openminds.v5.neuroimaging¶

In-depth metadata for neuroimaging experiments, including MRI acquisition and equipment.

Activities¶

class StaticMRIAcquisition(lookup_label=None, contrast_agents=None, custom_property_sets=None, description=None, device=None, distortion_corrections=None, end_time=None, inputs=None, is_part_of=None, motion_corrections=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, registration_data=None, specimen_orientation=None, start_time=None, study_targets=None, target_anatomy=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

contrast_agents (AmountOfChemical) – no description available
custom_property_sets (CustomPropertySet) – no description available
description (str) – Longer statement or account giving the characteristics of the static m r i acquisition.
device (MRIScannerUsage) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.
distortion_corrections (File) – no description available
end_time (datetime, time) – no description available
inputs (SubjectState, TissueSampleState) – Something or someone that is put into or participates in a process or machine.
is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.
lookup_label (str) – no description available
motion_corrections (File) – no description available
outputs (File) – Something or someone that comes out of, is delivered or produced by a process or machine.
performed_by (SoftwareAgent, Person) – no description available
preparation_design (PreparationType) – no description available
protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.
registration_data (File) – no description available
specimen_orientation (AnatomicalAxesOrientation) – no description available
start_time (datetime, time) – no description available
study_targets (AnatomicalCavity, AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, DeviceType, Disease, DiseaseModel, ElectricalStimulusType, ExternalBodyRegion, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, TissueStructure, VascularStructure, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.
target_anatomy (AnatomicalCavity, CellType, ExternalBodyRegion, MuscularStructure, NervousSystemStructure, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, SubcellularEntity, TissueStructure, VascularStructure, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available

class DynamicMRIAcquisition(lookup_label=None, behavioral_protocols=None, contrast_agents=None, custom_property_sets=None, delay_time=None, description=None, device=None, distortion_corrections=None, end_time=None, inputs=None, is_part_of=None, motion_corrections=None, number_of_discarded_volumes=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, registration_data=None, specimen_orientation=None, start_time=None, study_targets=None, target_anatomy=None, volume_acquisition_time=None, volume_timing=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

behavioral_protocols (BehavioralProtocol) – no description available
contrast_agents (AmountOfChemical) – no description available
custom_property_sets (CustomPropertySet) – no description available
delay_time (QuantitativeValue) – no description available
description (str) – Longer statement or account giving the characteristics of the dynamic m r i acquisition.
device (MRIScannerUsage) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.
distortion_corrections (File) – no description available
end_time (datetime, time) – no description available
inputs (SubjectState, TissueSampleState) – Something or someone that is put into or participates in a process or machine.
is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.
lookup_label (str) – no description available
motion_corrections (File) – no description available
number_of_discarded_volumes (int) – no description available
outputs (File) – Something or someone that comes out of, is delivered or produced by a process or machine.
performed_by (SoftwareAgent, Person) – no description available
preparation_design (PreparationType) – no description available
protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.
registration_data (File) – no description available
specimen_orientation (AnatomicalAxesOrientation) – no description available
start_time (datetime, time) – no description available
study_targets (AnatomicalCavity, AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, DeviceType, Disease, DiseaseModel, ElectricalStimulusType, ExternalBodyRegion, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, TissueStructure, VascularStructure, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.
target_anatomy (AnatomicalCavity, CellType, ExternalBodyRegion, MuscularStructure, NervousSystemStructure, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, SubcellularEntity, TissueStructure, VascularStructure, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available
volume_acquisition_time (QuantitativeValue) – no description available
volume_timing (QuantitativeValueArray) – no description available

Devices¶

class MRIScanner(name=None, contributions=None, description=None, internal_identifier=None, is_part_of=None, magnetic_field_strength=None, serial_number=None, type=None, usage=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

contributions (Organization, Person) – no description available
description (str) – Longer statement or account giving the characteristics of the m r i scanner.
internal_identifier (str) – Term or code that identifies the m r i scanner within a particular product.
magnetic_field_strength (QuantitativeValue) – no description available
name (str) – Word or phrase that constitutes the distinctive designation of the m r i scanner.
serial_number (str) – no description available
type (DeviceType, HardwareProduct) – Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.
is_part_of (Setup) – reverse of ‘has_parts’
usage (MRIScannerUsage) – reverse of ‘device’

class MRIScannerUsage(lookup_label=None, acceleration_factor=None, device=None, diffusion_encoding_parameters=None, dwell_time=None, echo_times=None, fat_suppression_technique=None, field_of_view=None, flip_angle=None, generation_device=None, gradient_correction=None, inversion_time=None, is_used_to_obtain=None, matrix_sizes=None, metadata_locations=None, mri_weighting=None, mt_pulse_shape=None, number_of_discarded_volumes=None, number_of_excitations=None, number_of_slices=None, parallel_acquisition_technique=None, phase_encoding_directions=None, placed_by=None, receiver_bandwidth=None, repetition_time=None, slice_angulations=None, slice_gap=None, slice_orientation=None, slice_thickness=None, slice_timing=None, spatial_encoding=None, spoiling_technique=None, total_read_out_time=None, transmitter_bandwidth=None, used_coils=None, used_in=None, used_specimen=None, voxel_size=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

acceleration_factor (int) – no description available
device (MRIScanner) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.
diffusion_encoding_parameters (File) – no description available
dwell_time (QuantitativeValue) – no description available
echo_times (QuantitativeValue) – no description available
fat_suppression_technique (MRIFatSuppressionTechnique) – no description available
field_of_view – no description available
flip_angle (QuantitativeValue) – no description available
gradient_correction (AnalysisTechnique) – no description available
inversion_time (QuantitativeValue) – no description available
lookup_label (str) – no description available
matrix_sizes (int) – no description available
metadata_locations (File, FileBundle) – no description available
mri_weighting (MRIWeighting) – no description available
mt_pulse_shape (PulseShape) – no description available
number_of_discarded_volumes (int) – no description available
number_of_excitations (int) – no description available
number_of_slices (int) – no description available
parallel_acquisition_technique (MRIParallelAcquisitionTechnique) – no description available
phase_encoding_directions (int) – no description available
receiver_bandwidth (QuantitativeValue) – no description available
repetition_time (QuantitativeValue) – no description available
slice_angulations (Real) – no description available
slice_gap (QuantitativeValue, QuantitativeValueRange) – no description available
slice_orientation (AnatomicalPlane) – no description available
slice_thickness (QuantitativeValue, QuantitativeValueRange) – no description available
slice_timing (QuantitativeValueArray) – no description available
spatial_encoding (SpatialEncoding) – no description available
spoiling_technique (MRISpoilingTechnique) – no description available
total_read_out_time (QuantitativeValue) – no description available
transmitter_bandwidth (QuantitativeValue) – no description available
used_coils (DeviceType, MRICoilUsage) – no description available
used_specimen (SubjectState, TissueSampleState) – no description available
voxel_size (QuantitativeValueArray) – Extent of the discrete elements comprising a three-dimensional entity.
generation_device (EphysStimulus) – reverse of ‘generated_by’
is_used_to_obtain (GridImage, GridImageSequence, GridImageStack, GridVolume, GridVolumeSequence, Measurement, RegularTimeSeries) – reverse of ‘obtained_with’
placed_by (ElectrodePlacement) – reverse of ‘devices’
used_in (CellPatching, DynamicMRIAcquisition, StaticMRIAcquisition) – reverse of ‘device’

class MRICoil(name=None, contributions=None, description=None, element_count=None, intended_mounting_location=None, internal_identifier=None, is_part_of=None, mounting_type=None, serial_number=None, type=None, usage=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

contributions (Organization, Person) – no description available
description (str) – Longer statement or account giving the characteristics of the m r i coil.
element_count (int) – no description available
intended_mounting_location (ExternalBodyRegion) – no description available
internal_identifier (str) – Term or code that identifies the m r i coil within a particular product.
mounting_type (DeviceMountingType) – no description available
name (str) – Word or phrase that constitutes the distinctive designation of the m r i coil.
serial_number (str) – no description available
type (DeviceType, HardwareProduct) – Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.
is_part_of (Setup) – reverse of ‘has_parts’
usage (MRICoilUsage) – reverse of ‘device’

class MRICoilUsage(lookup_label=None, active_elements=None, device=None, generation_device=None, is_used_to_obtain=None, metadata_locations=None, mounting_location=None, placed_by=None, signal_directionality=None, used_in=None, used_specimen=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

active_elements (str) – no description available
device (MRICoil) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.
lookup_label (str) – no description available
metadata_locations (File, FileBundle) – no description available
mounting_location (ExternalBodyRegion) – no description available
signal_directionality (SignalDirectionality) – no description available
used_specimen (SubjectState, TissueSampleState) – no description available
generation_device (EphysStimulus) – reverse of ‘generated_by’
is_used_to_obtain (GridImage, GridImageSequence, GridImageStack, GridVolume, GridVolumeSequence, Measurement, RegularTimeSeries) – reverse of ‘obtained_with’
placed_by (ElectrodePlacement) – reverse of ‘devices’
used_in (CellPatching, MRIScannerUsage) – reverse of devices, used_coils