Package: raveio 0.9.0.101

raveio: File-System Toolbox for RAVE Project

Includes multiple cross-platform read/write interfaces for 'RAVE' project. 'RAVE' stands for "R analysis and visualization of human intracranial electroencephalography data". The whole project aims at providing powerful free-source package that analyze brain recordings from patients with electrodes placed on the cortical surface or inserted into the brain. 'raveio' as part of this project provides tools to read/write neurophysiology data from/to 'RAVE' file structure, as well as several popular formats including 'EDF(+)', 'Matlab', 'BIDS-iEEG', and 'HDF5', etc. Documentation and examples about 'RAVE' project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>. For applications such as electrode localization, please check Zhengjia Wang, John F. Magnotti, Xiang Zhang, Michael S. Beauchamp (2023) <doi:10.1523/ENEURO.0328-23.2023>, or see 'citation("raveio")' for details.

Authors:Zhengjia Wang [aut, cre], John Magnotti [aut], Michael Beauchamp [aut], University of Pennsylvania [cph]

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manual.pdf |manual.html✨
card.svg |card.png
raveio/json (API)
NEWS

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

Bug tracker:https://github.com/beauchamplab/raveio/issues

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

On CRAN:

Conda:

4.07 score 9 stars 66 scripts 148 downloads 194 exports 117 dependencies

Last updated from:efd87d4ba6. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK183
source / vignettesOK235
linux-release-x86_64OK214
macos-release-arm64OK156
macos-oldrel-arm64OK105
windows-develOK151
windows-releaseOK155
windows-oldrelOK158
wasm-releaseOK151

Exports:add_module_registryants_coregants_morph_electrodeants_mri_to_templateants_preprocessingarchive_subjectas_rave_projectas_rave_subjectas_rave_unitas_yael_processAuxiliary_electrodebackup_fileBlackrockFilecache_rootcache_to_filearraycatglclear_cached_filescmd_afni_homecmd_dcm2niixcmd_executecmd_freesurfer_homecmd_fsl_homecmd_homebrewcmd_run_3dAllineatecmd_run_ants_coregcmd_run_ants_mri_to_templatecmd_run_dcm2niixcmd_run_flirtcmd_run_niftyreg_coregcmd_run_nipy_coregcmd_run_rcmd_run_recon_allcmd_run_recon_all_clinicalcmd_run_yael_preprocesscollapse_powercollapse2compose_channelconfigure_knitrconvert_blackrockconvert_electrode_table_to_bidsconvert_fst_to_csvconvert_fst_to_hdf5dir_create2ECoGTensorexport_tablefind_pathgenerate_referenceget_module_descriptionget_modules_registriesget_projectsget_val2glueh5_namesh5_validimport_electrode_tableIMPORT_FORMATSimport_tableingest_regressorinstall_modulesinstall_snippetinstall_subjectis_dry_runis_on_cranis_valid_ishis.blankis.zerolenthjoin_tensorslapply_asyncLazyFSTLazyH5LFP_electrodeLFP_referencelist_snippetsload_bids_ieeg_headerload_fstload_fst_or_h5load_h5load_jsonload_meta2load_snippetload_targetsload_yamlLOCATION_TYPESmgh_to_niiMNI305_to_MNI152module_addmodule_registrymodule_registry2new_electrodenew_referenceniftyreg_coregnormalize_commandline_pathpipelinepipeline_attachpipeline_buildpipeline_cleanpipeline_collectionpipeline_create_subject_pipelinepipeline_create_templatepipeline_debugpipeline_dep_targetspipeline_descriptionpipeline_evalpipeline_findpipeline_forkpipeline_from_pathpipeline_get_preferencespipeline_has_preferencespipeline_hasnamepipeline_install_githubpipeline_install_localpipeline_listpipeline_load_extdatapipeline_progresspipeline_readpipeline_renderpipeline_rootpipeline_runpipeline_run_barepipeline_save_extdatapipeline_set_preferencespipeline_settings_getpipeline_settings_setpipeline_setup_rmdpipeline_sharedpipeline_target_namespipeline_vartablepipeline_visualizepipeline_watchPipelineCollectionsPipelineResultPipelineToolspower_baselineprepare_subject_bareprepare_subject_bare0prepare_subject_phaseprepare_subject_powerprepare_subject_raw_voltage_with_epochprepare_subject_voltage_with_epochprepare_subject_waveletprepare_subject_with_blocksprepare_subject_with_epochprogress_with_loggerpy_nipy_coregrave_brainrave_directoriesrave_exportrave_importrave_server_configurerave_server_installrave_subject_format_conversionRAVEAbstarctElectrodeRAVEEpochraveio_confpathraveio_getoptraveio_resetoptraveio_setoptRAVEMetaSubjectRAVEPreprocessSettingsRAVEProjectRAVESubjectread_csv_ieegread_edf_headerread_edf_signalread_eeg_dataread_eeg_headerread_eeg_markerread_matread_mat2read_nsx_nevsafe_read_csvsafe_write_csvsave_fstsave_h5save_jsonsave_meta2save_yamlSIGNAL_TYPESSpike_electrodeTensortest_hdspeedtime_diff2transform_point_to_templatetransform_thinfilm_to_mni152update_local_snippeturl_neurosynthvalidate_raw_filevalidate_subjectvalidate_time_windowvoltage_baselinewith_future_parallelYAEL_IMAGE_TYPESyael_preprocessYAELProcess

Dependencies:abindbackportsbase64encbase64urlBHbitbit64bitopsbslibcachemcallrclicodetoolscommonmarkcpp11crayoncurldata.tabledigestdipsausdownloaderedfReaderevaluatefastmapfilearrayfontawesomefreesurferformatsfsfstfstcorefuturefuture.applygiftiglobalsgluegsignalhdf5rherehighrhtmltoolshtmlwidgetshttpuvieegioigraphIRdisplayIRkerneljquerylibjsonliteknitrlaterlatticelifecyclelistenvloggermagrittrMatrixmemoisemimemultitaperoro.niftiotelparallellypbdZMQpillarpkgconfigpkgfilecachepngpracmaprettyunitsprocessxprogressrpromisespsR.matlabR.methodsS3R.ooR.utilsR6rappdirsravepipelineravetoolsRcppRcppEigenRcppTOMLreadNSxremotesreprreticulaterlangrmarkdownRNiftiRNiftyRegrprojrootrpyANTsrpymatrstudioapisasssecretbaseservrshinysourcetoolsstringistringrtargetsthreeBraintibbletidyselecttinytexutf8uuidvctrswaveslimwithrxfunxml2xtableyaml

Readme and manuals

Help Manual

Help pageTopics
Register 'CT' or 'MR' images via ''ANTs''ants_coreg ants_morph_electrode ants_mri_to_template cmd_run_ants_coreg cmd_run_ants_mri_to_template
Process 'T1' weighted 'MRI' using ''ANTs''ants_preprocessing
Archive and share a subjectarchive_subject
Convert character to 'RAVEProject' instanceas_rave_project
Get 'RAVESubject' instance from characteras_rave_subject
Convert numeric number into print-friendly formatas_rave_unit
Create a 'YAEL' imaging processing instanceas_yael_process
Class definition for auxiliary channelsAuxiliary_electrode
Back up and rename the file or directorybackup_file
Class definition to load data from 'BlackRock' 'Micro-systems' filesBlackrockFile
Manipulate cached data on the file systemscache_path cache_root clear_cached_files
Generate and automatically cache a file arraycache_to_filearray
Print colored messagescatgl
External shell commands for 'RAVE'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
Process brain images for ''YAEL''cmd_run_yael_preprocess yael_preprocess
Collapse power array with given analysis cubescollapse_power collapse_power.array collapse_power.FileArray
Collapse high-dimensional tensor arraycollapse2 collapse2.array collapse2.FileArray collapse2.Tensor
Compose a "phantom" channel from existing electrodescompose_channel
Convert 'BlackRock' 'NEV/NSx' filesconvert_blackrock
Convert electrode tableconvert_electrode_table_to_bids
Force creating directory with checksdir_create2
'iEEG/ECoG' Tensor class inherit from 'Tensor'ECoGTensor
Export data frame to different common formatsexport_table import_table
Try to find path along the root directoryfind_path
Generate common average reference signal for 'RAVE' subjectsgenerate_reference
Get all possible projects in 'RAVE' directoryget_projects
Get value or return default if invalidget_val2
Returns all names contained in 'HDF5' fileh5_names
Check whether a 'HDF5' file can be opened for read/writeh5_valid
Import electrode table into subject meta folderimport_electrode_table
Ingest signals according to 'RAVE' repository epochingest_regressor
Install a subject from the internet, a zip file or a directoryinstall_subject
Check if current session is on 'CRAN'is_on_cran
Check if data is close to ``valid"is_valid_ish
Check If Input Has Blank Stringis.blank
Check If Input Has Zero Lengthis.zerolenth
Join Multiple Tensors into One Tensorjoin_tensors
Run 'lapply' in parallellapply_async
Definitions of electrode with 'LFP' signal typeLFP_electrode
Definitions of reference with 'LFP' signal typeLFP_reference
Read in description files from 'BIDS-iEEG' formatload_bids_ieeg_header
Function try to load 'fst' arrays, if not found, read 'HDF5' arraysload_fst_or_h5
Lazy Load 'HDF5' File via 'io_read_h5'load_h5
Load 'RAVE' subject meta dataload_meta2
A port to 'read_yaml'load_yaml
Convert 'FreeSurfer' ''mgh'' to 'Nifti'mgh_to_nii
Create new electrode channel instance or a reference signal instancenew_electrode new_reference
Register 'CT' to 'MR' images via ''NiftyReg''cmd_run_niftyreg_coreg niftyreg_coreg
Calculate power baselinepower_baseline power_baseline.array power_baseline.ECoGTensor power_baseline.FileArray power_baseline.rave_prepare_power
Prepare 'RAVE' single-subject dataprepare_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
Enhanced progress with logger messageprogress_with_logger
Register 'CT' to 'MR' images via ''nipy'' scriptcmd_run_nipy_coreg py_nipy_coreg
Load 'FreeSurfer' or 'AFNI/SUMA' brain from 'RAVE'rave_brain
Find and execute external command-line toolscmd_afni_home cmd_dcm2niix cmd_freesurfer_home cmd_fsl_home cmd_homebrew is_dry_run normalize_commandline_path rave_command_line_path
Returns a list of 'RAVE' directoriesrave_directories
Export 'RAVE' datarave_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
Import data into 'rave' projectsrave_import
Compatibility support for 'RAVE' 1.0 formatrave_subject_format_conversion
Validate raw files in 'rave' directoryIMPORT_FORMATS rave-raw-validation validate_raw_file
Install and configure 'RAVE' server as background service using shiny-serverrave-server rave_server_configure rave_server_install
Abstract definition of electrode class in RAVERAVEAbstarctElectrode
Definition for epoch classRAVEEpoch
The constant variablesLOCATION_TYPES MNI305_to_MNI152 raveio-constants SIGNAL_TYPES YAEL_IMAGE_TYPES
Defines 'RAVE' subject class for meta analysesRAVEMetaSubject
Defines preprocess configurationsRAVEPreprocessSettings
Definition for 'RAVE' project classRAVEProject
Defines 'RAVE' subject classRAVESubject
Read comma separated value file and ignore headersread_csv_ieeg
Read 'EDF(+)' or 'BDF(+)' file headersread_edf_header
Read 'EDF(+)' or 'BDF(+)' file signalsread_edf_signal
Read 'Matlab' filesread_mat read_mat2
Read 'BlackRock' event and signal filesread_nsx_nev
Load from 'BrainVision' fileread-brainvision-eeg read_eeg_data read_eeg_header read_eeg_marker
Read a 'fst' fileload_fst read-write-fst save_fst
Read comma separated value files with given column classessafe_read_csv
Save data to comma separated value files with backupssafe_write_csv
Save objects to 'HDF5' file without trivial checkssave_h5
Save or load R object in 'JSON' formatload_json save_json
Function to save meta data to 'RAVE' subjectsave_meta2
Write named list to filesave_yaml
Class definition for micro-wire spike channelsSpike_electrode
R6 Class for large Tensor (Array) in Hybrid ModeTensor
Simple hard disk speed testtest_hdspeed
Calculate time difference in secondstime_diff2
Calculate template 'MNI' coordinates for points on native braintransform_point_to_template transform_thinfilm_to_mni152
Get 'Neurosynth' website address using 'MNI152' coordinatesurl_neurosynth
Validate subject data integrityvalidate_subject
Validate time windows to be usedvalidate_time_window
Calculate voltage baselinevoltage_baseline voltage_baseline.array voltage_baseline.FileArray voltage_baseline.rave_prepare_subject_raw_voltage_with_epoch voltage_baseline.rave_prepare_subject_voltage_with_epoch
Enable parallel computing provided by 'future' package within the contextwith_future_parallel
Class definition of ''YAEL'' image pipelineYAELProcess