| Title: | FreeSurfer Brain Atlases for the 'ggseg' Ecosystem |
|---|---|
| Description: | FreeSurfer cortical and subcortical brain atlases for the 'ggseg' ecosystem. Provides unified 'ggseg_atlas' objects with 2D polygon geometry and 3D mesh or vertex data, for use with 'ggseg' and 'ggseg3d'. |
| Authors: | Athanasia Mo Mowinckel [aut, cre] (ORCID: <https://orcid.org/0000-0002-5756-0223>), Didac Vidal-Piñeiro [aut] (ORCID: <https://orcid.org/0000-0001-9997-9156>) |
| Maintainer: | Athanasia Mo Mowinckel <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.0.1.9000 |
| Built: | 2026-10-14 14:24:00 UTC |
| Source: | https://github.com/ggsegverse/ggsegFreeSurfer |
Atlas of the four FreeSurfer brainstem substructures (midbrain, pons,
medulla oblongata and superior cerebellar peduncle), as implemented in
FreeSurfer's segment_subregions brainstem (Iglesias et al. 2015).
Built from the cvs_avg35 template segmentation embedded in its
full-brain aseg, so slice views show the brainstem inside cerebral
cortex and white matter (rendered grey as anatomical context).
Substructure colours come from FreeSurfer's official LUT.
brainstem()brainstem()
A ggseg.formats::ggseg_atlas object (subcortical).
Iglesias JE, Van Leemput K, Bhatt P, Casillas C, Dutt S, Schuff N, Truran-Sacrey D, Boxer A, Fischl B (2015). "Bayesian segmentation of brainstem structures in MRI." NeuroImage, 113:184-195. doi:10.1016/j.neuroimage.2015.02.065
Other ggseg_atlases:
destrieux(),
dkt(),
hcpa(),
hippoamyg(),
hypothalamus(),
thalamus()
Other subcortical_atlases:
hcpa(),
hippoamyg(),
hypothalamus(),
thalamus()
Other freesurfer_atlases:
destrieux(),
dkt(),
hcpa(),
hippoamyg(),
hypothalamus(),
thalamus()
brainstem()brainstem()
Brain atlas for the Destrieux cortical parcellation
(aparc.a2009s) with 75 regions per hemisphere. Contains 2D
polygon geometry for ggseg::geom_brain().
destrieux()destrieux()
A ggseg.formats::ggseg_atlas object (cortical).
Destrieux C, Fischl B, Dale A, Halgren E (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage, 53(1), 1-15. doi:10.1016/j.neuroimage.2010.06.010
Other ggseg_atlases:
brainstem(),
dkt(),
hcpa(),
hippoamyg(),
hypothalamus(),
thalamus()
Other cortical_atlases:
dkt()
Other freesurfer_atlases:
brainstem(),
dkt(),
hcpa(),
hippoamyg(),
hypothalamus(),
thalamus()
destrieux() plot(destrieux())destrieux() plot(destrieux())
Cortical parcellation with 32 regions per hemisphere based on
the Desikan-Killiany-Tourville labeling protocol. Contains both
2D polygon geometry for ggseg::geom_brain() and 3D vertex
indices for ggseg3d::ggseg3d().
dkt()dkt()
A ggseg.formats::ggseg_atlas object (cortical).
Klein A, Tourville J (2012). 101 labeled brain images and a consistent human cortical labeling protocol. Frontiers in Neuroscience, 6:171. doi:10.3389/fnins.2012.00171
Other ggseg_atlases:
brainstem(),
destrieux(),
hcpa(),
hippoamyg(),
hypothalamus(),
thalamus()
Other cortical_atlases:
destrieux()
Other freesurfer_atlases:
brainstem(),
destrieux(),
hcpa(),
hippoamyg(),
hypothalamus(),
thalamus()
dkt() plot(dkt())dkt() plot(dkt())
Atlas of the hippocampus split into an anterior (head) and a posterior
(body and tail) part per hemisphere, after the common HCP-style
long-axis subdivision. The boundary is the midpoint of each
hippocampus's own anterior-posterior extent in the FreeSurfer aseg.
Built from the fsaverage5 aseg, so slice views show the hippocampus
inside cerebral cortex and white matter (rendered grey as anatomical
context).
hcpa()hcpa()
A ggseg.formats::ggseg_atlas object (subcortical).
Other ggseg_atlases:
brainstem(),
destrieux(),
dkt(),
hippoamyg(),
hypothalamus(),
thalamus()
Other subcortical_atlases:
brainstem(),
hippoamyg(),
hypothalamus(),
thalamus()
Other freesurfer_atlases:
brainstem(),
destrieux(),
dkt(),
hippoamyg(),
hypothalamus(),
thalamus()
hcpa()hcpa()
FreeSurfer segmentation of the hippocampal subfields (Iglesias et al.
2015) and the nuclei of the amygdala (Saygin et al. 2017), as produced
by segment_subregions hippo-amygdala. Built from the cvs_avg35
template segmentation embedded in fsaverage5's full aseg, so slice
views show the subregions inside cerebral cortex and white matter
(rendered grey as anatomical context), surrounded by the neighbouring
subcortical structures. Region colours come from FreeSurfer's official
LUT.
hippoamyg()hippoamyg()
A ggseg.formats::ggseg_atlas object (subcortical).
Iglesias JE, Augustinack JC, Nguyen K, Player CM, Player A, Wright M, Roy N, Frosch MP, McKee AC, Wald LL, Fischl B, Van Leemput K (2015). "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI." NeuroImage, 115:117-137. doi:10.1016/j.neuroimage.2015.04.042
Saygin ZM, Kliemann D, Iglesias JE, van der Kouwe AJW, Boyd E, Reuter M, Stevens A, Van Leemput K, McKee A, Frosch MP, Fischl B, Augustinack JC (2017). "High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas." NeuroImage, 155:370-382. doi:10.1016/j.neuroimage.2017.04.046
Other ggseg_atlases:
brainstem(),
destrieux(),
dkt(),
hcpa(),
hypothalamus(),
thalamus()
Other subcortical_atlases:
brainstem(),
hcpa(),
hypothalamus(),
thalamus()
Other freesurfer_atlases:
brainstem(),
destrieux(),
dkt(),
hcpa(),
hypothalamus(),
thalamus()
hippoamyg()hippoamyg()
Atlas of the five FreeSurfer hypothalamic subunits per hemisphere
(anterior-inferior, anterior-superior, posterior, tubular-inferior and
tubular-superior), as implemented in FreeSurfer's
mri_segment_hypothalamic_subunits (Billot et al. 2020). Built from the
cvs_avg35 template segmentation embedded in its full-brain aseg, so
slice views show the hypothalamus inside cerebral cortex and white
matter (rendered grey as anatomical context). Subunit colours come from
FreeSurfer's official LUT.
hypothalamus()hypothalamus()
A ggseg.formats::ggseg_atlas object (subcortical).
Billot B, Bocchetta M, Todd E, Dalca AV, Rohrer JD, Iglesias JE (2020). "Automated segmentation of the hypothalamus and associated subunits in brain MRI." NeuroImage, 223:117287. doi:10.1016/j.neuroimage.2020.117287
Other ggseg_atlases:
brainstem(),
destrieux(),
dkt(),
hcpa(),
hippoamyg(),
thalamus()
Other subcortical_atlases:
brainstem(),
hcpa(),
hippoamyg(),
thalamus()
Other freesurfer_atlases:
brainstem(),
destrieux(),
dkt(),
hcpa(),
hippoamyg(),
thalamus()
hypothalamus()hypothalamus()
Probabilistic atlas of the 26 thalamic nuclei per hemisphere
combining ex vivo MRI and histology, as implemented in FreeSurfer's
segmentThalamicNuclei.sh (Iglesias et al. 2018). Built from the
cvs_avg35 template segmentation embedded in its full-brain aseg,
so slice views show the thalamus inside cerebral cortex and white
matter (rendered grey as anatomical context). Nucleus colours come
from FreeSurfer's official LUT — the published Iglesias palette.
thalamus()thalamus()
A ggseg.formats::ggseg_atlas object (subcortical).
Iglesias JE, Insausti R, Lerma-Usabiaga G, Bocchetta M, Van Leemput K, Greve D, van der Kouwe A, Caballero-Gaudes C, Paz-Alonso P (2018). "A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology." NeuroImage, 183:314-326. doi:10.1016/j.neuroimage.2018.08.012
Other ggseg_atlases:
brainstem(),
destrieux(),
dkt(),
hcpa(),
hippoamyg(),
hypothalamus()
Other subcortical_atlases:
brainstem(),
hcpa(),
hippoamyg(),
hypothalamus()
Other freesurfer_atlases:
brainstem(),
destrieux(),
dkt(),
hcpa(),
hippoamyg(),
hypothalamus()
thalamus()thalamus()