Package: raveio 0.9.0.81

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, cph], John Magnotti [aut], Michael Beauchamp [aut], University of Pennsylvania [cph]

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raveio/json (API)
NEWS

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

Peer review:

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

Pkgdown:https://beauchamplab.github.io

On CRAN:

5.36 score 6 stars 1 packages 115 scripts 256 downloads 197 exports 112 dependencies

Last updated 4 hours agofrom:57bc8d8a5f. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 20 2024
R-4.5-winOKDec 20 2024
R-4.5-linuxOKDec 20 2024
R-4.4-winOKDec 20 2024
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R-4.3-winOKDec 20 2024
R-4.3-macOKDec 20 2024

Exports:%...!%%...>%%...T!%%...T>%add_module_registryants_coregants_morph_electrodeants_mri_to_templateants_preprocessingarchive_subjectas_rave_projectas_rave_subjectas_rave_unitas_yael_processbackup_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_tableinstall_modulesinstall_subjectis_dry_runis_on_cranis_valid_ishis.blankis.zerolenthjoin_tensorslapply_asyncLazyFSTLazyH5LFP_electrodeLFP_referenceload_bids_ieeg_headerload_fstload_fst_or_h5load_h5load_jsonload_meta2load_snippetload_targetsload_yamlLOCATION_TYPESmgh_to_niiMNI305_to_MNI152module_addmodule_registrymodule_registry2new_constrained_bindingnew_constrained_variablenew_constraintsnew_electrodenew_referencenew_variable_collectionniftyreg_coregnormalize_commandline_pathpipelinepipeline_attachpipeline_buildpipeline_cleanpipeline_collectionpipeline_create_subject_pipelinepipeline_create_templatepipeline_debugpipeline_dep_targetspipeline_descriptionpipeline_evalpipeline_findpipeline_forkPIPELINE_FORK_PATTERNpipeline_from_pathpipeline_get_preferencespipeline_has_preferencespipeline_hasnamepipeline_install_githubpipeline_install_localpipeline_listpipeline_load_extdatapipeline_progresspipeline_readpipeline_rootpipeline_runpipeline_run_barepipeline_save_extdatapipeline_set_preferencespipeline_settings_getpipeline_settings_setpipeline_setup_rmdpipeline_sharedpipeline_target_namespipeline_vartablepipeline_visualizepipeline_watchpower_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_setoptRAVEMetaSubjectRAVEPreprocessSettingsRAVEProjectRAVESubjectRAVEVariableRAVEVariableCollectionRAVEVariableConstraintsread_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_TYPESTensortest_hdspeedtime_diff2transform_point_to_templatetransform_thinfilm_to_mni152update_local_snippeturl_neurosynthvalidate_raw_filevalidate_subjectvalidate_time_windowvoltage_baselinewith_future_parallelYAEL_IMAGE_TYPESyael_preprocessYAELProcess

Dependencies:abindbackportsbase64encbase64urlBHbitbit64bitopsbslibcachemcallrcheckmateclicodetoolscommonmarkcpp11crayoncurldata.tabledigestdipsausdownloaderedfReaderevaluatefansifastmapfilearrayfontawesomefreesurferformatsfsfstfstcorefuturefuture.applygiftiglobalsgluegsignalhdf5rherehighrhtmltoolshtmlwidgetshttpuvigraphIRdisplayIRkerneljquerylibjsonliteknitrlaterlatticelifecyclelistenvmagrittrMatrixmemoisemimemultitaperoro.niftiparallellypbdZMQpillarpkgconfigpkgfilecachepngpracmaprocessxprogressrpromisespsR.matlabR.methodsS3R.ooR.utilsR6rappdirsravetoolsRcppRcppEigenRcppTOMLremotesreprreticulaterlangrmarkdownRNiftiRNiftyRegrprojrootrpymatrstudioapisasssecretbaseservrshinysourcetoolsstringistringrtargetsthreeBraintibbletidyselecttinytexutf8uuidvctrswaveslimwithrxfunxml2xtableyaml

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
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
Convert 'fst' files to other formatsconvert-fst convert_fst_to_csv convert_fst_to_hdf5
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
Install 'RAVE' modulesinstall_modules
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
R6 Class to Load 'fst' FilesLazyFST
Lazy 'HDF5' file loaderLazyH5
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 'hdf5r-package'load_h5
Load 'RAVE' subject meta dataload_meta2
A port to 'read_yaml'load_yaml
Convert 'FreeSurfer' ''mgh'' to 'Nifti'mgh_to_nii
Add new 'RAVE' (2.0) module to current projectmodule_add
'RAVE' module registryadd_module_registry get_modules_registries get_module_description module_registry module_registry2
Create ''RAVE'' constrained variablesnew_constrained_binding new_constrained_variable new_constraints
Create new electrode channel instance or a reference signal instancenew_electrode new_reference
Create a collection of constraint variablesnew_variable_collection
Register 'CT' to 'MR' images via ''NiftyReg''cmd_run_niftyreg_coreg niftyreg_coreg
Creates 'RAVE' pipeline instancepipeline pipeline_from_path
Combine and execute pipelinespipeline_collection
Install 'RAVE' pipelinespipeline_install pipeline_install_github pipeline_install_local
Get or change pipeline input parameter settingspipeline_settings_get pipeline_settings_get_set pipeline_settings_set
Configure ''rmarkdown'' files to build 'RAVE' pipelinesconfigure_knitr pipeline-knitr-markdown pipeline_setup_rmd
Connect and schedule pipelinesPipelineCollections
Pipeline result objectPipelineResult
Class definition for pipeline toolsPipelineTools
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
'RAVE' pipeline functionsload_targets pipeline_attach pipeline_build pipeline_clean pipeline_create_subject_pipeline pipeline_create_template pipeline_debug pipeline_dep_targets pipeline_description pipeline_eval pipeline_find pipeline_fork pipeline_get_preferences pipeline_hasname pipeline_has_preferences pipeline_list pipeline_load_extdata pipeline_progress pipeline_read pipeline_root pipeline_run pipeline_run_bare pipeline_save_extdata pipeline_set_preferences pipeline_shared pipeline_target_names pipeline_vartable pipeline_visualize pipeline_watch rave-pipeline
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
'RAVE' code snippetsload_snippet rave-snippet update_local_snippet
Abstract definition of electrode class in RAVERAVEAbstarctElectrode
Definition for epoch classRAVEEpoch
The constant variablesLOCATION_TYPES MNI305_to_MNI152 PIPELINE_FORK_PATTERN raveio-constants SIGNAL_TYPES YAEL_IMAGE_TYPES
Set/Get 'raveio' optionraveio-option raveio_confpath raveio_getopt raveio_resetopt raveio_setopt
Defines 'RAVE' subject class for meta analysesRAVEMetaSubject
Defines preprocess configurationsRAVEPreprocessSettings
Definition for 'RAVE' project classRAVEProject
Defines 'RAVE' subject classRAVESubject
Class definition of 'RAVE' constrained variableRAVEVariable
Class definition of 'RAVE' constrained variable collectionRAVEVariableCollection
Class definition for 'RAVE' variable constraintsRAVEVariableConstraints
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
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