| abs_tol |
Absolute tolerance for ODE integration |
| absolute_value |
Absolute value of the score at the time of assessment |
| accelerator |
Hardware accelerator: ‘cpu’, ‘gpu’, ‘tpu’ |
| acquisition |
Acquisition protocol or scanner information |
| acronym |
|
| active_contacts |
|
| additional_equations |
|
| additive |
Indicates whether the noise is additive |
| affect |
Affect function: what happens when the event triggers |
| affect_negative |
Affect on downcrossing (continuous events only) |
| affect_parameters |
Parameter symbols modifiable in the affect function |
| affect_states |
State variable symbols modifiable in the affect function |
| age |
|
| aggregate |
How to aggregate the result across dimensions |
| aggregation |
How to aggregate over time |
| algorithm |
Optimizer for this stage: ‘adam’, ‘adamw’, ‘sgd’, etc |
| algorithms |
Iterative parameter tuning algorithms (FIC, EIB, etc |
| amplitude |
|
| anatomicalAxesOrientation |
Add the axes orientation in standard anatomical terms (XYZ) |
| apply_every |
Apply update every N iterations |
| apply_on_dimension |
Which dimension to apply the transformation on |
| arguments |
Parameters/arguments for the function |
| atlas |
|
| autonomous |
Whether the system is autonomous (equations do not depend explicitly on time … |
| average |
Averaging mode across trials |
| axesOrigin |
Enter the origin (central point where all axes intersect) |
| axis |
Dimension along which the distribution is sampled |
| baseline_value |
Preoperative baseline value of the score |
| batch_size |
Batch size for vectorized operations (None = auto) |
| bc_type |
|
| bids |
BIDS filename entities for this dataset |
| bids_dir |
Path to BEP017-compliant BIDS directory for loading connectivity matrices |
| bothside |
Continue branch in both directions |
| boundaries |
|
| boundary_conditions |
|
| bounds |
Constraints on parameter values after update |
| branches |
Child branches to continue from detected bifurcation points (PO from Hopf, fo… |
| build_hash |
Deterministic hash/fingerprint of the resolved dependency set |
| call_args |
Arguments passed when calling the instance (call) |
| callable |
Software implementation reference (if software-based) |
| cases |
|
| center |
Add the center coordinate of this entity |
| class_call |
Class instantiation and call (alternative to callable/function) |
| class_reference |
Direct class reference (alternative to pipeline) |
| clinical_improvement |
Observed improvement relative to baseline based on a defined score |
| clinical_scores |
|
| coefficient |
|
| cohort |
BIDS cohort- entity (e |
| color |
Add the color code used for visual representation of this entity |
| comment |
|
| condition |
The condition for this block (e |
| condition_parameters |
Parameter symbols accessible in the condition function |
| condition_states |
State variable symbols accessible in the condition function |
| conditional |
|
| conditionals |
Conditional logic for piecewise equations |
| connectivity |
|
| connectivity_ref |
Reference to connectivity data (_conndata-network_connectivity |
| constructor_args |
Arguments passed to init when instantiating the class |
| contact_id |
Identifier (e |
| contacts |
List of physical contacts along the electrode |
| container_image |
Container image reference (e |
| continuation |
Override solver settings for this branch |
| continuations |
Numerical continuation and bifurcation analysis specifications |
| coordinate |
3D coordinate of the contact center in the defined coordinate space |
| coordinate_space |
|
| coordinates |
Node coordinates (x,y,z) in the given coordinate space |
| correlated |
|
| correlation |
|
| coupling |
Reusable coupling configurations referenced by edges (e |
| coupling_function |
Mathematical function defining the coupling |
| coupling_inputs |
|
| coupling_terms |
|
| coupling_variable |
Whether this state variable is transmitted to connected nodes through the cou… |
| data |
|
| data_file |
Path to companion data file |
| data_source |
|
| dataLocation |
|
| dataset_id |
|
| dataset_path |
Dataset path for array-valued parameters |
| date_created |
ISO 8601 (prov:generatedAtTime) |
| default |
|
| defaultImage |
Add all image files used as visual representation of this common coordinate s… |
| definition |
|
| degree |
Polynomial degree per mesh interval for collocation |
| delayed |
|
| delta_p |
Initial parameter offset from the bifurcation point |
| depends_on |
Algorithm to use as starting point for optimization |
| derivative_initial_value |
Initial value for the first time derivative, used when equation_order > 1 |
| derived_from |
|
| derived_from_model |
|
| derived_observations |
Observations derived from combining other observations |
| derived_parameters |
|
| derived_variables |
|
| description |
|
| descriptor |
Short alphanumeric identifier for the BIDS desc- filename entity (e |
| detect_bifurcation |
Bifurcation detection level |
| detect_fold |
Enable fold (limit point) detection |
| diagnosis |
|
| dimension |
Dimensionality of the coupling input (number of coupled values) |
| dimension_labels |
Ordered labels for the matrix columns (dim-1) when the matrix is non-square |
| directed |
Whether to generate a directed graph |
| discretization |
Discretization method for the branch solution |
| distance_unit |
Unit for distances/lengths in the network |
| distribution |
Distribution for sampling initial conditions per node |
| doi |
|
| domain |
|
| downsample_period |
Intermediate downsampling period (ms) |
| ds |
Initial arc-length step size |
| ds_max |
Maximum adaptive step size |
| ds_min |
Minimum adaptive step size |
| dt |
Time step (s) |
| dtype |
Data type for matrix values |
| duration |
|
| dynamics |
Dictionary of dynamics models keyed by name |
| ecosystem |
Package ecosystem or index (e |
| edge_matrix_files |
|
| edges |
List of directed edges with coupling references (optional, for explicit edge … |
| efield |
Metadata about the E-field result for this setting |
| electrode_id |
Unique identifier for this electrode |
| electrode_reference |
|
| electrodes |
|
| element |
Element/node index this range applies to |
| element_domains |
Per-element domain overrides for heterogeneous parameters |
| element_type |
|
| elements |
Connectivity (indices) or file reference to topology |
| engine |
Primary engine (must appear in environment |
| entities |
|
| environment |
|
| environment_type |
Category: conda, venv, docker, etc |
| equation |
|
| equation_order |
Order of the time derivative on the LHS |
| equation_type |
Type of equation: ‘differential’ (default) means dx/dt = rhs, ‘algebraic’ mea… |
| evaluator |
Who performed the rating (e |
| event_type |
Type of event trigger mechanism |
| events |
Events attached to this node (e |
| execution |
Per-optimization execution configuration (overrides experiment-level defaults… |
| explorations |
Parameter exploration/grid search specifications |
| explored_values |
Explicit explored values for this element |
| expression |
The equation to apply when the condition is met |
| extension |
|
| field |
Primary field being solved for (deprecated; use state_variables) |
| field_dynamics |
|
| file |
|
| find_fixpoint |
Whether to find a fixed point (steady state) before time integration |
| format |
Storage format in binary companion (dense, csr, coo) |
| free |
|
| free_parameters |
Parameters to optimize in this stage |
| freeze_parameters |
Parameters from previous stages to freeze (keep at optimized value but not up… |
| frequency |
|
| function |
Custom distribution function (PDF or sampling callable) |
| functions |
|
| gaussian |
Indicates whether the noise is Gaussian |
| generated_at |
Timestamp when this TimeSeries was generated |
| generated_by |
Software/agent identifier (prov:wasGeneratedBy) |
| geometry |
Optional file for geometry/ROI mask (e |
| graph_generator |
Graph generator specification |
| groups |
|
| handedness |
|
| has_reference |
|
| hash |
Build or artifact hash for exact reproducibility (wheel, sdist, image layer) |
| head |
|
| hemisphere |
Add the hemisphere of this entity |
| heterogeneous |
|
| hi |
Upper bound or stopping value |
| history |
|
| homepage |
|
| hyperparameters |
Stage-specific hyperparameters (e |
| id |
Unique node identifier |
| imaging_modality |
Type of imaging modality (BOLD, EEG, MEG, etc |
| includes |
Include update rules from other algorithms with optional argument overrides |
| incoming_states |
References to state variables from connected nodes (source) |
| initial_expression |
Analytic initial condition for the field |
| initial_state |
How to obtain the initial equilibrium |
| initial_value |
|
| inner_coupling |
For hierarchical coupling: inner coupling applied at regional level |
| input |
Simple input reference: name of previous function’s output in pipeline |
| integration |
Integration settings for optimization simulations (overrides experiment defau… |
| intensity |
Optional scalar or vector intensity parameter for noise |
| intermediate_expressions |
|
| iri |
|
| key |
Key/variable name within the file (for |
| keys |
Named keys for multi-dimensional coupling |
| label |
|
| labels_dimensions |
Mapping of dimension names to their labels (JSON-encoded dict) |
| labels_ordering |
Ordering of dimensions: Time, State Variable, Space, Mode |
| latex |
|
| learning_rate |
|
| learning_rate_schedule |
Learning rate schedule: ‘constant’, ‘linear’, ‘exponential’ |
| learning_rate_warmup |
Linear warmup of learning rate from 0 to learning_rate over n_iterations |
| lefthandside |
|
| license |
|
| linear_solver |
Linear solver for the Newton bordered system |
| lo |
Lower bound or starting value |
| loader |
Callable that loads the data (e |
| local_coupling_term |
|
| local_states |
References to state variables from local node (target) |
| log_scale |
Whether to use logarithmic spacing |
| loss |
Loss function call |
| manufacturer |
|
| max_bisection_steps |
Maximum bisection steps for bifurcation point localization |
| max_iterations |
|
| max_steps |
Maximum continuation steps |
| mesh |
|
| mesh_file |
Path to external mesh file (GIFTI, VTK, MSH, FreeSurfer, etc |
| mesh_format |
Explicit format override (gifti, freesurfer, meshio, vtk, gmsh) |
| mesh_intervals |
Number of mesh intervals (time slices) for collocation or trapezoid methods |
| method |
Discretization method |
| metric |
Metric equation for matching (e |
| modality |
Imaging modality or simulation output type |
| mode |
|
| model |
|
| model_equation_ref |
BIDS ModelEq reference: path to _eq |
| model_param_ref |
BIDS ModelParam reference: path to _param |
| model_type |
Coarse classification of this model (mean_field, neural_mass, phase_oscillato… |
| modes |
|
| modified |
|
| module |
|
| modules |
(Deprecated) Former ad-hoc list; use environment |
| n |
Number of points (alternative to step for grid exploration) |
| n_inversion |
Number of eigenvalue sign inversions to flag a bifurcation |
| n_iterations |
Number of iterations to run |
| n_parallel |
Parallel evaluations |
| n_regions |
Total number of regions |
| n_sections |
Number of shooting sections for shooting or Poincaré methods |
| n_threads |
Number of CPU threads per worker (-1 = auto-detect) |
| n_trials |
Number of independent trials per grid point |
| n_vertices |
Total number of vertices |
| n_workers |
Number of parallel workers (maps to pmap devices in JAX, processes in multipr… |
| name |
|
| nativeUnit |
Add the native unit that is used for this common coordinate space version |
| network |
|
| nev |
Number of eigenvalues to compute |
| newton_max_iterations |
Maximum Newton corrector iterations per step |
| newton_tol |
Absolute tolerance for Newton corrector convergence |
| node_mapping |
HDF5 dataset path for node-to-parent mapping |
| nodes |
List of nodes with individual dynamics (optional, for heterogeneous networks) |
| noise |
|
| noise_type |
|
| non_negative |
All values >= 0 |
| notes |
|
| number_of_elements |
Number of elements (triangles, quads, tetrahedra, etc |
| number_of_modes |
|
| number_of_nodes |
Number of nodes in the network (derived from nodes if not set) |
| number_of_stages |
|
| number_of_subjects |
Number of subjects in the tractography dataset |
| number_of_vertices |
Number of vertices in the mesh |
| objective |
What the algorithm optimizes for |
| observable |
Observable to compute at each point |
| observational_measures |
BEP017 measure names for observational targets (e |
| observations |
References to observations defined in the observations section |
| observed |
Observable functions computed from states, inputs, and parameters after simul… |
| ode_solver |
ODE solver for flow-based methods (shooting, poincaré) |
| on_region |
Mesh/atlas subset where BC applies |
| operator_type |
|
| operators |
|
| optimizations |
Parameter optimization configurations |
| optional |
|
| options |
Toolkit-specific string options (jacobian type, etc |
| originalLookupLabel |
Add the original label of this entity as defined in the parcellation terminol… |
| output |
Output variable names to include in simulation results |
| output_equation |
Output transformation equation (if equation-based) |
| outsym |
Output symbol names for the edge model |
| over |
Dimension to aggregate over (e |
| package |
Reference to the software package identity |
| parameters |
|
| parcellation |
Brain parcellation/atlas reference |
| parent_network |
Path/URI to parent (coarser) Network |
| parent_score |
If this score is a subscore of a broader composite |
| path |
|
| percent_change |
Percent change compared to preoperative baseline (positive = improvement) |
| period |
Sampling period for monitors (ms) |
| pipeline |
Ordered sequence of Functions |
| platform |
OS / architecture description (e |
| position |
Spatial coordinates (x, y, z) of the node |
| post_expression |
Post-processing expression applied after coupling |
| pre_expression |
Pre-processing expression applied before coupling |
| precision |
Floating point precision: ‘float32’ or ‘float64’ |
| preconditioner |
|
| preprocessing |
Optional preprocessing to apply after loading |
| processing_pipeline |
Processing pipeline used to generate the tractography |
| protocols |
All DBS protocols assigned to this subject |
| provenance |
W3C PROV-O aligned provenance |
| pulse_width |
|
| pycode |
Python code for the equation |
| quantity_kind |
Scalar, vector, or tensor |
| random_seed |
Base random seed for reproducibility |
| random_state |
|
| recon_path |
|
| reconstruction |
BIDS rec- entity (e |
| reference |
DOI, PMID or persistent identifier |
| references |
|
| region |
Brain region or anatomical label |
| region_mapping |
For hierarchical coupling: vertex-to-region mapping for aggregation |
| regional_connectivity |
For hierarchical coupling: region-to-region connectivity with weights and del… |
| regions |
|
| rel_tol |
Relative tolerance for ODE integration |
| relatedUBERONTerm |
Add the related anatomical entity as defined by the UBERON ontology |
| reported_optimum |
|
| repository |
|
| requirements |
|
| requires |
Observables required by this update rule |
| righthandside |
|
| role |
|
| run_id |
BIDS run number |
| sample |
|
| sampling_period |
Time between samples (inverse of sampling_rate) |
| sampling_period_unit |
Unit of the sampling period (e |
| sampling_rate |
Sampling rate in Hz |
| scale |
The scale this score belongs to, if applicable |
| scipy_ode_base |
|
| score |
|
| seed |
Random seed for reproducible graph generation |
| segmentation |
BIDS seg- entity (e |
| session_id |
BIDS session identifier |
| settings |
|
| sex |
|
| shape |
Matrix dimensions [N, M] |
| simulation_experiments |
|
| simulation_period |
Duration of each simulation step (e |
| size |
|
| skip_t |
Number of samples to skip at the start (transient removal) |
| software |
|
| software_environment |
Software environment used to generate this data |
| solver |
ODE solver for time_integration method |
| source |
|
| source_branch |
Name of a previously computed branch (for from_branch method) |
| source_code |
|
| source_experiment |
Reference to the SimulationExperiment that generated this TimeSeries |
| source_observations |
One or more observations to derive from |
| source_point |
Which point on the source branch: ‘endpoint’, ‘hopf:1’, ‘fold:2’, a step numb… |
| source_url |
Canonical source or repository URL |
| source_var |
Output variable from source node to use (e |
| sources |
|
| sparse |
Whether the coupling uses sparse representations |
| stages |
Ordered list of optimization stages |
| state |
Per-node initial state variable values, keyed by state variable name |
| state_variables |
|
| state_wise_sigma |
|
| step |
Step size |
| step_size |
|
| steps |
|
| stimulation |
|
| stimulation_variable |
|
| stimulus |
|
| structural_measures |
BEP017 measure names for structural connectivity (e |
| subject_id |
BIDS subject identifier |
| subjects |
|
| symbol |
|
| symmetry |
Edge symmetry type for NetworkDynamics |
| system_type |
|
| tail |
|
| tail_samples |
Number of samples from the end to use |
| target |
Target node ID (set for explicit edges, absent for template edges) |
| target_component |
Component to attach this event to |
| target_data |
Reference to empirical data observation for matching objectives |
| target_network |
Path or name of the Network whose nodes define the columns of a non-square (p… |
| target_parameter |
The parameter to update (e |
| target_structure |
Anatomical target structure from a brain atlas |
| target_value |
Target value for activity objectives |
| target_var |
Input variable on target node to connect to (e |
| target_variable |
State variable for activity targets (e |
| targets |
State variables this noise applies to; if omitted, applies globally |
| task_name |
BIDS task name for the simulation (e |
| template |
BIDS tpl- entity (e |
| tensor_coefficient |
Optional anisotropic tensor (e |
| terminology |
Add the parcellation terminology version used for this brain atlas version |
| threshold_applied |
Threshold value applied to the E-field simulation |
| time |
|
| time_dependent |
|
| time_integrator |
e |
| time_post_surgery |
Timepoint of assessment in days or months after implantation |
| time_range |
Time range for generated TimeSeries (for kernel generators) |
| time_scale |
Time unit for the integration / simulation |
| time_unit |
Default time unit for the network |
| timepoint |
Timepoint of assessment (e |
| timing_info |
|
| title |
|
| tol_stability |
Tolerance on real part of eigenvalue for stability boundary |
| tolerances |
Abs/rel tolerances |
| tractogram |
Reference to tractography data |
| trajectory |
The planned trajectory for electrode implantation |
| transforms |
Ordered list of transforms applied to edge property matrices |
| transient_time |
|
| trigger_times |
Predetermined trigger times for preset_time events |
| type |
Graph family name |
| unit |
Physical unit of measurement |
| update_expression |
|
| update_rules |
How parameters are updated each iteration |
| url |
(Deprecated) Use source_url |
| valid_diagonal |
Self-connections are meaningful |
| value |
|
| values |
|
| variable_of_interest |
|
| version |
Version of the instrument (e |
| version_spec |
Version or constraint specifier (e |
| vertex_to_region |
Array mapping each vertex index to its parent region index |
| voi |
Variable of interest index (which state variable to monitor) |
| volume_data |
Reference to raw or thresholded volume |
| warmup |
Whether to apply learning rate warmup to this update rule |
| warmup_from |
Previous stage to initialize from |
| warmup_source |
Reference to transient simulation result for history initialization (e |
| weighted |
Matrix entries carry weights (not just 0/1) |
| weighting |
|
| window_size |
Number of samples for windowed aggregation |
| x |
X coordinate |
| y |
Y coordinate |
| year |
|
| z |
Z coordinate |