Package: fmridataset 0.11.0.9000

Bradley Buchsbaum

fmridataset: Spatially Typed Annotated fMRI Datasets

Provides spatially typed, annotated observation-by-feature containers for functional magnetic resonance imaging (fMRI) data. The package aligns lazy numerical assays with observation metadata, feature metadata, experimental entities, and explicit neuroimaging spaces while retaining compatibility with NIfTI, HDF5, BIDS, and in-memory sources.

Authors:Bradley Buchsbaum [aut, cre]

fmridataset_0.11.0.9000.tar.gz
fmridataset_0.11.0.9000.zip(r-4.7-any)fmridataset_0.11.0.9000.zip(r-4.6-any)fmridataset_0.11.0.9000.zip(r-4.5-any)
fmridataset_0.11.0.9000.tgz(r-4.6-any)fmridataset_0.11.0.9000.tgz(r-4.5-any)
fmridataset_0.11.0.9000.tar.gz(r-4.7-any)fmridataset_0.11.0.9000.tar.gz(r-4.6-any)
fmridataset_0.11.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fmridataset/json (API)

# Install 'fmridataset' in R:
install.packages('fmridataset', repos = c('https://bbuchsbaum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bbuchsbaum/fmridataset/issues

Pkgdown/docs site:https://bbuchsbaum.github.io

On CRAN:

Conda:

6.07 score 3 packages 30 scripts 215 exports 67 dependencies

Last updated from:58c9f4c389. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK305
source / vignettesOK479
linux-releaseOK284
macos-releaseOK182
macos-oldrelOK204
windows-develOK263
windows-releaseOK282
windows-oldrelOK247
wasm-releaseOK152

Exports:active_assayadjacencyaligned_assay_setappend_provenanceappend_source_shardsapply_feature_validityas_array_sourceas_delarras_fmri_frameas_sampling_frameassayassaysassert_same_spaceauxiliary_tableaxis_blockaxis_block_dataaxis_blocksaxis_dataaxis_frameaxis_id_policyaxis_idsbasis_analysisbasis_projection_infobasis_spacebasis_space_from_decoderbasis_space_from_fmrilatentbasis_synthesisbind_observationsblock_applyblock_component_idsblock_componentsblock_manifestcanonical_bytescanonical_sha256canonicalization_contractcollect_assaycollect_spatial_mapscollection_common_spacecollection_digestcollection_framecollection_framescollection_idscollection_space_datacompare_frame_schemacompose_frame_linkscomposite_partcomposite_part_namescomposite_partscomposite_spacecontent_hashcontent_hash_contractcounting_sourceentitiesentityentity_blocksentity_dataentity_feature_validityentity_frameentity_idsentity_keyentity_namesentity_registryentity_registry_digestevent_dataevent_keyevent_tableexecute_block_planexecute_spatialexecution_pathexplainfault_sourcefds_frame_bindingsfds_frame_manifestfds_manifest_digestfds_schemafds_schema_versionfds_study_bindingsfds_study_manifestfds_study_manifest_digestfds_study_representationsfeature_axisfeature_blocksfeature_datafeature_idsfeature_mapfeature_map_digestfeature_map_from_targetfeature_map_operatorfeature_map_source_spacefeature_map_target_spacefeature_mapped_sourcefeaturesfilter_entitiesfilter_obsfmri_collectionfmri_framefmri_studyframe_from_fds_manifestframe_linkframe_schemaframe_schema_digesthas_temporal_schemahierarchy_completehierarchy_digesthierarchy_groupshierarchy_idshierarchy_indexhierarchy_levelshierarchy_relationsidentity_descriptorids_are_durableindex_spacekey_relationlocate_source_rowsmap_featuresmask_bankmask_bank_digestmask_valuesmemory_sourcen_featuresn_masksnative_shapenifti_array_sourcenifti_source_spaceobs_blocksobservation_axisobservation_idsobservation_validityobservationsopen_frameparcel_aggregationparcel_membershipparcel_spaceparcel_space_from_atlasparent_spaceplan_blocksprovenance_digestprovenance_graphprovenance_recordprovenance_recordsprovenance_tipsread_bids_boldreconstruct_spacerelationrelation_namesrelation_registryrelation_registry_digestrelationsreset_source_countsrestrict_spacerow_sharded_sourcesame_spaceselect_featuresshard_manifestsource_capabilitiessource_chunkssource_closesource_countssource_descriptorsource_dtypesource_errorsource_fingerprintsource_opensource_readsource_read_nativesource_realization_costsource_shapesource_viewspacespace_digestsparse_relationspatial_mapstudy_digeststudy_framestudy_framesstudy_from_fds_manifeststudy_idsstudy_linkstudy_linksstudy_tablestudy_tablessurface_spacesurface_space_from_neurosurftable_datatable_keytable_roletemporal_schemaunaligned_recordvalidate_against_schemavalidate_array_sourcevalidate_auxiliary_tablevalidate_entity_feature_validityvalidate_entity_registryvalidate_event_tablevalidate_fds_manifestvalidate_fds_study_manifestvalidate_feature_mapvalidate_fmri_collectionvalidate_fmri_studyvalidate_frame_schemavalidate_mask_bankvalidate_provenance_graphvalidate_relation_registryvalidate_unaligned_recordvalidity_coveragevalidity_entityvalidity_entity_idsvalidity_mask_bankvalidity_masked_sourcevalidity_matrixvalidity_spacevectorize_spacevolume_spacewrite_framezarr_array_source

Dependencies:assertthatbigassertrbigparallelrbigstatsrbitcachemclicodetoolscowplotcpp11dbscandeflistdelarrdigestdoParallelfarverfastmapffflockforeachfsfuturefuture.applygenericsggplot2globalsgluegtableisobanditeratorslabelinglatticelifecyclelistenvmagrittrMatrixmemoisemmapneuroim2parallellypatchworkpillarpkgconfigpspurrrR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRhpcBLASctlrlangrmioRNiftiRNiftyRegRSpectraS7scalesstringistringrtibbleutf8uuidvctrsviridisLitewithr

Feature spaces and maps
A masked volume | Views restrict the space | Same space, not merely same size | Parcels over a volume | Moving a frame between spaces | Bases and synthesis-only bases | Composite spaces | Where the package stops
Rendered fromfeature-spaces.Rmdusingknitr::rmarkdown

Last update: 2026-10-11
Started: 2026-09-07

Persistence, identity, and import
The FDS manifest | Identity domains | Fingerprints are not content hashes | HDF5 round trip | Import from BIDS | Choosing the right identity
Rendered frompersistence-and-import.Rmdusingknitr::rmarkdown

Last update: 2026-10-11
Started: 2026-09-07

Implementing an array source
The protocol | An RDS-backed source | Try it | Validate it | Composition comes for free | Checklist for a storage package
Rendered fromextending-sources.Rmdusingknitr::rmarkdown

Last update: 2026-09-13
Started: 2026-09-07

Frames: aligned fMRI data with explicit identity
Build a frame | Select by ID or by metadata | Views are lazy | Inspect without reading | Run structure is metadata | Durable and ephemeral IDs | Bind frames along observations | What a frame promises
Rendered fromfmridataset.Rmdusingknitr::rmarkdown

Last update: 2026-09-07
Started: 2026-09-07

Readme and manuals

Help Manual

Help pageTopics
Construct a strictly aligned assay setaligned_assay_set
Append immutable source shardsappend_source_shards
Apply one validity relation lazily to frame assaysapply_feature_validity
Serializable numerical array sourcesarray-source as_array_source source_capabilities source_chunks source_close source_dtype source_fingerprint source_open source_read source_read_native source_realization_cost source_shape
Convert an array source to a lazy delarr arrayas_delarr as_delarr.default
Coerce an object to the canonical frame protocolas_fmri_frame
Construct a typed auxiliary tableauxiliary_table
Validate and inspect a typed auxiliary tableauxiliary-table table_data table_key table_role validate_auxiliary_table
Construct an axis-aligned multivariate blockaxis_block axis_block_data block_components block_component_ids
Construct an annotated axisaxis_blocks axis_data axis_frame axis_ids
Construct a linear basis feature spacebasis_space
Construct a basis space from a synthesis dictionarybasis_space_from_decoder
Adapt fmrilatent spatial loadings to a basis feature spacebasis_space_from_fmrilatent
Inspect basis-space operatorsbasis-operators basis_analysis basis_projection_info basis_synthesis
Bind frames along observationsbind_observations
Apply a function to bounded feature blocksblock_apply
Inspect a frame block planblock_manifest
Encode and hash canonical R valuescanonical-encoding canonical_bytes canonical_sha256
Identity and canonicalization contractcanonicalization_contract
Collect one frame assay under an explicit memory budgetcollect_assay
Collect spatial maps through native or reconstructed readscollect_spatial_maps
Compute a deterministic collection digestcollection_digest
Access frames in an fMRI collectioncollection-accessors collection_frame collection_frames collection_ids
Summarize collection feature spacescollection-spaces collection_common_space collection_space_data
Compose source-to-target frame linkscompose_frame_links
Construct an ordered composite feature spacecomposite_space
Inspect composite feature-space partscomposite-parts composite_part composite_parts composite_part_names
Compute a numerical content hash of an array sourcecontent_hash content_hash.array_source content_hash.default content_hash.memory_source content_hash.row_sharded_source content_hash.source_view
Content-hash contractcontent_hash_contract
Developer tool: instrument an array sourcecounting_source reset_source_counts source_counts
Describe compressed entity-by-feature validityentity_feature_validity
Construct a keyed entity frameentity_frame
Construct and validate an entity registryentity_registry validate_entity_registry
Compute a stable entity-registry digestentity_registry_digest
Access entities from a frame or registryentities entity entity-accessors entity_names
Entity-frame accessorsentity-frame-accessors entity_blocks entity_data entity_ids entity_key
Construct a keyed event tableevent_table
Event-table accessorsevent-accessors event_data event_key
Execute a bounded frame block planexecute_block_plan
Stream an operation over spatial mapsexecute_spatial
Select a matrix or spatial execution pathexecution_path
Explain a frame without reading numerical valuesexplain
Developer tool: inject deterministic source failuresfault_source
Extract physical array bindings from a framefds_frame_bindings
Construct and validate an FDS v1 frame manifestfds_frame_manifest validate_fds_manifest
Compute a canonical FDS manifest digestfds_manifest_digest
FDS logical schema identityfds_schema fds_schema_version
Extract shared study-level physical bindingsfds_study_bindings
Construct and validate an FDS v2 study manifestfds_study_manifest validate_fds_study_manifest
Compute a canonical FDS study-manifest digestfds_study_manifest_digest
Extract canonical study representations for persistencefds_study_representations
Construct a spatial feature axisfeature_axis
Describe an explicit transformation between feature spacesfeature_map
Derive the canonical map owned by a parent-linked target spacefeature_map_from_target
Construct a lazy source transformed through a feature mapfeature_mapped_source
Validate and inspect feature mapsfeature-map-accessors feature_map_digest feature_map_operator feature_map_source_space feature_map_target_space validate_feature_map
Feature-space contractadjacency assert_same_space feature-space feature_data feature_ids native_shape n_features reconstruct_space reconstruct_space.surface_space restrict_space same_space space_digest vectorize_space
Validate and inspect entity-feature validityfeature-validity-accessors validate_entity_feature_validity validity_entity validity_entity_ids validity_mask_bank validity_matrix validity_space
Filter every study representation through one shared entity selectionfilter_entities
Filter frame observations using scalar metadatafilter_obs
Construct a collection of semantically equivalent fMRI framesfmri_collection
Construct a spatially typed annotated matrixfmri_frame
Construct a linked fMRI studyfmri_study
Reconstruct a frame from an FDS manifest and physical sourcesframe_from_fds_manifest
Describe a typed link between study representationsframe_link
Compute the canonical metadata-only frame schemaframe_schema
Frame accessorsactive_assay assay assays dim.fmri_frame dim.fmri_view features feature_blocks frame-accessors observations observation_axis observation_ids obs_blocks
Validate and compare canonical frame schemascompare_frame_schema frame-schema-validation frame_schema_digest validate_against_schema validate_frame_schema
Compute the deterministic digest of a hierarchy indexhierarchy_digest
Derive stable observation hierarchy indiceshierarchy_index
Access derived hierarchy index datahierarchy-accessors hierarchy_complete hierarchy_groups hierarchy_ids hierarchy_levels hierarchy_relations
Inspect axis ID durabilityaxis_id_policy id-policy ids_are_durable
Inspect typed identity domainsidentity_descriptor
Construct a generic indexed feature spaceindex_space
Describe a symbolic foreign-key relationkey_relation
Resolve logical observation rows to shardslocate_source_rows
Lazily transform a frame into a new feature domainmap_features
Construct a deduplicated, bit-packed bank of feature masksmask_bank
Validate and inspect a mask bankmask-bank-accessors mask_bank_digest mask_values n_masks validate_mask_bank
Construct an in-memory array sourcememory_source
Construct a pushdown-aware NIfTI array sourcenifti_array_source
Recover the spatial domain of a NIfTI sourcenifti_source_space
Resolve validity onto frame observationsobservation_validity
Construct a parent-linked parcel feature spaceparcel_space
Build a parcel space from a neuroatlas atlasparcel_space_from_atlas
Inspect parent-linked feature spaces and parcel-space operatorsparcel-operators parcel_aggregation parcel_membership parent_space
Plan bounded observation-by-feature blocksplan_blocks
Create a content-addressed provenance recordprovenance_record
Construct and inspect an immutable provenance graphappend_provenance provenance-graph provenance_digest provenance_graph provenance_records provenance_tips validate_provenance_graph
Read one subject's preprocessed BIDS BOLD data as an fmri_frameread_bids_bold
Construct a relation registryrelation_registry
Compute a stable relation-registry digestrelation_registry_digest
Access frame relationsrelation relation-accessors relations relation_names
Construct a manifest-backed row-sharded sourcerow_sharded_source
Select frame features using feature metadataselect_features
Inspect a row-sharded source manifestshard_manifest
Inspect and validate an array-source contractsource_descriptor validate_array_source
Build the structured conditions an array source may signalsource_error
Construct a lazy view over an array sourcesource_view
Feature-space accessorspace
Describe an explicit sparse or many-to-many relationsparse_relation
Recover a spatial map for one observationspatial_map
Compute a deterministic study digeststudy_digest
Reconstruct a study from semantic and physical componentsstudy_from_fds_manifest
Study representation accessorsstudy-accessors study_frame study_frames study_ids
Study link and table accessorsstudy-registries study_link study_links study_table study_tables
Construct a packed cortical surface feature spacesurface_space
Adapt a neurosurf geometry to a surface feature spacesurface_space_from_neurosurf
The observation-axis temporal contractas_sampling_frame has_temporal_schema temporal-schema temporal_schema
Construct a typed unaligned metadata recordunaligned_record
Validate a keyed event tablevalidate_event_table
Validate an fMRI collectionvalidate_fmri_collection
Validate a studyvalidate_fmri_study
Validate a relation registryvalidate_relation_registry
Validate a typed unaligned metadata recordvalidate_unaligned_record
Summarize feature coverage without imposing an analysis policyvalidity_coverage
Lazily mask invalid observation-feature cells with missing valuesvalidity_masked_source
Construct a packed volumetric feature spacevolume_space
Persist and reopen an fmri frameopen_frame write_frame
Construct an experimental Zarr array sourcezarr_array_source