| 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 |
| 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 |
|
| axesOrigin |
Enter the origin (central point where all axes intersect) |
| baseline_value |
Preoperative baseline value of the score |
| batch_size |
Batch size for vectorized operations (None = auto) |
| bc_type |
|
| bids_dir |
Path to BEP017-compliant BIDS directory for loading connectivity matrices |
| boundaries |
|
| boundary_conditions |
|
| bounds |
Constraints on parameter values after update |
| 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 |
| center_coordinates |
|
| 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 |
|
| color |
Add the color code used for visual representation of this entity |
| comment |
|
| condition |
The condition for this block (e |
| conditional |
|
| conditionals |
Conditional logic for piecewise equations |
| conduction_speed |
Conduction speed for computing delays from distances |
| 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 |
| 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 |
|
| data |
|
| data_source |
|
| dataLocation |
|
| dataset_id |
|
| default |
|
| defaultImage |
Add all image files used as visual representation of this common coordinate s… |
| definition |
|
| delayed |
|
| dependencies |
|
| depends_on |
Algorithm to use as starting point for optimization |
| derived_from |
|
| derived_from_model |
|
| derived_observations |
Observations derived from combining other observations |
| derived_parameters |
|
| derived_variables |
|
| description |
|
| diagnosis |
|
| dimension |
Dimensionality of the coupling input (number of coupled values) |
| directed |
Whether the edge is directed |
| discretization |
|
| distance_unit |
Unit for distances/lengths in the network (e |
| distribution |
For hierarchical coupling: distribution method (‘broadcast’, ‘weighted’) or c… |
| doi |
|
| domain |
|
| downsample_period |
Intermediate downsampling period (ms) |
| dt |
Time step (s) |
| dtype |
|
| duration |
|
| dynamics |
Dynamics model governing this node’s behavior |
| 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_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 |
|
| evaluator |
Who performed the rating (e |
| execution |
Per-optimization execution configuration (overrides experiment-level defaults… |
| explorations |
Parameter exploration/grid search specifications |
| explored_values |
|
| expression |
The equation to apply when the condition is met |
| extension |
|
| field |
Primary field being solved for (deprecated; use state_variables) |
| field_dynamics |
|
| file |
|
| format |
Data format: ‘npy’, ‘mat’, ‘csv’, ‘nifti’, etc |
| 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 |
Reference to a defined Function (by name) |
| functions |
|
| gaussian |
Indicates whether the noise is Gaussian |
| generated_at |
Timestamp when this TimeSeries was generated |
| geometry |
Optional file for geometry/ROI mask (e |
| global_coupling_strength |
Global scaling factor for all coupling weights |
| 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 |
Initial values for state variables |
| 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 |
|
| lo |
Lower bound or starting value |
| loader |
Callable that loads the data (e |
| local_coupling_term |
|
| local_dynamics |
Default dynamics model for all nodes (used when node |
| local_states |
References to state variables from local node (target) |
| log_scale |
Whether to use logarithmic spacing |
| loss |
Loss function call |
| manufacturer |
|
| max_iterations |
|
| mesh |
|
| method |
Integration method (euler, heun, rk4, etc |
| 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 |
| modes |
|
| modified |
|
| module |
|
| modules |
(Deprecated) Former ad-hoc list; use environment |
| n |
Number of points (alternative to step for grid exploration) |
| n_iterations |
Number of iterations to run |
| n_parallel |
Parallel evaluations |
| n_regions |
Total number of regions |
| n_threads |
Number of CPU threads per worker (-1 = auto-detect) |
| 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 |
|
| nodes |
List of nodes with individual dynamics (optional, for heterogeneous networks) |
| noise |
|
| noise_type |
|
| normalization |
Normalization equation for connectivity weights |
| notes |
|
| number_of_modes |
|
| number_of_nodes |
Number of nodes in the network (derived from nodes if not set) |
| number_of_regions |
Number of regions (derived from nodes if not set) |
| number_of_stages |
|
| number_of_subjects |
Number of subjects in the tractography dataset |
| 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 |
| on_region |
Mesh/atlas subset where BC applies |
| operator_type |
|
| operators |
|
| optimization |
Parameter optimization configurations |
| optional |
|
| 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) |
| over |
Dimension to aggregate over (e |
| package |
Reference to the software package identity |
| parameters |
|
| parcellation |
Brain parcellation/atlas reference |
| 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 |
| 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 |
|
| reference |
DOI, PMID or persistent identifier |
| references |
|
| region |
Brain region or anatomical label |
| region_labels |
|
| 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 |
|
| 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 |
|
| session_id |
BIDS session identifier |
| settings |
|
| sex |
|
| shape |
|
| 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 |
|
| source |
|
| source_code |
|
| source_experiment |
Reference to the SimulationExperiment that generated this TimeSeries |
| source_observations |
One or more observations to derive from |
| 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_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 |
|
| system_type |
|
| tail |
|
| tail_samples |
Number of samples from the end to use |
| target |
Target node ID |
| target_data |
Reference to empirical data observation for matching objectives |
| 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 |
| 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 |
Default time unit for the network (e |
| timepoint |
Timepoint of assessment (e |
| timing_info |
|
| title |
|
| tolerances |
Abs/rel tolerances |
| tractogram |
Reference to tractography data |
| trajectory |
The planned trajectory for electrode implantation |
| transient_time |
|
| type |
|
| unit |
|
| update_expression |
|
| update_rules |
How parameters are updated each iteration |
| url |
(Deprecated) Use source_url |
| 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 |
| weighting |
|
| window_size |
Number of samples for windowed aggregation |
| x |
X coordinate |
| y |
Y coordinate |
| year |
|
| z |
Z coordinate |