Package index • ggseg.extra

Create Brain Atlases

Turn a parcellation into a ggseg_atlas you can plot

create_cerebellar_from_annotation() experimental: Create cerebellar atlas from FreeSurfer annotation
create_cerebellar_from_gifti() experimental: Create cerebellar atlas from SUIT flatmap
create_cerebellar_from_volume() experimental: Create cerebellar atlas from volume segmentation
create_cortical_from_annotation() maturing: Create cortical atlas from FreeSurfer annotation
create_cortical_from_cifti() experimental: Create cortical atlas from a CIFTI file
create_cortical_from_gifti() experimental: Create cortical atlas from GIFTI annotation files
create_cortical_from_labels() experimental: Create brain atlas from label files
create_cortical_from_neuromaps() experimental: Create cortical atlas from a neuromaps annotation
create_subcortical_from_volume() experimental: Create brain atlas from subcortical segmentation
create_tract_from_tractography() experimental: Create brain atlas from white matter tracts
create_tract_from_volume() experimental: Create a white matter tract atlas from a label volume
create_wholebrain_from_volume() experimental: Create atlas from whole-brain volumetric parcellation

Shape an Atlas’s Geometry

Simplify, smooth and grow a finished atlas’s 2D outlines. These run on the returned atlas, not during the build, so retuning one is cheap.

atlas_polish() experimental: Simplify and smooth an atlas against a vertex budget
atlas_simplify(): Reduce an atlas's vertex count
atlas_smooth(): Round off an atlas's voxel staircase
atlas_dilate(): Grow or shrink an atlas's regions
context_pattern() experimental: The label pattern that matches an atlas's backdrop
count_vertices(): Count the vertices an atlas carries

Curate an Atlas

The atlas_region_* and atlas_view_* vocabulary, re-exported from ggseg.formats, plus the constructor that validates a hand-edited atlas. ?atlas-verbs groups them by what they change.

atlas-verbs: Atlas manipulation verbs, re-exported from ggseg.formats
reexports convert_legacy_brain_atlas atlas_context_remove atlas_core_add atlas_geom atlas_geometry_type atlas_labels atlas_meshes atlas_palette atlas_polygons atlas_region_contextual atlas_region_keep atlas_region_op atlas_region_remove atlas_region_rename atlas_regions atlas_sf atlas_type atlas_vertices atlas_view_gather atlas_view_keep atlas_view_remove atlas_view_remove_region atlas_view_remove_small atlas_view_reorder atlas_views ggseg_atlas is_ggseg_atlas: Objects exported from other packages

Atlas Repository

Create and maintain a ggseg atlas package

setup_atlas_repo(): Create a new ggseg atlas package
use_atlas_github_actions(): Add ggsegverse GitHub Actions workflows to a package
ggseg_atlas_github_actions(): Workflows use_atlas_github_actions() can write
sitrep(): Report on the ggseg.extra setup

Lookup Tables

Read, write and build FreeSurfer-style colour lookup tables

read_lut(): Read FreeSurfer LUT
write_lut(): Write FreeSurfer LUT
get_lut(): Read LUT and add hex colours
is_lut(): Check if object is a LUT
lut_add(): Add rows to a FreeSurfer LUT
lut_combine(): Combine FreeSurfer LUTs
lut_classify_anatomy(): Classify lookup-table labels as cortical, subcortical, or cerebellar
lut_generate_colors(): Generate a palette for a colourless lookup table

Subcortical Helpers

Compose slice views and anatomical context for subcortical atlases

subcortical_slabs(): Build subcortical slabs from a label bounding box

Anatomical Coregistration

Align an atlas volume to a FreeSurfer subject for anatomical context

coregister_volume(): Coregister an atlas volume to a FreeSurfer subject
project_volume_anatomical(): Project atlas labels onto FreeSurfer anatomical context
prepare_subcortical_anatomical(): Prepare an atlas for the subcortical pipeline with anatomical context
prepare_subcortical_mni152(): Embed MNI152 subcortical parcels in a FreeSurfer aseg for grey-brain context
aseg_subcortical_labels(): Lumped aseg subcortical structures a parcellation typically subdivides

Cerebellar Helpers

SUIT surfaces and MNI-to-SUIT transforms for cerebellar atlases

suit_flatmap_path(): Path to bundled SUIT flatmap surface
suit_3d_path(): Path to bundled SUIT 3D cerebellar surface
suit_deformation_field() experimental: Download SUIT deformation field for MNI-to-SUIT transforms
transform_mni_to_suit() experimental: Transform a volume from MNI space to SUIT cerebellar space
read_suit_parcellation() experimental: Read SUIT cerebellar parcellation from GIFTI

Reading Parcellation Files

Read the formats the creation pipelines accept

read_annotation_data(): Read annotation data from files
read_gifti_annotation(): Read GIFTI annotation files
read_cifti_annotation(): Read CIFTI annotation file
read_cifti_subcortical() experimental: Extract subcortical labels from a CIFTI file
read_neuromaps_annotation(): Read neuromaps annotation files
read_neuromaps_volume(): Read neuromaps volume annotation via surface projection
read_tractography(): Read tractography file

Utilities

mri_surf2surf_rereg(): Re-register an annotation file
label_to_region(): Derive an atlas region from a label
get_verbose(): Get verbose setting
as_verbosity(): Coerce a value to a verbosity level