# File IO for Intracranial Electroencephalography

## Documentation for package ‘ieegio’ version 0.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D I L M N P R S T V W

## -- A --

as_edf_channel | Write to 'EDF' format
as_ieegio_colormap | Convert to 'ieegio_colormap'
as_ieegio_colormap.threeBrain_colormap | Convert to 'ieegio_colormap'
as_ieegio_colortable | Convert to ieegio color table
as_ieegio_lookup | Convert to ieegio lookup table
as_ieegio_roi | Convert objects to "ieegio" region of interest
as_ieegio_roi.ants.core.ants_image.ANTsImage | Convert objects to "ieegio" region of interest
as_ieegio_roi.array | Convert objects to "ieegio" region of interest
as_ieegio_roi.character | Convert objects to "ieegio" region of interest
as_ieegio_roi.data.frame | Convert objects to "ieegio" region of interest
as_ieegio_roi.default | Convert objects to "ieegio" region of interest
as_ieegio_roi.fs.surface | Convert objects to "ieegio" region of interest
as_ieegio_roi.ieegio_roi | Convert objects to "ieegio" region of interest
as_ieegio_roi.ieegio_streamlines | Convert objects to "ieegio" region of interest
as_ieegio_roi.ieegio_surface | Convert objects to "ieegio" region of interest
as_ieegio_roi.ieegio_volume | Convert objects to "ieegio" region of interest
as_ieegio_roi.integer | Convert objects to "ieegio" region of interest
as_ieegio_roi.list | Convert objects to "ieegio" region of interest
as_ieegio_roi.matrix | Convert objects to "ieegio" region of interest
as_ieegio_roi.mesh3d | Convert objects to "ieegio" region of interest
as_ieegio_roi.nifti | Convert objects to "ieegio" region of interest
as_ieegio_roi.niftiImage | Convert objects to "ieegio" region of interest
as_ieegio_roi.numeric | Convert objects to "ieegio" region of interest
as_ieegio_streamlines | Read and write streamlines
as_ieegio_streamlines.character | Read and write streamlines
as_ieegio_streamlines.default | Read and write streamlines
as_ieegio_surface | Convert other surface formats to 'ieegio' surface
as_ieegio_surface.character | Convert other surface formats to 'ieegio' surface
as_ieegio_surface.default | Convert other surface formats to 'ieegio' surface
as_ieegio_surface.fs.surface | Convert other surface formats to 'ieegio' surface
as_ieegio_surface.ieegio_niml | Convert other surface formats to 'ieegio' surface
as_ieegio_surface.ieegio_surface | Convert other surface formats to 'ieegio' surface
as_ieegio_surface.mesh3d | Convert other surface formats to 'ieegio' surface
as_ieegio_transform | Convert to ieegio transform
as_ieegio_transform.array | Convert to ieegio transform
as_ieegio_transform.character | Convert to ieegio transform
as_ieegio_transform.ieegio_transforms | Convert to ieegio transform
as_ieegio_transform.list | Convert to ieegio transform
as_ieegio_transform.matrix | Convert to ieegio transform
as_ieegio_transform.NULL | Convert to ieegio transform
as_ieegio_volume | Convert objects to "ieegio" image volumes
as_ieegio_volume.ants.core.ants_image.ANTsImage | Convert objects to "ieegio" image volumes
as_ieegio_volume.array | Convert objects to "ieegio" image volumes
as_ieegio_volume.character | Convert objects to "ieegio" image volumes
as_ieegio_volume.ieegio_volume | Convert objects to "ieegio" image volumes
as_ieegio_volume.nifti | Convert objects to "ieegio" image volumes
as_ieegio_volume.niftiImage | Convert objects to "ieegio" image volumes
as_nifti_header | Internal method to extract header information from a 'NIfTI' file

## -- B --

burn_curve | Burn a curve trajectory into a volume
burn_volume | Burn image at given positions

## -- C --

calculate_color | Map data values or atlas keys to hex colors
colorspace_from_rgb | Color space conversion helpers
colorspace_to_rgb | Color space conversion helpers
convert-fst | Convert 'FST' files to other formats
convert_fst_to_csv | Convert 'FST' files to other formats
convert_fst_to_hdf5 | Convert 'FST' files to other formats

## -- D --

detect_roi_overlap | Detect whether two regions of interest overlap

## -- I --

ieegio_sample_data | Download sample files
imaging-streamlines | Read and write streamlines
imaging-surface | Read and write surface files
imaging-volume | Read and write volume data
install_pynwb | Install "NWB" via "pynwb"
io-trk | Read or write "TCK" streamlines
io-tt | Read "TT" streamline file
io-vtk-polys | Read or write surface mesh data in "VTK" format
io-vtk-streamlines | Read or write streamline data in "VTK" format
io_h5_names | Check whether a 'HDF5' file can be opened for read/write
io_h5_valid | Check whether a 'HDF5' file can be opened for read/write
io_read_ants_transform | Read 'ANTs' transform file
io_read_flirt_transform | Read FSL FLIRT transformation matrix
io_read_fs | Read and write surface files
io_read_fst | Low-level file read and write
io_read_fstarray_or_h5 | Function try to load 'FST' arrays, if not found, read 'HDF5' arrays
io_read_gii | Read and write surface files
io_read_h5 | Lazy Load 'HDF5' File
io_read_ini | Low-level file read and write
io_read_json | Low-level file read and write
io_read_mat | Low-level file read and write
io_read_mgz | Read and write volume data
io_read_nii | Read and write volume data
io_read_niml | Read an AFNI/SUMA NIML dataset
io_read_tck | Read or write "TCK" streamlines
io_read_trk | Read or write "TCK" streamlines
io_read_tt | Read "TT" streamline file
io_read_vtk_polys | Read or write surface mesh data in "VTK" format
io_read_vtk_streamlines | Read or write streamline data in "VTK" format
io_read_yaml | Low-level file read and write
io_write_fst | Low-level file read and write
io_write_gii | Read and write surface files
io_write_h5 | Save objects to 'HDF5' file without trivial checks
io_write_json | Low-level file read and write
io_write_mat | Low-level file read and write
io_write_mgz | Read and write volume data
io_write_mgz.ants.core.ants_image.ANTsImage | Read and write volume data
io_write_mgz.array | Read and write volume data
io_write_mgz.ieegio_mgh | Read and write volume data
io_write_mgz.ieegio_volume | Read and write volume data
io_write_mgz.nifti | Read and write volume data
io_write_mgz.niftiImage | Read and write volume data
io_write_nii | Read and write volume data
io_write_nii.ants.core.ants_image.ANTsImage | Read and write volume data
io_write_nii.array | Read and write volume data
io_write_nii.ieegio_mgh | Read and write volume data
io_write_nii.ieegio_nifti | Read and write volume data
io_write_nii.nifti | Read and write volume data
io_write_nii.niftiImage | Read and write volume data
io_write_tck | Read or write "TCK" streamlines
io_write_trk | Read or write "TCK" streamlines
io_write_vtk_polys | Read or write surface mesh data in "VTK" format
io_write_vtk_streamlines | Read or write streamline data in "VTK" format
io_write_yaml | Low-level file read and write

## -- L --

LazyFST | R6 Class to Load 'FST' Files
LazyH5 | Lazy 'HDF5' file loader
low-level-read-write | Low-level file read and write

## -- M --

merge.ieegio_surface | Merge two "ieegio" surfaces
merge.ieegio_volume | Merge "ieegio" volumes

## -- N --

new_space | Define a coordinate space
niml_as_surface | Read an AFNI/SUMA NIML dataset
niml_find | Read an AFNI/SUMA NIML dataset
NWBHDF5IO | Creates a 'NWBHDF5IO' file container

## -- P --

plot.ieegio_colormap_continuous | Plot a color map legend
plot.ieegio_colormap_discrete | Plot a color map legend
plot.ieegio_surface | Plot '3D' surface objects
plot.ieegio_volume | Plot '3D' volume in anatomical slices
print.ieegio_roi | Convert objects to "ieegio" region of interest
print.ieegio_roi_overlap_result | Detect whether two regions of interest overlap
pynwb_module | Install "NWB" via "pynwb"

## -- R --

read_bci2000 | Read 'BCI2000' data file
read_brainvis | Read 'BrainVision' data
read_colormap | Read a color map file
read_edf | Read 'EDF' or 'BDF' data file
read_nsx | Read ('BlackRock') 'NEV' 'NSx' data
read_nwb | Read 'NWB' format
read_streamlines | Read and write streamlines
read_surface | Read and write surface files
read_volume | Read and write volume data
resample_volume | Down-sample or super-sample volume
resolve_roi_as | Resolve a region of interest into a chosen representation

## -- S --

SignalDataCache | Class definition for signal cache
surface_to_surface | Transform surface between coordinate spaces

## -- T --

transform_flirt2ras | Convert FLIRT transform to world (RAS) coordinates
transform_orientation | Create transform between coordinate orientations

## -- V --

volume_to_surface | Create smooth surface from volume mask or data

## -- W --

write_colormap | Write a color map to file
write_edf | Write to 'EDF' format
write_streamlines | Read and write streamlines
write_surface | Read and write surface files
write_volume | Read and write volume data