Subcortical Atlases in MNI space

Below you find information about how and where to obtain subcortical atlases suitable for 2D/3D-visualization using Lead-DBS.   If an atlas you know of is missing, please contact us. Also, we are interested in distributing subcortical atlases preinstalled within Lead-DBS, if possible.

Looking for atlases of the cortex / whole-brain parcellations? Please see this page.

Please read our philosophy on including code and datasets into Lead-DBS. In brief, inclusion of datasets does not mean endorsement or approval of the datasets you find within Lead-DBS.

DISTAL Atlas (Ewert 2017)

This atlas was created especially for use in Lead-DBS and combines multimodal MRI-, histology- and connectivity data into the same atlas to precisely define DBS targets and surrounding structures in 2009b NLIN Asym ICBM space (the most modern “MNI space” in highest resolution currently available). The histology of this atlas is based on the Chakravarty atlas (see below).

  • Current Version is 1.1. | Older Versions:

Subsection of the DISTAL atlas visualized with three typical DBS electrodes

Human Motor Thalamus in 3D Stereotactic Coordinates

By Ilinsky I. and Kultas-Ilinsky H-K.

Continuous series of thalamic nuclear maps in three stereotactic planes obtained from a single brain plus the original series of sagittal histological sections and a set of sagittal MRIs from the same brain are available at the site

This is a unique set of images in that the motor related nuclei are outlined based on an immunocytochemical marker specific for terminal zone of each motor-related subcortical afferent system such as cerebellar, pallidal and nigral. These territories are shown within the Talairach coordinate system and their correspondence to Hassler’s parcellations of the motor related nuclei as well as Jones-Morel outlines is discussed in an accompanying manuscript Ilinsky et al., 2015, available at the site referenced below. Also comparison with some related DTI tractography data is given.

CIT168 Reinforcement Learning Atlas (Pauli 2017)

Initially built to study structures involved in reinforcement learning processes, this atlas captures all primary DBS targets and structures of interest. Probabilistic atlas based on manual segmentations on HCP data.

How to obtain the atlas:

Related citations:

  • Current Version is 1.1. | Older Versions:

Thalamic DBS Connectivity atlas (Akram 2018)

This atlas parcellates the thalamus based on connectivity – including a region predominantly connected to the contralateral dentate via the dentatorubrothalamic tract.

MNI PD25 atlas (Xiao 2017)

This atlas is defined on a specialized, Parkinson Disease specific template based on multispectral imaging that visualizes primary target regions such as the subthalamic nucleus. Key structures were defined on MRI, further structures were added using the same histological data introduced in the Chakravarty atlas (see above).

Computational Brain Anatomy Lab Merged Atlas (CoBrALab Atlas) in MNI Space (Pipitone 2014)

The CoBrALab produces manually segmented MNI-based atlases of brain anatomy on their 5 high-resolution (0.3 mm isotropic) T1 and T2 templates for use with their registration-based segmentation pipeline MAGeTbrain. In order to enable usage of their atlases for common-space localization in MNI space, they applied the MAGeTbrain pipeline to all publicly available MNI space templates in order to provide MNI space localization. These atlases contain the thamalus, globlus paladus, striatum, hippocampus with its subfields and whitematter, and the amydalaya.

How to obtain the atlas:

Related citations:

Enhanced tissue probability maps (Lorio 2016)

The enhanced Tissue Probability Maps are a set of gray-, white- and csf- priors for segmentation of subcortical structures using SPM based on manual labelling of iron and myelin specific parameter maps of nearly 100 individuals aged 25-75yo. Not specifically a subcortical atlas (with strict boundaries for each nucleus), they are still a highly valuable source for patient-specific segmentation and normalization with specific focus on the subcortex. Lead-DBS uses the TPMs to generate customized space-specific TPMs for each “space” that you use (for instance, a TPM for the default ICBM 2009b NLIN Asym space is generated based on the Lorio et al. enhances TPMs).

Brainstem connectome (Meola 2016)

This set of canonical fiber tracts in MNI space have been defined using human connectome project data and include fibertracts that are relevant to DBS surgery such as the dentato-rubro-thalamic tracts, the corticospinal tract and many more. The set of fibers was kindly provided for distribution within Lead-DBS by Antonio Meola from Brigham’s and Womens Hospital in Boston. You can read more about the fiber atlas here. You may contact Antonio in case of questions using our contact us webform.

Electrophysiological Atlas of STN Activity (Horn 2017)

In this atlas, beta power estimates recorded from >50 PD patients were mapped to the subthalamic nucleus, forming an electrophysiological target for DBS.

Electrophysiological Atlas of GPi Activity (Neumann 2017)

In this atlas, theta power estimates recorded from 27 dystonia patients were mapped to the internal pallidum, forming an electrophysiological target for DBS. Literature based similar sweetspots are also included.

Accolla 2014 STN functional zones atlas

Atlas with a parcellation of the BGHAT-volume (see above) of the STN into three functional zones (sensorimotor,associative, limbic) based on diffusion-based tractography.

Ultra-high field atlas for DBS planning

Atlas including STN, pallidum and red nucleus made on 7T data from 12 healthy controls. The templates on which the atlas is defined is not in MNI space but can be used within Lead-DBS for normalizations, as well (instead of using an MNI template). Also, there is an MNI version ported from template to MNI space available within Lead-DBS.

How to obtain the atlas:

  • An MNI version of the atlas comes preinstalled within Lead-DBS
  • Original 7T template space atlases and templates can be downloaded via the Lead-DBS spaces menu, as well
  • The raw data can be downloaded here

Related citations:

Melbourne Subcortex Atlas (Tian 2020)

This hierarchical functional MRI Atlas of the human subcortex features

  • Volumetric parcellation of the human subcortex representing consensus among more than 1000 healthy adults.
  • Available in four hierarchical scales as well as 3 and 7 Tesla versions.
  • Personalizable to represent individual variation in regional boundaries.
  • Seamlessly integratable into established cortex-only parcellation atlases.
  • Includes subdivisions of the striatum, thalamus, hippocampus, amygdala and globus pallidus.

Atlas of the Basal Ganglia and Thalamus (ABGT)

This atlas was generated in a hybrid manner using both structural and functional information. Components of the basal ganglia were first defined structurally with the “atlas of the basal ganglia” (ATAG; Keuken et al., 2014), including the striatum, globus pallidus externus (GPe) and internus (GPi), subthalamic nucleus (STN), and substantia nigra (SN). We also localized the spatial extent of the thalamus based on the Morel atlas (Morel et al., 1997; Krauth et al., 2010). Due to the relatively small size of the GPi, GPe, STN, and SN, these components were kept in consistent with ATAG without any additional processing. For the striatum and thalamus, we then performed a masked independent component analysis (ICA) based functional parcellation (Moher Alsady et al., 2016) to divide them into functionally distinctive subdivisions.

DBS targets atlas

Atlas defining DBS targets for nine diseases in MNI space. A systematic literature research defined optimal stimulation targets for each disease in AC/PC (functional) coordinates that were warped into MNI space based on a probabilistic mapping via an age-matched cohort.

  • Current Version is 1.1. | Older Versions:


Histological atlas that has been normalized to MNI-Space.

Optimal for STN or thalamic targets. In case your DBS target is the ventral intermediate nucleus (VIM), please note that this nucleus (commonly appearing in Walker or Hassler nomenclatures of thalamic nuclei) is not directly represented in this atlas which follows the Jones / Hirai & Jones nomenclatures.

The VLpv is the nucleus of the atlas best corresponding to the VIM although it may not be exactly the same. For more information about conversions between thalamic nomenclatures e.g. see Paxinos, G. (2012). The Human Nervous System. Academic Press.

Chakravarty 2006 Atlas

To the best of our knowledge, this atlas is the most detailed subcortical atlas available. Since its structural descriptions are in nomenclature of the Schaltenbrand-Wahren atlas, it also is very relevant to the field of DBS.

Please note that the original version of this atlas was registered to the MNI colin space whereas Lead-DBS conventionally uses the MNI152 ICBM 2009 space. These spaces are similar, but a 2009b version of the same data exists in the DISTAL atlas (see above). Alternatively, the same data was used to create the MNI PD25 atlas – which again uses a slightly different template space based on patients suffering from Parkinson’s Disease (see below).

How to obtain the atlas:

Related citations:

2D slice visualization of the atlas

THOMAS Atlas (Saranathan 2019)

THOMAS (Thalamus optimized multi-atlas segmentation) is a thalamic nuclei segmentation method based on 7T white matter nulled MP-RAGE which has been manually segmented by a trained neuroradiologist, following the Morel atlas. This atlas has been generated by label fusion of the 20 atlases warped to MNI space from a local averaged template space.

How to obtain the atlas:

  • The atlas comes pre-installed with Lead-DBS.

Related citations:

Nigral organization atlas (Zhang 2017)

An atlas displaying the anatomical and functional organization of the human substantia nigra (SN) using diffusion and functional MRI data from the Human Connectome Project.

How to obtain the atlas:

  • The atlas comes pre-installed with LEAD-DBS.
  • The atlas can be downloaded from Neurovault.

Related citations:


An atlas of the basal ganglia that is based on 7T MR imaging

ATAG-Atlas STN young–middle-aged–elderly

An atlas of the STN based on 7T MR imaging

PPN Histological Atlas (Alho 2017)

In this atlas, the pedunculopontine nucleus has been segmented based on postmortem MRI and histology.

BigBrain (Amunts 2013)

Not in particular an atlas but rather a highly detailed whole-brain histological map available in MNI/ICBM 152 2009b nonlinear symmetric space.

GPi probabilistic parcellation atlas (Moreira da Silva 2016)

An atlas parcellating the GPi by structural connectivity to brainstem, GPe and cortical regions.

Zhang thalamic connectivity atlas (Zhang 2008)

An atlas parcellating the thalamus into Motor/Premotor, Somatosensory, Parietal/Occipital, Prefrontal and Temporal functional zones based on functional and structural connectivity.

Oxford Thalamic Connectivity Atlas (Behrens 2003)

An atlas parcellating the thalamus into seven functional zones based on structural connectivity.

Thalamic Connectivity Atlas (Horn 2016)

A reproduction of the Oxford thalamic connectivity atlas – obtained on 169 subjects of the NKI-RS enhanced dataset and computed entirely within ICBM 2009b (MNI152) nonlinear space.

Harvard Ascending Arousal Network Atlas

An atlas focusing on the Ascending Arousal Network of the brainstem which also includes the pedunculo-pontine nucleus targeted for freezing of gait with DBS. Also, the ventral tegmental area is included.

Ahsan 2007 Basal ganglia atlas

An atlas of the basal ganglia based on MR-imaging data – including pallidum, substantia nigra, thalamus and more. The subthalamic nucleus is not included.


An atlas of the basal ganglia based on MR-imaging data

Functional Striatum parcellation atlas (Choi 2012)

As in the Yeo 2011 brain parcellation atlas, 1000 rs-fMRI scans were used to create this striatal parcellation atlas.

How to obtain the atlas:

Related citations:

PPN atlas (Snijders 2016)

Not really an “atlas” but rather an MNI coordinate defining the position of the PPN within MNI space. Lined out by an experienced neuroanatomist using multiple MNI templates and the Bigbrain dataset.

AICHA subcortical regions

The AICHA atlas is an atlas of intrinsic connectivity of homotopic areas. It also features a subcortical section functionally parcellating the thalamus and other deep nuclei such as Caudate, Pallidum, Putamen and Amygdama.

Harvard-Oxford subcortical/cortical atlas

A widely used atlas of subcortical structures. Does not separate between subparts of the pallidum / thalamus and does not contain a volume for the subthalamic nucleus. In the context of DBS, this atlas can for example be used for whole pallidum, thalamus, nucleus accumbens, as well as subcortical subcallosal cortex visualization.

Exemplary use of the HO-Atlas – target structures for DBS in depression.

MIDA model

One of the most detailed image-based anatomical head models available for computational life sciences.
If you are interested in whole-head anatomy, this is probably your atlas of choice. Regarding DBS, it contains interesting structures such as blood vessels, ventricles and subcortical structures such as thalamus and pallidum.

Please note that this atlas is not registered into MNI space which limits its use with Lead-DBS.

CFA subcortical shape atlas

An atlas based on MRI data


An atlas of the basal ganglia based on histological data

Brainstem Connectome Atlas

This is a probabilistic atlas of 23 brainstem bundles using high-quality connectome imaging data and advanced analysis techniques.  Rigorous quality control on connectome imaging data from the Human Connectome Project (HCP) were performed and only accepted high-quality imaging data with minimal residual distortions for atlas construction.

brainstem connectome atals

Fornix FMRIB FA Template

This atlas merged younger-older adult template of the fornix and demonstrated its utility for studies of aging and preclinical Alzheimer’s disease (AD).

Fornix FMRIB FA Template

DBS Tractography Atlas

A collection of manually curated dMRI-based tracts relevant to deep brain stimulation.

How to obtain the atlas:

  • The atlas comes preinstalled within Lead-DBS

Related citations:

  • Erik H. Middlebrooks et al. Neuroimaging Advances in Deep Brain Stimulation: Review of Indications, Anatomy, and Brain Connectomics. American Journal of Neuroradiology

Cerebellar Functional Networks (Buckner 2011)

This atlas is from rs-fMRI data acquired in 1000 young healthy adults that were registered using nonlinear deformation of the cerebellum in combination with surface-based alignment of the cerebral cortex.

Nucleus Accumbens atlas (Cartmell 2019)

Taking advantage of the distinct structural connectivity of nucleus accumbens subregions, this probabilistic atlas was generated using tractography-based segmentation results from 245 Human Connectome Project subjects. Segmentation results were corroborated using data from several modalities including MRI-based measures of function and microstructure and human post-mortem immunohistochemical staining. The atlas closely matches the traditional core and shell divisions based on cytoarchitecture.

Thalamic Functional Atlas (Kumar 2017)

This altas is based on resting state-fMRI to investigate the functional anatomy of the thalamus

Zona Incerta Atlas (Lau 2020)

This atlas shows direct visualization and characterization of the human zona incerta and surrounding structures.