{ "_id": "6a102e5aacfb0bcc41c943af", "Package": "fmristore", "Type": "Package", "Title": "Efficient Storage of fMRI Data", "Version": "0.1.0", "Authors@R": "person(given = \"Bradley\",\nfamily = \"Buchsbaum\",\nrole = c(\"aut\", \"cre\"),\nemail = \"brad.buchsbaum@gmail.com\",\ncomment = c(ORCID = \"0000-0002-1108-4866\"))", "Description": "Provides efficient storage and retrieval of functional\nmagnetic resonance imaging (fMRI) data using HDF5 format. The\npackage offers S4 classes and methods for working with dense\nand sparse representations of 4D neuroimaging data, latent\nspace decompositions, and spatially clustered voxel time\nseries. It includes memory-efficient access patterns for large\ndatasets and integrates with the neuroim2 package for standard\nneuroimaging data structures.", "License": "GPL (>= 3)", "URL": "https://github.com/bbuchsbaum/fmristore,\nhttps://bbuchsbaum.github.io/fmristore/", "BugReports": "https://github.com/bbuchsbaum/fmristore/issues", "Encoding": "UTF-8", "Language": "en-US", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Collate": "'all_class.R' 'all_generic.R' 'assertions.R' 'cluster_array.R'\n'cluster_experiment.R' 'constants.R' 'constructors.R'\n'fmristore-package.R' 'globals.R' 'h5_utils.R' 'h5neurovec.R'\n'h5neurovecseq.R' 'h5neurovol.R' 'io_h5_generic.R'\n'io_h5_helpers.R' 'io_write_h5.R' 'labeled_vec.R'\n'latent_vec.R' 'memory_utils.R' 'neurovecseq_h5.R'\n'read_dataset_methods.R' 'write_cluster_result.R'\n'write_dataset_methods.R' 'write_parcellated_scan_h5.R'\n'zzz_example_helpers.R'", "Remotes": [ "bbuchsbaum/neuroim2", "bbuchsbaum/fmrilatent", "bbuchsbaum/albersdown" ], "Config/Needs/website": "albersdown", "Config/pak/sysreqs": "make libhdf5-dev libicu-dev", "Repository": "https://bbuchsbaum.r-universe.dev", "Date/Publication": "2026-03-29 15:11:58 UTC", "RemoteUrl": "https://github.com/bbuchsbaum/fmristore", "RemoteRef": "HEAD", "RemoteSha": "0b834048f20f6a9cfc3c0bc36fa171ca71558359", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 14:12:52 UTC", "User": "root" }, "Author": "Bradley Buchsbaum [aut, cre] (ORCID:\n)", "Maintainer": "Bradley Buchsbaum ", "MD5sum": "48349f9e888d4f284ebd26986e932266", "_user": "bbuchsbaum", "_type": "src", "_file": "fmristore_0.1.0.tar.gz", "_fileid": "8da99b6c1a56f9288cd476f12ea17bd813fdca52c47472f29226f56246e7f95d", "_filesize": 1992041, "_sha256": "8da99b6c1a56f9288cd476f12ea17bd813fdca52c47472f29226f56246e7f95d", "_created": "2026-05-11T14:12:52.000Z", "_published": "2026-05-22T10:22:18.122Z", "_distro": "noble", "_jobs": [ { "job": 77360818304, "time": 211, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6920862664" }, { "job": 77360818934, "time": 202, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6920858884" }, { "job": 77360818631, "time": 193, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6920853671" }, { "job": 77360818688, "time": 210, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6920859392" }, { "job": 77360818011, "time": 382, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6920781950" }, { "job": 77360818150, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7158239576" }, { "job": 77360818621, "time": 232, "config": "windows-devel", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 77360818638, "time": 180, "config": "windows-oldrel", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 77360818444, "time": 241, "config": "windows-release", "r": "4.6.0", "check": "FAIL", "artifact": "" } ], "_buildurl": "https://github.com/r-universe/bbuchsbaum/actions/runs/25675148838", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bbuchsbaum/fmristore", "_commit": { "id": "0b834048f20f6a9cfc3c0bc36fa171ca71558359", "author": "bbuchsbaum ", "committer": "bbuchsbaum ", "message": "Fix pkgdown CI deployment: add Remotes, system deps, and site badge\n\nAdd Remotes field for GitHub-only dependencies (neuroim2, fmrilatent,\nalbersdown) so pak can resolve them in CI. Add HDF5 and system library\ninstall step to pkgdown workflow matching R-CMD-check. 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}, { "page": "cash-H5ParcellatedMultiScan-method", "title": "Accessor Methods for H5ParcellatedMultiScan Access Slots/Properties using `$`", "concept": [ "H5Parcellated" ], "topics": [ "$,H5ParcellatedMultiScan-method" ] }, { "page": "as_h5-methods", "title": "Generic function to convert R objects to HDF5 format", "topics": [ "as_h5", "as_h5,ClusteredNeuroVec-method", "as_h5,LabeledVolumeSet-method", "as_h5,LatentNeuroVec-method", "as_h5,NeuroVec-method", "as_h5,NeuroVecSeq-method" ] }, { "page": "as_h5-NeuroVol-method", "title": "Convert a NeuroVol to HDF5 Format (as_h5 Method)", "topics": [ "as_h5,NeuroVol-method" ] }, { "page": "as.array.LatentNeuroVec", "title": "Convert LatentNeuroVec to Array", "topics": [ "as.array.LatentNeuroVec" ] }, { "page": "as.data.frame-methods", "title": "Convert to Data Frame", "concept": [ "H5Cluster" ], "topics": [ "as.data.frame", "as.data.frame,H5ParcellatedScanSummary-method" ] }, { "page": "as.matrix-methods", "title": "Convert to Matrix", "concept": [ "H5Cluster" ], "topics": [ "as.matrix", "as.matrix,H5ParcellatedScanSummary-method" ] }, { "page": "basis-methods", "title": "Get the basis matrix (temporal components)", "topics": [ "basis" ] }, { "page": "close", "title": "Close an Object", "concept": [ "H5Parcellated" ], "topics": [ "close", "close,H5NeuroVec-method", "close,H5NeuroVecSeq-method", "close,H5NeuroVol-method", "close,H5ParcellatedMultiScan-method", "close,H5ParcellatedScan-method", "close,H5ParcellatedScanSummary-method", "close,LabeledVolumeSet-method" ] }, { "page": "cluster_metadata", "title": "Get cluster metadata", "topics": [ "cluster_metadata" ] }, { "page": "cluster_metadata-methods", "title": "Get cluster metadata", "concept": [ "H5Parcellated" ], "topics": [ "cluster_metadata,H5ParcellatedMultiScan-method" ] }, { "page": "clusters-methods", "title": "Get the cluster map object", "concept": [ "H5Parcellated" ], "topics": [ "clusters", "clusters,H5ParcellatedArray-method", "clusters,H5ParcellatedMultiScan-method" ] }, { "page": "configure_memory_warnings", "title": "Configure Memory Usage Warnings", "topics": [ "configure_memory_warnings" ] }, { "page": "detect_h5_type", "title": "Detect the type of data in an HDF5 file", "topics": [ "detect_h5_type" ] }, { "page": "get_memory_settings", "title": "Get Current Memory Warning Settings", "topics": [ "get_memory_settings" ] }, { "page": "H5_ATTRS", "title": "HDF5 Attribute Constants", "topics": [ "H5_ATTRS" ] }, { "page": "H5_DSETS", "title": "HDF5 Dataset Name Constants", "topics": [ "H5_DSETS" ] }, { "page": "H5_PATHS", "title": "HDF5 Path Constants", "topics": [ "H5_PATHS" ] }, { "page": "h5file", "title": "Get the HDF5 file object", "topics": [ "h5file" ] }, { "page": "h5file-methods", "title": "Get the HDF5 file object via generic", "concept": [ "H5Parcellated" ], "topics": [ "h5file,H5NeuroVecSeq-method", "h5file,H5ParcellatedArray-method", "h5file,H5ParcellatedMultiScan-method", "h5file,H5ParcellatedScan-method", "h5file,H5ParcellatedScanSummary-method" ] }, { "page": "H5NeuroVec", "title": "H5NeuroVec Constructor", "topics": [ "H5NeuroVec" ] }, { "page": "H5NeuroVec-class", "title": "H5NeuroVec Class", "topics": [ "H5NeuroVec-class" ] }, { "page": "H5NeuroVecSeq", "title": "H5NeuroVecSeq constructor", "topics": [ "H5NeuroVecSeq" ] }, { "page": "H5NeuroVecSeq-class", "title": "H5NeuroVecSeq Class", "topics": [ "H5NeuroVecSeq-class" ] }, { "page": "H5NeuroVol", "title": "H5NeuroVol Constructor", "topics": [ "H5NeuroVol" ] }, { "page": "H5NeuroVol-class", "title": "H5NeuroVol Class", "topics": [ "H5NeuroVol-class" ] }, { "page": "H5ParcellatedMultiScan", "title": "Constructor for H5ParcellatedMultiScan Objects", "concept": [ "H5Parcellated" ], "topics": [ "H5ParcellatedMultiScan" ] }, { "page": "H5ParcellatedMultiScan-class", "title": "H5ParcellatedMultiScan Class", "concept": [ "H5Cluster" ], "topics": [ "H5ParcellatedMultiScan-class" ] }, { "page": "H5ParcellatedScan", "title": "Constructor for H5ParcellatedScan Objects", "topics": [ "H5ParcellatedScan" ] }, { "page": "H5ParcellatedScan-class", "title": "H5ParcellatedScan Class", "concept": [ "H5Parcellated" ], "topics": [ "H5ParcellatedScan-class" ] }, { "page": "H5ParcellatedScanSummary", "title": "Constructor for H5ParcellatedScanSummary Objects", "topics": [ "H5ParcellatedScanSummary" ] }, { "page": "H5ParcellatedScanSummary-class", "title": "H5ParcellatedScanSummary Class", "concept": [ "H5Parcellated" ], "topics": [ "H5ParcellatedScanSummary-class" ] }, { "page": "LabeledVolumeSet-class", "title": "LabeledVolumeSet Class", "topics": [ "LabeledVolumeSet-class" ] }, { "page": "LatentNeuroVec", "title": "LatentNeuroVec constructor (re-exported from fmrilatent)", "topics": [ "LatentNeuroVec" ] }, { "page": "LatentNeuroVec-io", "title": "HDF5 I/O for LatentNeuroVec", "topics": [ "LatentNeuroVec-io" ] }, { "page": "loadings-methods", "title": "Get the loadings matrix (spatial components)", "topics": [ "loadings" ] }, { "page": "make_run_full", "title": "Constructor for H5ParcellatedScan Objects", "concept": [ "H5Cluster" ], "topics": [ "make_run_full" ] }, { "page": "make_run_summary", "title": "Constructor for H5ParcellatedScanSummary Objects", "concept": [ "H5Cluster" ], "topics": [ "make_run_summary" ] }, { "page": "map-methods", "title": "Get the index map volume", "topics": [ "map" ] }, { "page": "mask", "title": "Get the mask volume", "topics": [ "mask" ] }, { "page": "mask-methods", "title": "Get the mask object via generic", "concept": [ "H5Parcellated" ], "topics": [ "mask,H5ParcellatedArray-method", "mask,H5ParcellatedMultiScan-method", "mask,LatentNeuroVec-method" ] }, { "page": "matrix_concat", "title": "Concatenate Cluster Summary Matrices Across Runs (Generic)", "concept": [ "H5Parcellated" ], "topics": [ "matrix_concat", "matrix_concat,H5ParcellatedMultiScan-method" ] }, { "page": "n_scans", "title": "Get the number of scans", "topics": [ "n_scans" ] }, { "page": "n_scans-methods", "title": "Get number of scans", "concept": [ "H5Parcellated" ], "topics": [ "n_scans,H5NeuroVecSeq-method", "n_scans,H5ParcellatedMultiScan-method" ] }, { "page": "neurovecseq_to_h5", "title": "Convert NeuroVecSeq to HDF5", "topics": [ "neurovecseq_to_h5" ] }, { "page": "offset", "title": "Get the offset vector", "topics": [ "offset" ] }, { "page": "read_dataset", "title": "Read Dataset from HDF5", "topics": [ "read_dataset", "read_dataset,H5File-method" ] }, { "page": "read_dataset-character-method", "title": "Read Dataset from HDF5 File", "topics": [ "read_dataset,character-method" ] }, { "page": "read_labeled_vec", "title": "Read a Labeled Neuroimaging Volume Set from HDF5", "topics": [ "read_labeled_vec" ] }, { "page": "scan_metadata", "title": "Get scan metadata", "topics": [ "scan_metadata" ] }, { "page": "scan_metadata-methods", "title": "Get scan metadata", "concept": [ "H5Parcellated" ], "topics": [ "scan_metadata,H5ParcellatedMultiScan-method" ] }, { "page": "scan_names", "title": "Get the scan names", "topics": [ "scan_names" ] }, { "page": "scan_names-methods", "title": "Get scan names", "concept": [ "H5Parcellated" ], "topics": [ "scan_names,H5NeuroVecSeq-method", "scan_names,H5ParcellatedMultiScan-method" ] }, { "page": "series-methods", "title": "Extract Time Series Data", "concept": [ "H5Cluster" ], "topics": [ "series", "series,H5NeuroVec,integer-method", "series,H5NeuroVec,matrix-method", "series,H5NeuroVec,numeric-method", "series,H5ParcellatedScan,matrix-method", "series,H5ParcellatedScan,numeric-method", "series,H5ParcellatedScanSummary,ANY-method" ] }, { "page": "series_concat", "title": "Concatenate Voxel Time Series Across Runs (Generic)", "concept": [ "H5Parcellated" ], "topics": [ "series_concat", "series_concat,H5ParcellatedMultiScan,numeric-method" ] }, { "page": "show-H5NeuroVec-method", "title": "Display an H5NeuroVec object", "topics": [ "show,H5NeuroVec-method" ] }, { "page": "show-H5NeuroVol-method", "title": "Show Method for H5NeuroVol", "topics": [ "show,H5NeuroVol-method" ] }, { "page": "show-methods", "title": "Show Method for H5ParcellatedScanSummary", "concept": [ "H5Cluster" ], "topics": [ "show,H5ParcellatedMultiScan-method", "show,H5ParcellatedScan-method", "show,H5ParcellatedScanSummary-method" ] }, { "page": "show-LabeledVolumeSet-method", "title": "show method for LabeledVolumeSet", "topics": [ "show,LabeledVolumeSet-method" ] }, { "page": "validate_latent_file", "title": "Validate HDF5 File Against Latent Spec", "topics": [ "validate_latent_file" ] }, { "page": "write_cluster_result", "title": "Write Clustering Results to HDF5", "topics": [ "write_cluster_result" ] }, { "page": "write_dataset", "title": "Write Dataset to HDF5", "topics": [ "write_dataset", "write_dataset,ClusteredNeuroVec-method", "write_dataset,H5NeuroVec-method", "write_dataset,H5NeuroVol-method", 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Regions (Clusters)", "Step 3: Create Some fMRI Data", "Step 4: Save Using the New Simple Interface", "Step 5: Load Using the New Simple Interface", "Step 6: Extract and Visualize Data", "Understanding Single Scan vs Multi-Scan Containers", "Single Scan: H5ParcellatedScanSummary", "Multi-Scan: H5ParcellatedMultiScan", "Converting ClusteredNeuroVec Objects", "When to Use Each Format", "Advanced Example: Multiple Runs with Summary Data", "Create Multiple Runs", "Save Multiple Runs", "Automatic Type Detection", "Working with Multiple Runs", "Creating Summary Data", "Key Functions Summary", "write_dataset() - Save Your Data", "read_dataset() - Load Your Data", "detect_h5_type() - Identify File Contents", "Memory Efficiency Tips", "When to Use H5ParcellatedMultiScan", "Cleanup", "Next Steps" ], "created": "2025-08-19 15:15:35", "modified": "2026-03-29 15:02:43", "commits": 6 }, { "source": "fmristore-overview.Rmd", "filename": "fmristore-overview.html", "title": "fmristore: Efficient Storage for Neuroimaging Data", "author": "fmristore Package", "engine": "knitr::rmarkdown", "headings": [ "Why fmristore?", "Quick Start: Choose Your Storage Format", "Data Conversion Workflows", "1. Converting neuroim2 ClusteredNeuroVec", "2. Converting Regular NeuroVec to HDF5", "3. Creating Multi-Scan Experiments", "Performance Comparison", "Best Practices", "1. Memory Management", "2. Choosing Between Single and Multi-Scan", "3. Data Access Patterns", "Common Use Cases", "Use Case 1: Single Subject, Multiple Runs", "Use Case 2: Storing Subject Maps with LabeledVolumeSet", "Use Case 3: Resting State Connectivity from Parcellated Data", "Advanced Features", "Latent Representations", "Working with Atlas Labels", "Troubleshooting", "Common Issues and Solutions", "Next Steps", "Format Chooser" ], "created": "2025-08-23 16:50:44", "modified": "2026-03-29 15:02:43", "commits": 3 }, { "source": "H5Neuro.Rmd", "filename": "H5Neuro.html", "title": "Getting Started with HDF5 Neuroimaging Data", "author": "fmristore Package", "engine": "knitr::rmarkdown", "headings": [ "Why Use HDF5 for Neuroimaging?", "Quick Start: 3D Brain Volumes", "Working with fMRI Time Series (4D Data)", "Loading Existing HDF5 Files", "Best Practices", "1. Always Close Your Files", "2. Use Chunk Sizes Wisely", "3. Memory vs Speed Trade-off", "Common Use Cases", "Preprocessing Large Datasets", "Region of Interest Analysis", "Summary" ], "created": "2025-05-19 02:32:00", "modified": "2026-03-29 15:02:43", "commits": 6 }, { "source": "H5ParcellatedScan.Rmd", "filename": "H5ParcellatedScan.html", "title": "Working with Individual Scans: H5ParcellatedScan and H5ParcellatedScanSummary", "author": "fmristore Package", "engine": "knitr::rmarkdown", "headings": [ "How are individual scans organized?", "The Data Hierarchy", "Step 1: Create Sample Data Using the New Interface", "Create Multiple fMRI Runs with Different Characteristics", "Save Mixed Full and Summary Data", "Converting neuroim2 ClusteredNeuroVec Objects", "Creating a ClusteredNeuroVec", "Converting to HDF5: Single Scan (Default)", "Converting to HDF5: Multi-Scan Container", "Step 2: Load the Data with read_dataset()", "Step 3: Accessing Individual Scans from the Container", "Understanding Individual Scan Properties", "H5ParcellatedScan: Operations on Individual Full Scans", "Extract Time Series from Individual Voxels", "Extract Time Series for All Voxels in a Cluster", "Compare Task vs Rest Scans (Individual Scan Analysis)", "H5ParcellatedScanSummary: Operations on Individual Summary Scans", "Extract and Analyze Summary Data", "Compute Cluster-to-Cluster Correlations", "Practical Usage Guidelines", "Choose H5ParcellatedScan when you need:", "Choose H5ParcellatedScanSummary when you need:", "Key Individual Scan Operations Summary", "Memory and Performance Considerations", "Clean Up", "Key Takeaways", "Next Steps" ], "created": "2025-08-19 15:15:35", "modified": "2026-03-29 15:02:43", "commits": 6 }, { "source": "LabeledVolumeSet.Rmd", "filename": "LabeledVolumeSet.html", "title": "Working with Multiple Brain Maps using LabeledVolumeSet", "author": "fmristore Package", "engine": "knitr::rmarkdown", "headings": [ "What is a LabeledVolumeSet?", "Quick Example: Storing Statistical Maps", "Step 1: Create Example Data", "Step 2: Create Brain Mask", "Step 3: Save with Labels", "Step 4: Load and Access", "Real-World Use Case: Group Analysis Results", "Working with Subject-Specific Maps", "Create Subject Data", "Add Activation Patterns", "Save Subject Maps", "Compute Group Statistics", "Advanced: Efficient Access Patterns", "Best Practices", "1. Use Meaningful Labels", "2. Organize Your Analysis", "3. 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