Subset: model_extracted¶
Filled by a language model reading the source. The value is a claim about a publication, so it carries evidence in the extraction record and the only way to change it is to re-run the extractor.
Every field is in exactly one of deterministic and model_extracted, which is what pondie.schema.checks.field_provenance enforces. Neither generates a standalone schema: the two are interleaved down every path from the tree root, so pruning to either alone strands the other's fields.
URI: model_extracted
Identifier and Mapping Information¶
Annotations¶
| property | value |
|---|---|
| generates_schema | False |
Schema Source¶
- from schema: https://neurostuff.org/schemas/neuroimaging-study-storage
Slots in subset¶
| Slot | Description |
|---|---|
| acquired_count | Number for whom data were acquired or who were scanned |
| acquisition_duration_seconds | Total usable acquisition or recording duration in seconds |
| acquisition_voxel_size_mm | Original acquisition voxel size [x, y, z] in millimeters, before interpolatio... |
| acquisitions | The acquisition protocols used to collect data for this task |
| age_maximum | Oldest age reported for the group |
| age_mean | Mean participant age in the unit given by age_unit |
| age_median | Median participant age for the group |
| age_minimum | Youngest age reported for the group |
| age_standard_deviation | Standard deviation of participant age in the unit given by age_unit |
| age_unit | Unit used for age summaries, normally years but potentially months, weeks, or... |
| agent | The drug, agent, or stimulation target this arm received, as the source names... |
| allocation | How participants came to be in the arm they were in |
| alpha_level | Family-wise, false-discovery, or nominal alpha threshold when reported |
| analyses | Distinct analyses or inferential tests reported by the study, including those... |
| analysis | For a result, the analysis whose findings these are |
| analysis_id | Identifier of the sibling Analysis record for this component, when it is sepa... |
| analysis_type | The component's own method, when it is known and differs from the others |
| anchor_kind | For an anchor, what it defines |
| approached_count | Number of prospective participants approached for this group |
| arm | The arm this cohort was allocated to |
| arm_kind | What class of thing this arm received |
| arms | The arms of the study, active and comparator alike |
| assessment | The assessment whose measurements supply a continuous term, **including when ... |
| assessment_type | Broad type, such as cognitive test, clinical scale, diagnostic interview, que... |
| assessments | Assessments whose measurements were used in or selected the sample for this a... |
| assignment_structure | How the compared cohorts came about |
| atlas | The atlas, parcellation or template it came from, as named -- AAL, WFU_Pickat... |
| axis | What the qualifier varies |
| blinding | Who was kept unaware of the assignment |
| brain_coverage | How much of the brain the acquired volume contained |
| caption | Table caption describing the table's contents |
| category | The distribution bucket counted by this entry, labelled as the study writes i... |
| cells | What this contrast compared: one entry per level of a model term that entered... |
| classes | The classes discriminated |
| clinical_characteristics | Disease duration, severity, treatment status, or other clinically relevant su... |
| cluster_extent_threshold | Minimum surviving cluster extent in voxels, vertices, or the unit stated in t... |
| clusterwise_threshold_value | Numeric cluster-level threshold for retaining clusters |
| column_headings | Ordered leaf column headings retained to aid interpretation of extracted valu... |
| competing_models | Other models the reported model was compared against |
| component_id | Identifier of the component or latent variable within the decomposition, as r... |
| component_label | The source's name for the component, such as a network label, or for what a l... |
| components | The independently defined effects that were combined |
| condition | The experimental condition this class corresponds to, when it is one |
| condition_kind | What kind of state this was: an active task state, a rest or fixation period,... |
| conditions | The conditions this task was made of |
| connectivity_method | Method used to estimate connectivity |
| consented_count | Number who consented or assented to participate |
| coordinate_sets | Every group of coordinates the paper reports, in its tables or its text, with... |
| coordinate_space | Coordinate reference space or template the spatial results are reported in, s... |
| correction_regions | The regions correction was restricted to -- what correction_scope: roi name... |
| correction_scope | Whether the multiple-comparison correction searched the whole acquired volume... |
| count | Number of participants assigned to this category |
| crossblock_covariance_percent | Percentage of crossblock covariance this latent variable accounts for, as rep... |
| decoded_variable | The variable the classifier or discriminability test predicted |
| defines_regions | Regions this analysis produced: a localizer's clusters, or peaks of a contras... |
| definition | Precise statement of the tested effect in the source's own words, minimally c... |
| definition_method | How the region was delimited, which is a statement about independence: one dr... |
| degrees_of_freedom_denominator | Denominator degrees of freedom, used alone for t, correlation, and chi_square |
| degrees_of_freedom_numerator | Numerator degrees of freedom, normally populated only for f and likelihood_ra... |
| denominator | Number of participants used as the denominator for the percentage |
| description | Overall study design in narrative form, including observational or interventi... |
| design | The study's design outside its tasks: how participants were assigned, the arm... |
| design_type | How the task's events were modelled in time |
| details | The method that produced the map and its method-specific payload |
| device | The scanner, amplifier, or recording system this acquisition was made on, by ... |
| devices | The scanners, amplifiers, or recording systems the study collected data on |
| diagnostic_instrument | The study assessment that established this group's defining condition -- the ... |
| diagnostic_system | Classification system and edition under which this group's `medical_condition... |
| dimensionality_selection_method | How the number of components was chosen, as reported -- minimum description l... |
| direction | How this cell entered the contrast: the weight's sign for a categorical level... |
| echo_time_seconds | Echo time in seconds, as a list of one value per echo |
| edges | Named region pairs, when the source reports specific edges |
| education_summary | Aggregate education level and the measurement or coding system used |
| eeg_channel_count | Number of simultaneously recorded EEG channels |
| eeg_placement_scheme | Electrode placement system, such as the 10-20 or 10-10 system |
| eeg_reference | Reference scheme and location used for the raw recording |
| effect | What was tested about the map |
| enrolled_count | Number enrolled after screening and before acquisition |
| estimator | Estimation method, such as OLS, WLS, maximum likelihood, restricted maximum l... |
| ethnicity_distribution | Aggregate ethnic distribution using the study-reported category labels |
| excluded_count | Number excluded after consent, enrollment, acquisition, and quality control |
| exclusion_criteria | Screening, imaging-safety, clinical, behavioral, or quality-control criteria ... |
| explanation | What specifically could not be represented, in the source's own terms |
| external_datasets | Named external datasets used, cited, or made available by the study |
| family | The statistic used, independent of the thresholding procedure |
| footer | Table notes, abbreviations, threshold statements, and footnotes |
| functional_form | Shape of the term's relationship to the measure |
| gender_distribution | Aggregate self-described gender distribution, kept separate from phenotypic s... |
| generalization | Train/test split for cross-decoding, when the analysis generalized across set... |
| group | The cohort this entry refers to, by identifier |
| groups | The participant cohorts the analysis ran on, and how many participants each c... |
| handedness_distribution | Aggregate handedness distribution |
| height_threshold_type | Meaning of height_threshold_value, such as p, q, t, z, or F |
| height_threshold_value | The threshold applied to each element's statistic, before correction and befo... |
| hrf_model | The haemodynamic response basis the design matrix was built with: a canonical... |
| hypothesis | The study's own statement of what it expected to find, quoted from the paper ... |
| image_units | Units encoded in the PET image, such as Bq/mL or SUV |
| implementation | Procedure that computed the conjunction, recorded separately from the hypothe... |
| inclusion_criteria | Eligibility requirements that a participant had to satisfy for membership in ... |
| inference_level | Level at which inference is made, such as voxel, vertex, cluster, region, net... |
| inference_settings | The thresholding and correction this analysis was reported under, by identifi... |
| inference_target | What the statistical test was about: the strength of a connection, which of s... |
| inputs_from | The models whose fitted output this model was estimated on: the first-level G... |
| instructions | Task- or paradigm-specific instructions given to participants |
| interaction_with | The other terms this term is a product of -- what makes this column an intera... |
| interpretations | The source's own statement of what this analysis found and what it means, typ... |
| kind | What kind of test these cells describe, stated as well as encoded |
| label | The source's wording for this level in this comparison, when it differs from ... |
| level | The level represented by this cell, matching a `FactorLevel |
| levels | The levels of a categorical term, and for each the entities carrying it |
| magnetic_field_strength_tesla | Nominal static magnetic field strength in tesla |
| manufacturer | Company that made the device, as reported, such as Siemens, GE, Philips, Brai... |
| map_quantity | What the values of the reported map represent -- a loading, a weight, a PLS s... |
| measure | The scientific quantity of the map, by identifier, independent of the statist... |
| measures | The scientific quantities the study measured, used by one or more analyses |
| mediation | The mediation model this effect's quantity is a path through |
| mediator | The intervening term, by identifier |
| medical_condition | Medical, neurological, psychiatric, developmental, or physiological condition... |
| medication_status | Whether the cohort was medicated, unmedicated, drug-naive, or withdrawn, and ... |
| medications | The drugs or other agents this cohort was taking, as the source names them, o... |
| method | The algorithm that produced the components, which decides what their values a... |
| method_label | The method's name as the source gives it |
| modality | Imaging or recording modality |
| modality_label | The source's own name for the modality or recording technique, verbatim |
| mode_of_administration | Tracer administration mode, such as bolus, infusion, or bolus plus infusion |
| model | Model or product name of the device, as reported, such as Prisma, Signa, Achi... |
| model_estimation | The model this analysis's contrast was taken from: its family, estimator, sta... |
| model_estimations | Model estimation records used by one or more analyses |
| model_family | Normalized statistical model family, which is the queryable form |
| model_representation_notes | Model components that could not be represented or were represented only appro... |
| model_settings | Essential estimator, variance, autocorrelation, covariance, regularization, a... |
| model_type | The source's own wording for the model, minimally cleaned, such as mass- univ... |
| modulatory_input | Modulatory input of the model, for DCM and related methods |
| mr_acquisition_type | Acquisition dimensionality, such as 2D or 3D; useful for distinguishing proto... |
| multiple_comparison_method | Correction method, such as FWE, FDR, Bonferroni, permutation, Monte Carlo, or... |
| n | Number of participants from this cohort included in this analysis |
| name | Short arm label as the source states it, for example methylphenidate, sham tD... |
| neighborhood_definition | Voxel or vertex adjacency or connectivity rule used for cluster formation |
| neural_representation | How the neural pattern was defined, such as the voxel set or time window used |
| nirs_channel_count | Total number of NIRS channels, including short-separation channels |
| nirs_placement_scheme | Standard placement system or listed optode positions, such as 10-20, Cz, or P... |
| nirs_system_type | Instrument principle, such as continuous-wave, frequency-domain, or time-doma... |
| null_hypothesis | Which null hypothesis was tested |
| number_of_tests | Number of statistical tests considered by the multiple-comparison procedure |
| number_of_volumes | Number of acquired volumes contributing to the recording, when reported; a pr... |
| order | Position of this occasion in the study's sequence, counting from 1 |
| outcome | Whether anything survived the threshold this analysis was tested at: a cluste... |
| paradigm | The name with every qualifier that says how this version varies taken off and... |
| path | The path through the mediation model represented by this effect's map |
| percentage | Percentage of the relevant group in this category |
| performance_measures | Behavioral variables recorded and summaries used to verify task performance |
| performance_metrics | The performance measures reported for this map, one entry each |
| permutation_count | Number of permutations, randomizations, or simulations used for inference |
| polarity_semantics | Whether the sign of the reported map carries meaning |
| population_characteristics | How this cohort deviates from the typical, where no other field covers it... |
| preprocessing | The pipelines that produced the data this model was fitted to |
| preprocessings | Preprocessing pipelines applied before statistical analysis |
| presentation_software | Stimulus-presentation software name, version, and operating system when repor... |
| prespecification | Whether this contrast was planned before the data were seen or arrived at aft... |
| pulse_sequence_type | General pulse sequence family, such as EPI, MPRAGE, SPGR, or spin echo |
| purpose | What this table is for |
| qualifier | The qualifier as the name prints it |
| race_distribution | Aggregate racial distribution using the study-reported category labels |
| reason | The kind of obstacle that prevented structuring, selected from a short vocabu... |
| reason_first_class_type_not_used | Why no first-class details subclass fits this method |
| reason_no_modality_class_used | Why this is not an MRI, EEG, FNIRS, or PET record |
| reconstructed_voxel_size_mm | Reconstructed PET voxel size [x, y, z] in millimeters |
| recorded_signal_types | Raw or derived channel signal types, such as continuous-wave amplitude, optic... |
| recording_type | Recording organization, such as continuous, discontinuous, or epoched |
| recruitment_dates | Free-text recruitment period when the source does not support a precise norma... |
| recruitment_method | How, where, and from what setting participants were recruited |
| reference_value | Numeric reference this measure was compared against, when reported -- chance ... |
| references | Works the source cites for this task, exactly as it writes them: an author-ye... |
| region | The region whose signal supplies this term: a seed timecourse, an ROI mean co... |
| region_type | What kind of thing the region is, which definition_method does not settle: ... |
| regions | The regions the analysis ran over -- its search space, what `spatial_scope: r... |
| relation | Direction of this measure relative to its own reference_value |
| relation_to_intervention | Where this occasion sits relative to the intervention |
| repetition_time_seconds | Time between the start of successive acquired volumes, in seconds |
| reporting_framework | The classification system the study used for these categories, in its own wor... |
| response_modality | How participants responded |
| result_kind | For a result, the kind of analysis that produced it |
| result_reporting | Whether the paper reports inferential analyses of its own |
| role | What these coordinates are for |
| salience_threshold | The criterion deciding which elements count as reliable contributors, as repo... |
| sample_overlap_count | How many of this group were in that prior report, when the source says so |
| sample_source | Where this group's participants came from |
| sample_source_reference | The dataset name, or the prior publication as the source cites it: an author-... |
| sampling_frequency_hz | Sampling frequency of the recording in hertz |
| scan_type | Whether the analyzed PET data were acquired or summarized as a static or dyna... |
| search_volume | Reported search volume, mask size, or number of vertices or voxels used for i... |
| second_block | What the brain block was decomposed against, one value per additional block, ... |
| second_block_assessments | The measures forming a behavioural or clinical block, by identifier, when the... |
| second_block_detail | What each non-assessment block held, in the source's words: the seed regions ... |
| seed_regions | Seed or source regions, by identifier |
| selection_criterion | How this component was selected for reporting |
| sex_distribution | Aggregate phenotypic sex distribution |
| short_channel_count | Number of short-separation channels; zero indicates none |
| similarity_metric | Similarity or distance metric |
| smoothing_fwhm_mm | Full width at half maximum of the applied spatial smoothing kernel, in millim... |
| socioeconomic_status_summary | Aggregate socioeconomic status and the instrument or proxy used to measure it |
| software | Software packages or methods used, including version and revision identifiers |
| source_definition | The source's own definition of the term, and the origin of a continuous term ... |
| source_detector_distances_mm | Reported source-detector separations in millimeters |
| source_label | The paper's own term for the measure |
| source_region | Source region of the edge, by identifier |
| source_table_analysis | The key of the coordinate-parse analysis this analysis's results were read fr... |
| spatial_resolution_mm | Reported reconstructed spatial resolution, such as FWHM dimensions, in millim... |
| spatial_scope | Spatial domain of the analysis modelled |
| spatial_unit | The element this model was fitted over |
| species | The species of this cohort |
| specific_metric | Named metric when type is intentionally broad, such as fractional anisotropy,... |
| stage | Stage of analysis, in the source's terms: run, session, subject and group are... |
| statistic | The statistic this effect was tested with, and its degrees of freedom |
| steps | Ordered free-text preprocessing operation names, listed in execution order; e... |
| stimuli | The materials presented to participants, in the source's own terms -- the sti... |
| stimulus_content | What the task's stimuli were about when that holds across all its conditions ... |
| stimulus_modality | The sensory channel the stimuli were delivered through |
| structured_details | JSON-encoded method-specific payload, when the method has structure worth kee... |
| table_number | Printed identifier such as Table 2 or Supplementary Table S4 |
| tables | The source tables reporting results for this analysis |
| target_region | Target region of the edge, by identifier |
| target_regions | Target regions, by identifier |
| tasks | The participant paradigms that contextualize this analysis |
| term | The model term this cell belongs to, by identifier |
| terms | The terms this stage was specified with -- the columns of its design matr... |
| tfce_parameters | TFCE parameters such as height and extent exponents when reported |
| tfce_used | Whether threshold-free cluster enhancement was used |
| time_from_intervention | Elapsed time between the intervention and this occasion, in the source's own ... |
| timepoints | The occasions on which data were collected |
| title | Table title, when distinct from the caption |
| total_components | Number of components or latent variables the decomposition produced |
| tracer_name | Name of the injected tracer compound |
| tracer_radionuclide | Radioisotope labeling the tracer, such as C11, F18, or O15 |
| type | Normalized quantity, for cross-study queries |
| unit | The unit the measure is reported in, when the source gives one and it carries... |
| uptake_time_seconds | Interval from tracer administration to the start of the analyzed scan window,... |
| validation_scheme | Cross-validation or resampling scheme, such as leave-one-run-out |
| value | The value as reported, in the source's own scale: a percentage and a proporti... |
| variance_explained_percent | Percentage of the brain block's variance this component accounts for, as repo... |
| variant_qualifiers | The words of name that paradigm leaves out, each with the axis it varies ... |
| variation_level | Whether this term moves within a participant or only across the sample |
| wavelengths_nm | Nominal emitted wavelengths in nanometers |
Enumerations in subset¶
| Enumeration | Description |
|---|---|
| Allocation | How participants came to be in the arm they were in |
| AnalysisOutcome | Whether the tested effect produced any finding at the threshold the source ap... |
| AnalysisType | The method that produced the statistical map, independent of what was tested ... |
| AnchorKind | What an anchor coordinate set defines |
| ArmKind | What class of thing an arm received |
| AssignmentStructure | How the cohorts a study compares came about |
| Blinding | Who was kept unaware of the assignment |
| BrainCoverage | Extent of the brain contained in an acquired volume |
| ConditionKind | What kind of state a condition was, in itself |
| ConjunctionImplementation | Procedure used to compute the conjunction, which is not the same statement as... |
| ConnectivityMethod | Method used to estimate connectivity |
| CoordinateRole | What a set of reported coordinates is, by what it is to the study and not by ... |
| DecompositionMethod | The algorithm that produced the components or latent variables, which decides... |
| DesignType | How a task's events were modelled in time -- not what the task was or what it... |
| Direction | How a term entered or came out of an analysis, using one vocabulary for every... |
| EffectKind | What kind of test an effect's cells describe |
| EffectPath | The path through a mediation model represented by an effect's map |
| FunctionalForm | Shape of a term's relationship to the measure |
| InferenceTarget | What the connectivity analysis drew inference about |
| MapQuantity | What the values of a component or latent-variable map represent |
| MeasureFamily | Broad imaging or signal family, for coarse filtering |
| MeasureType | Normalized scientific quantity of the map, for cross-study queries |
| ModelFamily | Statistical model family used to estimate the effect |
| NotStructurableReason | Why a grounded effect has no stable structured decomposition |
| NullHypothesis | The null hypothesis tested by a conjunction |
| PerformanceRelation | Direction of a decoding performance metric relative to its reference value |
| PolaritySemantics | Whether the sign of a component map carries meaning |
| Prespecification | Whether a contrast was planned before the data were seen |
| RegionDefinition | How a region was delimited, which records independence: a region drawn from t... |
| RegionType | What kind of thing a region is |
| ResponseModality | How participants responded during a task |
| ResultKind | The kind of analysis a result came from, coarse enough to read from a table... |
| ResultReporting | Whether a paper reports inferential analyses of its own |
| SampleSource | Where a participant group came from |
| SecondBlock | What a decomposition crossed the brain block with, one value per block |
| SpatialScope | Spatial domain of the analysis, and a meta-analysis inclusion criterion |
| SpatialUnit | The element an analysis was carried out over: the surface-versus-volume disti... |
| Species | Species of a participant cohort |
| StatisticFamily | Test statistic family for the tested effect, independent of the thresholding ... |
| StimulusModality | The sensory channel a task's stimuli were delivered through |
| TablePurpose | What a table is for |
| TaskVariantAxis | What a task-name qualifier varies about its paradigm |
| TermType | Whether a model term is categorical or continuous |
| TimepointRelation | Where an occasion sits relative to the intervention |
| VariationLevel | The level at which a term varies -- whether it moves within a participant or ... |