as_ieegio_roi to mark an image volume, surface,
point cloud, or streamlines object as a region of interest, recording
the selection criteria (intensity bounds, threshold expressions, arc
length filters) rather than applying them right awayresolve_roi_as to carry out those criteria and
convert the region into a chosen representation (volume, point cloud,
surface, or streamlines), always in world RAS coordinates
so two resolved regions can be compared directlydetect_roi_overlap to test whether two regions
overlap, with distance tolerance, an optional interior test for closed
surfaces, and per-unit hit ratios written back onto the second
regionio_read_niml and niml_find to read
AFNI and SUMA NIML datasets,
supporting every storage form (plain text, binary and
base64 in either byte order, optionally gzip
compressed) and every column type, including String,
Line, complex, rgb, and
rgbaniml_as_surface and an
as_ieegio_surface method for NIML objects;
read_surface now recognizes '.niml.dset' files
and decides between annotations and measurements from the dataset
itselfread_colormap now reads the AFNI label
table from NIML datasets that store it in binary formHDF5 back-end is now resolved at run time, choosing
among readNSx, h5lite, hdf5r, and
h5py; hdf5r is no longer required and has been
removed from Suggestsh5py back-end returning 32-bit integer
datasets as double, which turned the missing value sentinel into a large
negative numbersanitize argument to
read_streamlines and as_ieegio_streamlines
that discards tracts which are not lines and points with missing
coordinates; set it to FALSE to read a file exactly as
writtenas_ieegio_volume choosing an integer data type
for arrays that contain InfNIML sample datasets and std.141
inflated surfaces to example dataio_read_vtk_polys and
io_write_vtk_polys to read and write surface meshes stored
in VTK polygon formats (legacy .vtk,
XML-based .vtp, .pvtp,
.vtu, and HDF5-based .vtpb),
including vertex colors and vertex-wise measurements;
read_surface and write_surface now recognize
these formatspar not reset after
showing surfacesYBA696 atlas to example databurn_curve to burn electrode trajectories
(e.g. depth/sEEG leads or DBS shafts) into a
volume given start and end positions in image native RAS
coordinates, with configurable radius and per-segment colorsmerge mode to burn_curve so newly
burned trajectories can be composted onto an existing volume instead of
overwriting itR graphics plot method for
ieegio_surface objects as an alternative to the default
r3js rendering, useful for static figures and environments
without WebGLget_channel so channels can be looked up by label
(in addition to index) for BCI2000 and
BrainVision formatsmat_to_quaternion to correctly handle handedness
changes, aligning the quaternion sign convention with
FreeSurferCRAN check issuesMCP tools
(can be loaded via package ravepipeline and
ellmer)new_space and as_ieegio_transform to
define coordinate spaces and chain transformsio_read_ants_transform to read ANTs
affine and displacement field transformsio_read_flirt_transform to read
FSL FLIRT affine transformsvolume_to_surface and
surface_to_surface for mapping data between volumes and
surfacesplot.ieegio_volume intensity windowing using
percentile-based display range (2-98 percentiles), following conventions
from FSLeyes, AFNI, MRIcroGL, and
SPMCT vs MRI data:
excludes zeros by default but includes them when lower percentile is
below -500 (indicating CT with -1024 background)as_nifti_header as a workaround when
RNifti is missing (not installed or running in
WebAssembly)Githubwrite_edf to save signals as continuous
EDF formatYBA atlas (690 segments) to example dataHDF5 checking error messagesLazyFST classgzipped is ignored in
io_write_nii.arrayLazyH5 fall back to alternatives when HDF5
is not supported in wasmr3js by defaultBrainVision annotation bugsSTL format (to support importing
to BrainLab)trk,
tck, tt, vtk)freesurfer surfaces also appends orientation
information at the end.ravetools to help speed up sample
volumes using C++GIfTI
formatwrite_surface not working when writing to
FreeSurfer measurement (curvature) formatas_ieegio_surface does not require verticesh5py loadermat_to_quaternion always returns non-negative
w nowdim and length to volume
objectEDF formatRGB[A]) formatscal_min and
cal_max is setr3js for visualizing surfacesresample_volume to sample images (currently only
nearest neighbor)burn_volume to burn contacts (positions given in
the image native RAS coordinate) with any given colorsio_h5_names returning wrong names when using with
h5pyLazyH5 for down-stream
packagesas_ieegio_volume and
as_ieegio_surface to enclose volume or surface dataPythonh5py as an alternative back-end supportTorig (index to tkr coordinate
transform) issue
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