Package: fmridataset 0.8.9

Bradley Buchsbaum

fmridataset: Unified Container for fMRI Datasets

Provides a unified S3 class 'fmri_dataset' for representing functional magnetic resonance imaging (fMRI) data from various sources including raw NIfTI files, BIDS projects, pre-loaded NeuroVec objects, and in-memory matrices. Features lazy loading, flexible data access patterns, and integration with neuroimaging analysis workflows.

Authors:Bradley Buchsbaum [aut, cre]

fmridataset_0.8.9.tar.gz
fmridataset_0.8.9.zip(r-4.7)fmridataset_0.8.9.zip(r-4.6)fmridataset_0.8.9.zip(r-4.5)
fmridataset_0.8.9.tgz(r-4.6-any)fmridataset_0.8.9.tgz(r-4.5-any)
fmridataset_0.8.9.tar.gz(r-4.7-any)fmridataset_0.8.9.tar.gz(r-4.6-any)
fmridataset_0.8.9.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:

5.21 score 2 packages 49 scripts 112 exports 70 dependencies

Last updated from:0d3a0a595e. Checks:6 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK452
source / vignettesOK308
linux-release-x86_64OK449
macos-release-arm64OK281
macos-oldrel-arm64OK251
windows-develERROR493
windows-releaseERROR488
windows-oldrelERROR455
wasm-releaseOK186

Exports:%||%all_selectorall_timepointsanalyze_runas_delarras_delayed_arrayas_fmri_groupas.matrix_datasetbackend_closebackend_get_databackend_get_dimsbackend_get_loadingsbackend_get_maskbackend_get_metadatabackend_openbackend_reconstruct_voxelsbids_h5_datasetbids_h5_scan_backendblockidsblocklenscollect_chunkscompress_bids_studycreate_backenddata_chunkdata_chunksencoding_infoexec_strategyfilter_subjectsfmri_cache_infofmri_cache_resizefmri_clear_cachefmri_datasetfmri_dataset_legacyfmri_groupfmri_h5_datasetfmri_latent_datasetfmri_mem_datasetfmri_seriesfmri_study_datasetfmri_zarr_datasetgenerate_benchmark_datagenerate_example_eventsgenerate_example_fmri_datagenerate_example_maskgenerate_example_pathsget_backend_registryget_component_infoget_confoundsget_dataget_data_matrixget_latent_scoresget_loadingsget_maskget_run_durationget_run_lengthsget_spatial_loadingsget_total_durationget_TRgroup_mapgroup_reduceh5_backendh5_shared_connectionindex_selectoris_backend_registeredis.fmri_seriesis.sampling_frameiter_subjectslatent_backendlatent_datasetleft_join_subjectslist_backend_namesmask_selectormask_to_logicalmask_to_volumematrix_backendmatrix_datasetmutate_subjectsn_runsn_subjectsn_timepointsnew_fmri_seriesnifti_backendparcellation_infoparticipantsprint_dataset_inforead_fmri_configreconstruct_voxelsregister_backendresolve_indicesresolve_selectorresolve_timepointsroi_selectorsample_subjectssamplesscan_manifestseriessessionssphere_selectorstream_subjectsstudy_backendstudy_to_groupsubject_idssubjectssubjects<-subset_bids_h5tasksunregister_backendvalidate_fmri_groupvoxel_selectorwith_rowDatawrite_fmri_configzarr_backend

Dependencies:assertthatbigassertrbigparallelrbigstatsrbitcachemclicodetoolscowplotcpp11dbscandeflistdelarrdigestdoParallelfarverfastmapffflockfmrihrfforeachfsfuturefuture.applygenericsggplot2globalsgluegtableisobanditeratorsjsonlitelabelinglatticelifecyclelistenvmagrittrMatrixmemoisemmapneuroim2numDerivparallellypatchworkpillarpkgconfigpracmapspurrrR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRhpcBLASctlrlangrmioRNiftiRNiftyRegRSpectraS7scalesstringistringrtibbleutf8vctrsviridisLitewithr

Architecture Overview
Layer Diagram | The Backend Contract | Dataset Classes | matrix_dataset | fmri_file_dataset | latent_dataset | fmri_study_dataset | Temporal Structure | Extension Points | Adding a New Backend | BIDS + HDF5 as a Concrete Example | Object Zoo | Related Vignettes
Rendered fromarchitecture-overview.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2025-08-14

BIDS H5 Archive: Compressing a Study into a Single File
Which compression mode should you use? | How do you create an archive? | Parcellated mode | Latent mode | How do you open an archive? | Exploring the study | Subsetting by task, subject, or session | Accessing data | Events | Confounds | Chunked iteration | Group operations | Latent-mode extras | Parcellation metadata | Next steps
Rendered frombids-h5-archive.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2026-03-29

Getting Started with fmridataset
Motivation | Creating a Dataset | Accessing Data | Temporal Structure | Event Tables | Chunked Processing | Run-wise Processing | File-based Datasets | See Also | Session Information
Rendered fromfmridataset-intro.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2025-05-31

Study-Level Analysis: From Single Subjects to Group Studies
Create per-subject datasets | Compose into fmri_study_dataset() | Access data | Chunked iteration | Group operations with fmri_group() | Next steps
Rendered fromstudy-level-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2025-06-10

Writing Custom Storage Backends
The six-method contract | backend_open(backend) | backend_close(backend) | backend_get_dims(backend) | backend_get_mask(backend) | backend_get_data(backend, rows = NULL, cols = NULL) | backend_get_metadata(backend) | Minimal working example: CSV backend | Registering your backend | Validation | Testing
Rendered frombackend-development-basics.Rmdusingknitr::rmarkdown

Last update: 2026-06-18
Started: 2025-08-26

Readme and manuals

Help Manual

Help pageTopics
All Voxels Series Selectorall_selector
Convert backend to a delarr lazy matrixas_delarr as_delarr.default as_delarr.matrix_backend as_delarr.nifti_backend as_delarr.study_backend
Convert Backend to DelayedArrayas_delayed_array as_delayed_array.default as_delayed_array.matrix_backend as_delayed_array.nifti_backend as_delayed_array.study_backend
Convert Dataset Objects to DelayedArrayas_delayed_array,fmri_file_dataset-method as_delayed_array,fmri_mem_dataset-method as_delayed_array,matrix_dataset-method as_delayed_array-dataset
Coerce a data frame into an fmri_groupas_fmri_group
Convert fmri_series to Tibbleas_tibble.fmri_series
Convert fmri_study_dataset to a tibble or lazy matrixas_tibble.fmri_study_dataset
Convert to Matrix Datasetas.matrix_dataset
Convert fmri_series to Matrixas.matrix.fmri_series
Open a BIDS HDF5 Study Archivebids_h5_dataset
Get Block IDs from Sampling Frameblockids blockids.fmri_dataset blockids.sampling_frame
Get Block Lengths from Objectsblocklens blocklens.fmri_dataset blocklens.sampling_frame
Collect all chunks from a chunk iteratorcollect_chunks
Compress a BIDS Study into a Single HDF5 Archivecompress_bids_study
Create Backend Instancecreate_backend
Create a Data Chunk Objectdata_chunk
Create Data Chunks for Processingdata_chunks
Create Data Chunks for fmri_file_dataset Objectsdata_chunks.fmri_file_dataset
Create Data Chunks for fmri_mem_dataset Objectsdata_chunks.fmri_mem_dataset
Create Data Chunks for fmri_study_dataset Objectsdata_chunks.fmri_study_dataset
Create Data Chunks for matrix_dataset Objectsdata_chunks.matrix_dataset
Dimensions of fmri_seriesdim.fmri_series
Get Encoding Metadata from a Latent-Mode BIDS H5 Datasetencoding_info encoding_info.bids_h5_study_dataset
Create an Execution Strategy for Data Processingexec_strategy
Filter subjects in an fmri_groupfilter_subjects
Get cache information and statisticsfmri_cache_info
Resize the fmridataset cachefmri_cache_resize
Clear fmridataset cachefmri_clear_cache
Create an fMRI Dataset Object from a Set of Scansfmri_dataset
Legacy fMRI Dataset Constructorfmri_dataset_legacy
Create an fmri_group (one row per subject)fmri_group
Create an fMRI Dataset Object from H5 Filesfmri_h5_dataset
Create an fMRI Dataset Object from LatentNeuroVec Files or Objectsfmri_latent_dataset
Create an fMRI Memory Dataset Objectfmri_mem_dataset
fmri_series: fMRI Time Series Containerfmri_series
Helpers for fmri_series spatial and temporal selectionfmri_series_resolvers
Create an fmri_study_datasetfmri_study_dataset
Create an fMRI Dataset from Zarr Arraysfmri_zarr_dataset
Generic Functions for fMRI Dataset Operationsgenerics
Get Registered Backend Informationget_backend_registry
Get Component Informationget_component_info
Get Confound Regressors from a BIDS H5 Datasetget_confounds get_confounds.bids_h5_study_dataset
Get Data from fMRI Dataset Objectsget_data
Get Data Matrix from fMRI Dataset Objectsget_data_matrix
Get Latent Scores from Datasetget_latent_scores
Get Spatial Loadings from a Latent-Mode BIDS H5 Datasetget_loadings get_loadings.bids_h5_study_dataset
Get Mask from fMRI Dataset Objectsget_mask
Get Run Duration from Sampling Frameget_run_duration get_run_duration.fmri_dataset get_run_duration.sampling_frame
Get Run Lengths from Sampling Frameget_run_lengths get_run_lengths.fmri_dataset get_run_lengths.sampling_frame
Get Spatial Loadings from Datasetget_spatial_loadings
Get Total Duration from Sampling Frameget_total_duration get_total_duration.fmri_dataset get_total_duration.sampling_frame
Get TR (Repetition Time) from Sampling Frameget_TR get_TR.fmri_dataset get_TR.sampling_frame
Map a function over subjects in an fmri_groupgroup_map
Reduce over subjects in a single passgroup_reduce
Index-based Series Selectorindex_selector
Check if Backend is Registeredis_backend_registered
Check if object is an fmri_seriesis.fmri_series
Test if Object is a Sampling Frameis.sampling_frame
Iterate subjects one-by-one (streaming)iter_subjects
Latent Dataset Interfacelatent_dataset
Left join additional subject metadataleft_join_subjects
List Registered Backend Nameslist_backend_names
Mask-based Series Selectormask_selector
Matrix Dataset Constructormatrix_dataset
Mutate subject-level attributesmutate_subjects
Get Number of Runs from Sampling Framen_runs n_runs.fmri_dataset n_runs.fmri_study_dataset n_runs.sampling_frame
Number of subjects in a groupn_subjects
Get Number of Timepoints from Sampling Framen_timepoints n_timepoints.fmri_dataset n_timepoints.sampling_frame
Number of columns in fmri_seriesncol.fmri_series
Number of rows in fmri_seriesnrow.fmri_series
Get Parcellation Information from a BIDS H5 Datasetparcellation_info parcellation_info.bids_h5_study_dataset
Get Participant IDs from a Datasetparticipants participants.bids_h5_study_dataset
Print Methods for fmridataset Objectsprint print.chunkiter print.data_chunk print.fmri_dataset print.matrix_dataset summary.fmri_dataset
Print Backend Registryprint.backend_registry
Print Method for fmri_series Objectsprint.fmri_series
Print Methods for Series Selectorsprint.series_selector
read a basic fMRI configuration fileread_fmri_config
Reconstruct Voxel-Space Data from a Latent-Mode BIDS H5 Datasetreconstruct_voxels reconstruct_voxels.bids_h5_study_dataset reconstruct_voxels.latent_dataset
Register a Storage Backendregister_backend
Resolve Indices from Series Selectorresolve_indices
ROI-based Series Selectorroi_selector
Sample subjects from an fmri_groupsample_subjects
Get Sample Indices from Sampling Framesamples samples.fmri_dataset samples.sampling_frame
Get Scan Manifest from a BIDS H5 Datasetscan_manifest scan_manifest.bids_h5_study_dataset
Deprecated alias for 'fmri_series'series
Series Selector Classes for fMRI Dataseries_selector
Get Session Names from a Datasetsessions sessions.bids_h5_study_dataset
Spherical ROI Series Selectorsphere_selector
Stream subjects with optional orderingstream_subjects
Study Backendstudy_backend
Convert a BIDS H5 Study Dataset to an fmri_groupstudy_to_group study_to_group.bids_h5_study_dataset study_to_group.fmri_study_dataset
Get Subject IDs from Multi-Subject Datasetsubject_ids subject_ids.fmri_study_dataset
Access the subjects tibble stored inside an fmri_groupsubjects subjects<-
Subset a BIDS H5 Study Datasetsubset_bids_h5
Get Task Names from a Datasettasks tasks.bids_h5_study_dataset
Unregister a Backendunregister_backend
Validate an fmri_group objectvalidate_fmri_group
Voxel Coordinate Series Selectorvoxel_selector
Attach rowData metadata to a lazy matrixwith_rowData
Write fMRI configuration filewrite_fmri_config