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.

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).

Subsection of the DISTAL atlas visualized with three typical DBS electrodes

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).

2D slice visualization of the atlas

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).

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.

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:

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.


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.

Human 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.

How to obtain the atlas:

  • For information about the atlas, see this link
  • An MNI space version of the atlas is in preparation

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