{ "_id": "6a1f2868b401979e734234c8", "Package": "raveio", "Type": "Package", "Title": "File-System Toolbox for RAVE Project", "Version": "0.9.0.101", "Language": "en-US", "Authors@R": "c(\nperson(\"Zhengjia\", \"Wang\", email = \"dipterix.wang@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"John\", \"Magnotti\", email = \"john.magnotti@pennmedicine.upenn.edu\", role = c(\"aut\")),\nperson(\"Michael\", \"Beauchamp\", email = \"michael.beauchamp@pennmedicine.upenn.edu\", role = c(\"aut\")),\nperson(\"University of Pennsylvania\", role = c(\"cph\"))\n)", "Description": "Includes multiple cross-platform read/write interfaces for\n'RAVE' project. 'RAVE' stands for \"R analysis and visualization\nof human intracranial electroencephalography data\". The whole\nproject aims at providing powerful free-source package that\nanalyze brain recordings from patients with electrodes placed\non the cortical surface or inserted into the brain. 'raveio' as\npart of this project provides tools to read/write\nneurophysiology data from/to 'RAVE' file structure, as well as\nseveral popular formats including 'EDF(+)', 'Matlab',\n'BIDS-iEEG', and 'HDF5', etc. Documentation and examples about\n'RAVE' project are provided at , and the\npaper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp\n(2020) . For applications\nsuch as electrode localization, please check Zhengjia Wang,\nJohn F. Magnotti, Xiang Zhang, Michael S. Beauchamp (2023)\n, or see 'citation(\"raveio\")'\nfor details.", "BugReports": "https://github.com/beauchamplab/raveio/issues", "URL": "https://beauchamplab.github.io/raveio/", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "SystemRequirements": "little-endian platform", "Config/pak/sysreqs": "cmake libfftw3-dev git libglpk-dev make libhdf5-dev\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3\nlibzmq3-dev zlib1g-dev", "Repository": "https://dipterix.r-universe.dev", "Date/Publication": "2026-04-28 19:40:51 UTC", "RemoteUrl": "https://github.com/beauchamplab/raveio", "RemoteRef": "HEAD", "RemoteSha": "efd87d4ba61e9ff5fbb8ee19f9a3bb8d00591b87", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 18:55:08 UTC", "User": "root" }, "Author": "Zhengjia Wang [aut, cre],\nJohn Magnotti [aut],\nMichael Beauchamp [aut],\nUniversity of Pennsylvania [cph]", "Maintainer": "Zhengjia Wang ", "MD5sum": "234a28a2d10e3b04f1a9eabc5b683109", "_user": 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"extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/raveio.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_releases": [ { "version": "0.0.3", "date": "2020-08-14" }, { "version": "0.0.4", "date": "2021-08-05" }, { "version": "0.0.5", "date": "2021-10-13" }, { "version": "0.0.6", "date": "2022-05-30" }, { "version": "0.0.7", "date": "2022-06-20" }, { "version": "0.0.8", "date": "2022-08-25" }, { "version": "0.0.9", "date": "2022-10-14" }, { "version": "0.1.0", "date": "2023-03-15" }, { "version": "0.9.0", "date": "2023-07-16" } ], "_exports": [ "add_module_registry", "ants_coreg", "ants_morph_electrode", "ants_mri_to_template", "ants_preprocessing", "archive_subject", "as_rave_project", "as_rave_subject", "as_rave_unit", "as_yael_process", "Auxiliary_electrode", "backup_file", "BlackrockFile", "cache_root", "cache_to_filearray", "catgl", "clear_cached_files", "cmd_afni_home", "cmd_dcm2niix", "cmd_execute", "cmd_freesurfer_home", "cmd_fsl_home", "cmd_homebrew", "cmd_run_3dAllineate", "cmd_run_ants_coreg", "cmd_run_ants_mri_to_template", "cmd_run_dcm2niix", "cmd_run_flirt", "cmd_run_niftyreg_coreg", "cmd_run_nipy_coreg", "cmd_run_r", "cmd_run_recon_all", "cmd_run_recon_all_clinical", "cmd_run_yael_preprocess", "collapse_power", "collapse2", "compose_channel", "configure_knitr", "convert_blackrock", "convert_electrode_table_to_bids", "convert_fst_to_csv", "convert_fst_to_hdf5", "dir_create2", "ECoGTensor", "export_table", "find_path", "generate_reference", "get_module_description", "get_modules_registries", "get_projects", "get_val2", "glue", "h5_names", "h5_valid", "import_electrode_table", "IMPORT_FORMATS", "import_table", "ingest_regressor", "install_modules", "install_snippet", "install_subject", "is_dry_run", "is_on_cran", "is_valid_ish", "is.blank", "is.zerolenth", "join_tensors", "lapply_async", "LazyFST", "LazyH5", "LFP_electrode", "LFP_reference", "list_snippets", "load_bids_ieeg_header", "load_fst", "load_fst_or_h5", "load_h5", "load_json", "load_meta2", "load_snippet", "load_targets", "load_yaml", "LOCATION_TYPES", "mgh_to_nii", "MNI305_to_MNI152", "module_add", "module_registry", "module_registry2", "new_electrode", "new_reference", "niftyreg_coreg", "normalize_commandline_path", "pipeline", "pipeline_attach", "pipeline_build", "pipeline_clean", "pipeline_collection", "pipeline_create_subject_pipeline", "pipeline_create_template", "pipeline_debug", "pipeline_dep_targets", "pipeline_description", "pipeline_eval", "pipeline_find", "pipeline_fork", "pipeline_from_path", "pipeline_get_preferences", "pipeline_has_preferences", "pipeline_hasname", "pipeline_install_github", "pipeline_install_local", "pipeline_list", "pipeline_load_extdata", "pipeline_progress", "pipeline_read", "pipeline_render", "pipeline_root", "pipeline_run", "pipeline_run_bare", "pipeline_save_extdata", "pipeline_set_preferences", "pipeline_settings_get", "pipeline_settings_set", "pipeline_setup_rmd", "pipeline_shared", "pipeline_target_names", "pipeline_vartable", "pipeline_visualize", "pipeline_watch", "PipelineCollections", "PipelineResult", "PipelineTools", "power_baseline", "prepare_subject_bare", "prepare_subject_bare0", "prepare_subject_phase", "prepare_subject_power", "prepare_subject_raw_voltage_with_epoch", "prepare_subject_voltage_with_epoch", "prepare_subject_wavelet", "prepare_subject_with_blocks", "prepare_subject_with_epoch", "progress_with_logger", "py_nipy_coreg", "rave_brain", "rave_directories", "rave_export", "rave_import", "rave_server_configure", "rave_server_install", "rave_subject_format_conversion", "RAVEAbstarctElectrode", "RAVEEpoch", "raveio_confpath", "raveio_getopt", "raveio_resetopt", "raveio_setopt", "RAVEMetaSubject", "RAVEPreprocessSettings", "RAVEProject", "RAVESubject", "read_csv_ieeg", "read_edf_header", "read_edf_signal", "read_eeg_data", "read_eeg_header", "read_eeg_marker", "read_mat", "read_mat2", "read_nsx_nev", "safe_read_csv", "safe_write_csv", "save_fst", "save_h5", "save_json", "save_meta2", "save_yaml", "SIGNAL_TYPES", "Spike_electrode", "Tensor", "test_hdspeed", "time_diff2", "transform_point_to_template", "transform_thinfilm_to_mni152", "update_local_snippet", "url_neurosynth", "validate_raw_file", "validate_subject", "validate_time_window", "voltage_baseline", "with_future_parallel", "YAEL_IMAGE_TYPES", "yael_preprocess", "YAELProcess" ], "_help": [ { "page": "ants_coreg", "title": "Register 'CT' or 'MR' images via ''ANTs''", "topics": [ "ants_coreg", "ants_morph_electrode", "ants_mri_to_template", "cmd_run_ants_coreg", "cmd_run_ants_mri_to_template" ] }, { "page": "ants_preprocessing", "title": "Process 'T1' weighted 'MRI' using ''ANTs''", "topics": [ "ants_preprocessing" ] }, { "page": "archive_subject", "title": "Archive and share a subject", "topics": [ "archive_subject" ] }, { "page": "as_rave_project", "title": "Convert character to 'RAVEProject' instance", "topics": [ "as_rave_project" ] }, { "page": "as_rave_subject", "title": "Get 'RAVESubject' instance from character", "topics": [ "as_rave_subject" ] }, { "page": "as_rave_unit", "title": "Convert numeric number into print-friendly format", "topics": [ "as_rave_unit" ] }, { "page": "as_yael_process", "title": "Create a 'YAEL' imaging processing instance", "topics": [ "as_yael_process" ] }, { "page": "Auxiliary_electrode", "title": "Class definition for auxiliary channels", "topics": [ "Auxiliary_electrode" ] }, { "page": "backup_file", "title": "Back up and rename the file or directory", "topics": [ "backup_file" ] }, { "page": "BlackrockFile", "title": "Class definition to load data from 'BlackRock' 'Micro-systems' files", "topics": [ "BlackrockFile" ] }, { "page": "cache_path", "title": "Manipulate cached data on the file systems", "topics": [ "cache_path", "cache_root", "clear_cached_files" ] }, { "page": "cache_to_filearray", "title": "Generate and automatically cache a file array", "topics": [ "cache_to_filearray" ] }, { "page": "catgl", "title": "Print colored messages", "topics": [ "catgl" ] }, { "page": "cmd-external", "title": "External shell commands for 'RAVE'", "topics": [ "cmd-external", "cmd_execute", "cmd_run_3dAllineate", "cmd_run_dcm2niix", "cmd_run_flirt", "cmd_run_r", "cmd_run_recon_all", "cmd_run_recon_all_clinical" ] }, { "page": "yael_preprocess", "title": "Process brain images for ''YAEL''", "topics": [ "cmd_run_yael_preprocess", "yael_preprocess" ] }, { "page": "collapse_power", "title": "Collapse power array with given analysis cubes", "topics": [ "collapse_power", "collapse_power.array", "collapse_power.FileArray" ] }, { "page": "collapse2", "title": "Collapse high-dimensional tensor array", "topics": [ "collapse2", "collapse2.array", "collapse2.FileArray", "collapse2.Tensor" ] }, { "page": "compose_channel", "title": "Compose a \"phantom\" channel from existing electrodes", "topics": [ "compose_channel" ] }, { "page": "convert_blackrock", "title": "Convert 'BlackRock' 'NEV/NSx' files", "topics": [ "convert_blackrock" ] }, { "page": "convert_electrode_table_to_bids", "title": "Convert electrode table", "topics": [ "convert_electrode_table_to_bids" ] }, { "page": "dir_create2", "title": "Force creating directory with checks", "topics": [ "dir_create2" ] }, { "page": "ECoGTensor", "title": "'iEEG/ECoG' Tensor class inherit from 'Tensor'", "topics": [ "ECoGTensor" ] }, { "page": "export_table", "title": "Export data frame to different common formats", "topics": [ "export_table", "import_table" ] }, { "page": "find_path", "title": "Try to find path along the root directory", "topics": [ "find_path" ] }, { "page": "generate_reference", "title": "Generate common average reference signal for 'RAVE' subjects", "topics": [ "generate_reference" ] }, { "page": "get_projects", "title": "Get all possible projects in 'RAVE' directory", "topics": [ "get_projects" ] }, { "page": "get_val2", "title": "Get value or return default if invalid", "topics": [ "get_val2" ] }, { "page": "h5_names", "title": "Returns all names contained in 'HDF5' file", "topics": [ "h5_names" ] }, { "page": "h5_valid", "title": "Check whether a 'HDF5' file can be opened for read/write", "topics": [ "h5_valid" ] }, { "page": "import_electrode_table", "title": "Import electrode table into subject meta folder", "topics": [ "import_electrode_table" ] }, { "page": "ingest_regressor", "title": "Ingest signals according to 'RAVE' repository epoch", "topics": [ "ingest_regressor" ] }, { "page": "install_subject", "title": "Install a subject from the internet, a zip file or a directory", "topics": [ "install_subject" ] }, { "page": "is_on_cran", "title": "Check if current session is on 'CRAN'", "topics": [ "is_on_cran" ] }, { "page": "is_valid_ish", "title": "Check if data is close to ``valid\"", "topics": [ "is_valid_ish" ] }, { "page": "is.blank", "title": "Check If Input Has Blank String", "topics": [ "is.blank" ] }, { "page": "is.zerolenth", "title": "Check If Input Has Zero Length", "topics": [ "is.zerolenth" ] }, { "page": "join_tensors", "title": "Join Multiple Tensors into One Tensor", "topics": [ "join_tensors" ] }, { "page": "lapply_async", "title": "Run 'lapply' in parallel", "topics": [ "lapply_async" ] }, { "page": "LFP_electrode", "title": "Definitions of electrode with 'LFP' signal type", "topics": [ "LFP_electrode" ] }, { "page": "LFP_reference", "title": "Definitions of reference with 'LFP' signal type", "topics": [ "LFP_reference" ] }, { "page": "load_bids_ieeg_header", "title": "Read in description files from 'BIDS-iEEG' format", "topics": [ "load_bids_ieeg_header" ] }, { "page": "load_fst_or_h5", "title": "Function try to load 'fst' arrays, if not found, read 'HDF5' arrays", "topics": [ "load_fst_or_h5" ] }, { "page": "load_h5", "title": "Lazy Load 'HDF5' File via 'io_read_h5'", "topics": [ "load_h5" ] }, { "page": "load_meta2", "title": "Load 'RAVE' subject meta data", "topics": [ "load_meta2" ] }, { "page": "load_yaml", "title": "A port to 'read_yaml'", "topics": [ "load_yaml" ] }, { "page": "mgh_to_nii", "title": "Convert 'FreeSurfer' ''mgh'' to 'Nifti'", "topics": [ "mgh_to_nii" ] }, { "page": "new_electrode", "title": "Create new electrode channel instance or a reference signal instance", "topics": [ "new_electrode", "new_reference" ] }, { "page": "niftyreg_coreg", "title": "Register 'CT' to 'MR' images via ''NiftyReg''", "topics": [ "cmd_run_niftyreg_coreg", "niftyreg_coreg" ] }, { "page": "power_baseline", "title": "Calculate power baseline", "topics": [ "power_baseline", "power_baseline.array", "power_baseline.ECoGTensor", "power_baseline.FileArray", "power_baseline.rave_prepare_power" ] }, { "page": "rave-prepare", "title": "Prepare 'RAVE' single-subject data", "topics": [ "prepare_subject_bare", "prepare_subject_bare0", "prepare_subject_phase", "prepare_subject_power", "prepare_subject_raw_voltage_with_epoch", "prepare_subject_voltage_with_epoch", "prepare_subject_wavelet", "prepare_subject_with_blocks", "prepare_subject_with_epoch", "rave-prepare" ] }, { "page": "progress_with_logger", "title": "Enhanced progress with logger message", "topics": [ "progress_with_logger" ] }, { "page": "py_nipy_coreg", "title": "Register 'CT' to 'MR' images via ''nipy'' script", "topics": [ "cmd_run_nipy_coreg", "py_nipy_coreg" ] }, { "page": "rave_brain", "title": "Load 'FreeSurfer' or 'AFNI/SUMA' brain from 'RAVE'", "topics": [ "rave_brain" ] }, { "page": "rave_command_line_path", "title": "Find and execute external command-line tools", "topics": [ "cmd_afni_home", "cmd_dcm2niix", "cmd_freesurfer_home", "cmd_fsl_home", "cmd_homebrew", "is_dry_run", "normalize_commandline_path", "rave_command_line_path" ] }, { "page": "rave_directories", "title": "Returns a list of 'RAVE' directories", "topics": [ "rave_directories" ] }, { "page": "rave_export", "title": "Export 'RAVE' data", "topics": [ "rave_export", "rave_export.default", "rave_export.rave_prepare_power", "rave_export.rave_prepare_subject_raw_voltage_with_epoch", "rave_export.rave_prepare_subject_voltage_with_epoch" ] }, { "page": "rave_import", "title": "Import data into 'rave' projects", "topics": [ "rave_import" ] }, { "page": "rave_subject_format_conversion", "title": "Compatibility support for 'RAVE' 1.0 format", "topics": [ "rave_subject_format_conversion" ] }, { "page": "rave-raw-validation", "title": "Validate raw files in 'rave' directory", "topics": [ "IMPORT_FORMATS", "rave-raw-validation", "validate_raw_file" ] }, { "page": "rave-server", "title": "Install and configure 'RAVE' server as background service using shiny-server", "topics": [ "rave-server", "rave_server_configure", "rave_server_install" ] }, { "page": "RAVEAbstarctElectrode", "title": "Abstract definition of electrode class in RAVE", "topics": [ "RAVEAbstarctElectrode" ] }, { "page": "RAVEEpoch", "title": "Definition for epoch class", "topics": [ "RAVEEpoch" ] }, { "page": "raveio-constants", "title": "The constant variables", "topics": [ "LOCATION_TYPES", "MNI305_to_MNI152", "raveio-constants", "SIGNAL_TYPES", "YAEL_IMAGE_TYPES" ] }, { "page": "RAVEMetaSubject", "title": "Defines 'RAVE' subject class for meta analyses", "topics": [ "RAVEMetaSubject" ] }, { "page": "RAVEPreprocessSettings", "title": "Defines preprocess configurations", "topics": [ "RAVEPreprocessSettings" ] }, { "page": "RAVEProject", "title": "Definition for 'RAVE' project class", "topics": [ "RAVEProject" ] }, { "page": "RAVESubject", "title": "Defines 'RAVE' subject class", "topics": [ "RAVESubject" ] }, { "page": "read_csv_ieeg", "title": "Read comma separated value file and ignore headers", "topics": [ "read_csv_ieeg" ] }, { "page": "read_edf_header", "title": "Read 'EDF(+)' or 'BDF(+)' file headers", "topics": [ "read_edf_header" ] }, { "page": "read_edf_signal", "title": "Read 'EDF(+)' or 'BDF(+)' file signals", "topics": [ "read_edf_signal" ] }, { 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