Package: ravecore 0.1.1.6

Zhengjia Wang

ravecore: Core File Structures and Workflows for 'RAVE'

Defines storage standard for Read, process, and analyze intracranial electroencephalography and deep-brain stimulation in 'RAVE', a reproducible framework for analysis and visualization of iEEG by Magnotti, Wang, and Beauchamp, (2020, <doi:10.1016/j.neuroimage.2020.117341>). Supports brain imaging data structure (BIDS) <https://bids.neuroimaging.io> and native file structure to ingest signals from 'Matlab' data files, hierarchical data format 5 (HDF5), European data format (EDF), BrainVision core data format (BVCDF), or BlackRock Microsystem (NEV/NSx); process images in Neuroimaging informatics technology initiative (NIfTI) and 'FreeSurfer' formats, providing brain imaging normalization to template brain, facilitating 'threeBrain' package for comprehensive electrode localization via 'YAEL' (your advanced electrode localizer) by Wang, Magnotti, Zhang, and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>).

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

ravecore_0.1.1.6.tar.gz
ravecore_0.1.1.6.zip(r-4.7)ravecore_0.1.1.6.zip(r-4.6)ravecore_0.1.1.6.zip(r-4.5)
ravecore_0.1.1.6.tgz(r-4.6-any)ravecore_0.1.1.6.tgz(r-4.5-any)
ravecore_0.1.1.6.tar.gz(r-4.7-any)ravecore_0.1.1.6.tar.gz(r-4.6-any)
ravecore_0.1.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ravecore/json (API)
NEWS

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

Bug tracker:https://github.com/rave-ieeg/ravecore/issues

Pkgdown/docs site:https://rave.wiki

On CRAN:

Conda:

4.41 score 1 packages 1 scripts 742 downloads 111 exports 123 dependencies

Last updated from:32dcb87cce. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK211
source / vignettesOK253
linux-release-x86_64OK216
macos-release-arm64OK170
macos-oldrel-arm64OK132
windows-develOK152
windows-releaseOK139
windows-oldrelOK284
wasm-releaseOK168

Exports:ants_coregarchive_subjectas_rave_projectas_rave_subjectas_yael_processAuxiliary_electrodebackup_filecache_rootclear_cached_filescmd_afni_homecmd_dcm2niixcmd_dry_runcmd_executecmd_freesurfer_homecmd_fsl_homecmd_homebrewcmd_run_3dAllineatecmd_run_ants_coregcmd_run_dcm2niixcmd_run_freesurfer_recon_allcmd_run_freesurfer_recon_all_clinicalcmd_run_fsl_flirtcmd_run_niftyreg_coregcmd_run_nipy_coregcmd_run_rcmd_run_yael_preprocesscollapse_powercollapse2compose_channelconvert_electrode_table_to_bidsexport_tablegenerate_atlases_from_templategenerate_referenceget_available_morph_to_templateget_projectsglimpse_voltage_filearrayglimpse_voltage_repository_with_blockshas_rave_subjectIMPORT_FORMATSimport_from_brainvisimport_from_edfimport_from_h5_mat_per_blockimport_from_h5_mat_per_channelimport_from_nevnsximport_tableinstall_openneuroinstall_subjectLFP_electrodeLFP_referenceload_meta2LOCATION_TYPESMNI305_to_MNI152new_electrodenew_rave_subjectnew_referenceniftyreg_coregnormalize_commandline_pathplot_volume_slicespower_baselineprepare_subject_bareprepare_subject_bare0prepare_subject_phase_with_blocksprepare_subject_phase_with_epochsprepare_subject_powerprepare_subject_power_with_blocksprepare_subject_power_with_epochsprepare_subject_raw_voltage_with_blocksprepare_subject_raw_voltage_with_epochsprepare_subject_time_frequency_coefficients_with_blocksprepare_subject_time_frequency_coefficients_with_epochsprepare_subject_voltage_with_blocksprepare_subject_voltage_with_epochsprepare_subject_with_blocksprepare_subject_with_epochspy_nipy_coregrave_brainrave_legacy_subject_format_conversionrave_pathRAVEAbstarctElectrodeRAVEEpochRAVEPreprocessSettingsRAVEProjectRAVESubjectRAVESubjectBaseRepositoryRAVESubjectEpochPhaseRepositoryRAVESubjectEpochPowerRepositoryRAVESubjectEpochRawVoltageRepositoryRAVESubjectEpochRepositoryRAVESubjectEpochTimeFreqCoefRepositoryRAVESubjectEpochVoltageRepositoryRAVESubjectRecordingBlockPhaseRepositoryRAVESubjectRecordingBlockPowerRepositoryRAVESubjectRecordingBlockRawVoltageRepositoryRAVESubjectRecordingBlockTimeFreqCoefRepositoryRAVESubjectRecordingBlockVoltageRepositoryrscript_pathrun_waveletsave_meta2SIGNAL_TYPESsnapshot_projectsnapshot_subjectSpike_electrodetransform_point_to_templatetransform_thinfilm_to_mni152validate_condition_groupingsvalidate_subjectvalidate_time_windowYAEL_IMAGE_TYPESyael_macaqueyael_preprocessYAELProcess

Dependencies:abindbackportsbase64encbase64urlBHbidsrbitbit64bitopsbslibcachemcallrcheckmateclicodetoolscommonmarkcpp11crayoncurldata.tabledigestdipsausdownloaderevaluatefastmapfilearrayfontawesomefreesurferformatsfsfstfstcorefuturefuture.applygiftiglobalsgluegsignalhdf5rherehighrhtmltoolshtmlwidgetshttpuvieegioigraphIRdisplayIRkerneljquerylibjsonliteknitrlaterlatticelifecyclelistenvloggermagrittrMatrixmemoisemimemultitapernanotimeoro.niftiotelparallellypbdZMQpillarpkgconfigpkgfilecachepngpracmaprettyunitsprocessxprogressrpromisespsR.matlabR.methodsS3R.ooR.utilsR6rappdirsravepipelineravetoolsRcppRcppCCTZRcppDateRcppEigenRcppTOMLreadNSxremotesreprreticulaterlangrmarkdownRNiftiRNiftyRegrprojrootrpyANTsrpymatrstudioapiS7sasssecretbaseservrshinysourcetoolsstringistringrtargetsthreeBraintibbletidyselecttinytexutf8uuidvctrswaveslimwithrxfunxml2xtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Archive and share a subjectarchive_subject
Convert character to 'RAVEProject' instanceas_rave_project as_rave_project.character
Create a 'YAEL' imaging processing instanceas_yael_process
Class definition for auxiliary channelsAuxiliary_electrode
Back up and rename the file or directorybackup_file
Manipulate cached data on the file systemscache_path cache_root clear_cached_files
Align images using 'AFNI'cmd_run_3dAllineate
Register a computerized tomography (CT) image to MRI via 'ANTs'ants_coreg cmd_run_ants_coreg
Convert DICOM to NIfTI via ''dcm2niix''cmd_run_dcm2niix
Workflow: 'FreeSurfer' surface reconstructioncmd_run_freesurfer_recon_all cmd_run_freesurfer_recon_all_clinical
Run 'FSL' linear registrationcmd_run_fsl_flirt
Run a built-in 'YAEL' imaging processing workflowcmd_run_yael_preprocess yael_preprocess
External shell commands for 'RAVE'cmd-external cmd_execute cmd_run_r
Collapse power array with given analysis cubescollapse_power collapse_power.array collapse_power.FileArray
Collapse high-dimensional tensor arraycollapse2 collapse2.array collapse2.FileArray collapse2.RAVEFileArray collapse2.Tensor
Compose a phantom channel from existing electrodescompose_channel
Convert electrode tableconvert_electrode_table_to_bids
Export data frame to different common formatsexport_table import_table
Create brain atlases from templategenerate_atlases_from_template
Generate common average reference signal for 'RAVE' subjectsgenerate_reference
Get names of available non-linear transforms to the templatesget_available_morph_to_template
Get all possible projects in 'RAVE' default directoryget_projects
Visualizes repositories with interactive plotsglimpse-repository glimpse_voltage_filearray glimpse_voltage_repository_with_blocks
Import signal data into 'RAVE'import-signals import_from_brainvis import_from_edf import_from_h5_mat_per_block import_from_h5_mat_per_channel import_from_nevnsx
Install data-sets from OpenNeuroinstall_openneuro
Install a subject from the internet, a zip file or a directoryinstall_subject
Definitions of electrode with local field potential signal typeLFP_electrode
Definitions of reference with local field potential signal typeLFP_reference
Load or save meta data to 'RAVE' subjectload_meta2 meta-data save_meta2
Create new electrode channel instance or a reference signal instancenew_electrode new_reference
Get 'RAVESubject' instance from characteras_rave_subject has_rave_subject new_rave_subject
Register a computerized tomography (CT) image to MRI via ''NiftyReg''cmd_run_niftyreg_coreg niftyreg_coreg
Plot volume slices into scalable vector graphics SVG imagesplot_volume_slices
Calculate power baselinepower_baseline power_baseline.array power_baseline.FileArray power_baseline.rave_prepare_power
'RAVE' repository: basicprepare_subject_bare prepare_subject_bare0
'RAVE' repository: with entire recording blocksprepare_subject_phase_with_blocks prepare_subject_power_with_blocks prepare_subject_raw_voltage_with_blocks prepare_subject_time_frequency_coefficients_with_blocks prepare_subject_voltage_with_blocks prepare_subject_with_blocks
'RAVE' repository: with epochsprepare_subject_phase_with_epochs prepare_subject_power prepare_subject_power_with_epochs prepare_subject_raw_voltage_with_epochs prepare_subject_time_frequency_coefficients_with_epochs prepare_subject_voltage_with_epochs prepare_subject_with_epochs
Register a computerized tomography (CT) image to MRI via ''nipy''cmd_run_nipy_coreg py_nipy_coreg
Load 'FreeSurfer' brain from 'RAVE'rave_brain
Find external command-line toolscmd_afni_home cmd_dcm2niix cmd_dry_run cmd_freesurfer_home cmd_fsl_home cmd_homebrew normalize_commandline_path rave_cmd_tools rscript_path
Legacy support for 'RAVE' 1.0 formatrave_legacy_subject_format_conversion
Find file paths based on storagerave_path
Abstract definition of electrode class in 'RAVE'RAVEAbstarctElectrode
'RAVE' constantsIMPORT_FORMATS LOCATION_TYPES MNI305_to_MNI152 ravecore-constants SIGNAL_TYPES YAEL_IMAGE_TYPES
Definition for epoch classRAVEEpoch
Defines preprocess configurationsRAVEPreprocessSettings
Definition for 'RAVE' project classRAVEProject
Defines 'RAVE' subject classRAVESubject
'RAVE' class for base repositoryRAVESubjectBaseRepository
'RAVE' class for epoch repository - time-frequency phaseRAVESubjectEpochPhaseRepository
'RAVE' class for epoch repository - time-frequency powerRAVESubjectEpochPowerRepository
'RAVE' class for epoch repository - raw voltageRAVESubjectEpochRawVoltageRepository
'RAVE' class for epoch repositoryRAVESubjectEpochRepository
'RAVE' class for epoch repository - time-frequency (internal)RAVESubjectEpochTimeFreqBaseRepository
'RAVE' class for epoch repository - time-frequencyRAVESubjectEpochTimeFreqCoefRepository
'RAVE' class for epoch repository - voltageRAVESubjectEpochVoltageRepository
'RAVE' class for loading time-frequency phase componentsRAVESubjectRecordingBlockPhaseRepository
'RAVE' class for loading time-frequency power componentsRAVESubjectRecordingBlockPowerRepository
'RAVE' class for blocks of voltage repositoryRAVESubjectRecordingBlockRawVoltageRepository
'RAVE' class for loading entire recording block repositoryRAVESubjectRecordingBlockRepository
'RAVE' class for loading entire block of time-frequency coefficientsRAVESubjectRecordingBlockTimeFreqBaseRepository
'RAVE' class for loading time-frequency coefficientsRAVESubjectRecordingBlockTimeFreqCoefRepository
'RAVE' class for blocks of voltage repositoryRAVESubjectRecordingBlockVoltageRepository
Apply Morlet-Wavelet to subjectrun_wavelet
Create overview report for given project or subjectsnapshot_project snapshot_subject
Class definition for micro-wire spike channelsSpike_electrode
Calculate template 'MNI' coordinates for points on native braintransform_point_to_template transform_thinfilm_to_mni152
Validate and normalize a list of user-supplied condition groupings.validate_condition_groupings
Validate subject data integrityvalidate_subject
Validate time windows to be usedvalidate_time_window
Run YAEL-based FreeSurfer reconstruction for macaque brainsyael_macaque
Class definition of 'YAEL' image pipelineYAELProcess