole_brain` and `correction_scope: roi`,
      and the two differing is the ordinary case rather than a contradiction.

      A domain the enum cannot name is written here as free text. An inference level
      such as "cluster level" is not a scope and belongs in `inference_level`.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedSpatialScope
  correction_regions:
    name: correction_regions
    description: 'The regions correction was restricted to -- what `correction_scope:
      roi` names, as `Analysis.regions` names what `spatial_scope: roi` restricts
      the search space to. Empty for a whole-brain correction.

      Not the analysis''s search space. Naming the correction mask on the analysis
      instead says the model was fitted within it, which is a different claim about
      what the paper did.'
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: Region
    multivalued: true
    inlined: false
  search_volume:
    name: search_volume
    description: Reported search volume, mask size, or number of vertices or voxels
      used for inference.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedString
  neighborhood_definition:
    name: neighborhood_definition
    description: Voxel or vertex adjacency or connectivity rule used for cluster formation.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedString
  tfce_used:
    name: tfce_used
    description: Whether threshold-free cluster enhancement was used.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedBoolean
  tfce_parameters:
    name: tfce_parameters
    description: TFCE parameters such as height and extent exponents when reported.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedString
  permutation_count:
    name: permutation_count
    description: Number of permutations, randomizations, or simulations used for inference.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedInteger
  alpha_level:
    name: alpha_level
    description: Family-wise, false-discovery, or nominal alpha threshold when reported.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedNumber
  number_of_tests:
    name: number_of_tests
    description: Number of statistical tests considered by the multiple-comparison
      procedure.
    from_schema: https://neurostuff.org/schemas/neuroimaging-study-extraction/analysis
    rank: 1000
    owner: InferenceSettings
    domain_of:
    - InferenceSettings
    range: ExtractedInteger