Package index

Create Brain Atlases

Functions to create brain atlases for ggseg and ggseg3d

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_wholebrain_from_volume() experimental

Create atlas from whole-brain volumetric parcellation

Atlas Manipulation

Functions to manipulate and manage brain atlases

atlas_smooth() atlas_simplify()

Smooth and simplify atlas 2D contours

Atlas Repository

Create and manage ggseg atlas packages

setup_atlas_repo()

Create a new ggseg atlas package

setup_sitrep()

Check ggseg.extra setup status

Color Tables

Read, write, and manipulate FreeSurfer color tables

read_lut() read_ctab() deprecated

Read FreeSurfer LUT

write_lut() write_ctab() deprecated

Write FreeSurfer LUT

is_lut() is_ctab() deprecated

Check if object is a LUT

get_lut() get_ctab() deprecated

Read LUT and add hex colours

lut_add()

Add rows to a FreeSurfer LUT

lut_combine()

Combine FreeSurfer LUTs

Subcortical Helpers

Compose slice views and anatomical context for subcortical atlases

subcortical_slabs() subcortical_views() deprecated

Build subcortical slabs from a label bounding box

aseg_context()

Reduce a subcortical atlas to focus regions on grey anatomical context

aseg_hidden_labels()

Standard FreeSurfer aseg labels stripped from a subcortical atlas

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

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

Utilities

General package utilities

read_annotation_data()

Read annotation data from files

read_cifti_annotation()

Read CIFTI annotation file

read_gifti_annotation()

Read GIFTI annotation files

read_neuromaps_annotation()

Read neuromaps annotation files

read_neuromaps_volume()

Read neuromaps volume annotation via surface projection

reexports convert_legacy_brain_atlas

Objects exported from other packages

read_tractography()

Read tractography file

mri_surf2surf_rereg()

Re-register an annotation file

get_verbose()

Get verbose setting

is_verbose()

Get verbosity level

as_verbosity()

Coerce a value to a verbosity level