Skip to contents

Create cerebellar atlas from volume segmentation

Source: R/atlas_cerebellar.R
create_cerebellar_from_volume.Rd

[Experimental]

Creates a cerebellar atlas from a NIfTI segmentation volume. Uses the bundled SUIT 3D surface for volume-to-surface sampling and the SUIT flatmap for 2D polygon generation. Per-region 3D meshes are tessellated from the volume for 3D rendering.

Usage

create_cerebellar_from_volume(
  input_volume = NULL,
  decimate = 0.5,
  verbose = get_verbose(),
  ...,
  input_lut = NULL,
  atlas_name = NULL,
  output_dir = NULL,
  min_coverage = NULL,
  cleanup = NULL,
  skip_existing = NULL
)

Arguments

input_volume

Path to a cerebellar segmentation volume (NIfTI).

decimate

Mesh decimation factor between 0 and 1. Reduces the number of faces in 3D meshes using quadric edge decimation (via Rvcg::vcgQEdecim()). A value of 0.5 reduces faces by 50%. Set to NULL to skip decimation. Requires the Rvcg package. Default is 0.5.

verbose

How much to print: 0 silent, 1 progress (the default), 2 adds FreeSurfer's own output. TRUE and FALSE mean 1 and 0. Falls back to options("ggseg.extra.verbose"), then GGSEG_EXTRA_VERBOSE.

...

Not used. Present so that a mistyped or misplaced argument is reported against this function rather than silently ignored; anything passed here is an error. Geometry is shaped after the build: see atlas_polish(), or atlas_simplify(), atlas_smooth() and atlas_dilate() individually.

input_lut

Optional path to a colour lookup table file, or a data.frame with columns idx, label, and optionally R, G, B. Either may also carry a hemi column ("left", "right" or "midline") that sets each region's hemisphere; a row left NA, or a table without the column, has it read from the label's name, and any other value is an error. write_lut() stores the column in a file. If NULL, labels are auto-generated from volume values.

atlas_name

Name for the atlas. If NULL, derived from the input filename. It also names the folder of intermediate files inside output_dir, so it must be a single name without path separators.

output_dir

Where to put the intermediate files. Defaults to tempdir(), from options("ggseg.extra.output_dir") or GGSEG_EXTRA_OUTPUT_DIR.

min_coverage

Smallest share of core labels that must end up with 2D geometry, between 0 and 1. A build that falls below it warns and names the labels that have no shape; the warning fires whatever verbose is set to, because a region that cannot be drawn is data loss rather than progress chatter. The build itself still returns, so a long pipeline is never thrown away over a threshold. Use 0 to turn the check off. Defaults to 0.8, or to options("ggseg.extra.min_coverage"), then GGSEG_EXTRA_MIN_COVERAGE.

cleanup

Remove the intermediate files afterwards. Default TRUE, from options("ggseg.extra.cleanup") or GGSEG_EXTRA_CLEANUP.

The intermediate files live in a folder named after the atlas inside output_dir, and the whole folder is removed. A build therefore refuses to start if that folder already holds files it did not write, since removing it would take them too. Choose another output_dir or atlas_name, or pass FALSE to build there and keep everything.

skip_existing

Reuse a step's intermediate files when they already exist, instead of running the step. Default FALSE, from options("ggseg.extra.skip_existing") or GGSEG_EXTRA_SKIP_EXISTING.

A cache records which ggseg.extra wrote it, not what it was built from, so reuse cannot tell that the volume or lookup table has changed. Reuse is therefore asked for rather than assumed, and is reported when it happens. To continue an interrupted build, either pass TRUE or leave the finished steps out of steps.

Value

A ggseg_atlas object of type "cerebellar" with both sf geometry and 3D meshes.

See also

atlas_polish() to simplify and round off the result, which most builds want next.

Other atlas creation: create_cerebellar_from_annotation(), create_cerebellar_from_gifti(), create_cortical_from_annotation(), create_cortical_from_cifti(), create_cortical_from_gifti(), create_cortical_from_labels(), create_cortical_from_neuromaps(), create_subcortical_from_volume(), create_tract_from_tractography(), create_tract_from_volume(), create_wholebrain_from_volume()

Examples

if (FALSE) { # \dontrun{
atlas <- create_cerebellar_from_volume("cerebellar_parcellation.nii.gz")
} # }