# Reinforcement Learning Atlas Please refer to the parent wiki of this OSF project for detailed documentation: [https://osf.io/r2hvk/wiki/home/][1] ## Nucleus Coverage This component of the subcortical atlas covers the principal nuclei associated with reinforcement learning: Putamen (Pu) Caudate Nucleus (Ca) Nucleus Acumbens (NAC) Extended Amygdala (EXA) Globus Pallidus, Internal (GPi) Globus Pallidus, External (GPe) Ventral Pallidum (VeP) Substantia Nigra, Pars Compacta (SNc) Substantia Nigra, Pars Reticulata (SNr) Subthalamic Nucleus (STH) Hypothalamus (HN) Parabrachial Pigmented Nucleus (PBP) Ventral Tegmental Area (VTA) Red Nucleus (RN) Habenular Nuclei (HN) Mammilary Nucleus (MN) ## Contents This component contains reference T1w and T2w templates and the probabilistic reinforcement learning atlas with associated statistical reports for inter- and intra-observer similarities. 3D structural templates and 4D probabilistic atlas images are provided in both the native CIT168 700 um space and the MNI152 2009c nonlin asym 1 mm space for generalizability. All images are in compressed Nifti-1 format. ## NeuroVault We invite interested readers to explore the atlas and anatomical labels on the neurovault.org website ([https://neurovault.org/collections/3145/][2]). ## Region Deliniation Our primary reference for regional delineation was the online Allen Institute Adult 34 year old human atlas (\href{url}{http://atlas.brain-map.org}) with the third edition of the Mai-Paxinos-Voss atlas (2008) as a secondary reference. Tissue boundaries were characterized as either explicit, with clear contrast between neighboring regions, or implicit, where low tissue contrast forces the observer to use surrounding landmarks to estimate the boundary location when labeling. ### Caudate Nucleus (Ca): The Ca is hypointense in T1w and hyperintense in T2w templates with clear, high contrast boundaries at almost all points. The only exception is at it's low contrast ventral boundary with the nucleus accumbens (NAC). The current atlas includes the tail of the caudate as it travels caudally and ventrally around the lateral ventricle. ### Putamen (Pu): Similar to the Ca, the Pu boundaries are well-defined in both T1w and T2w templates except at the ventral boundary with the NAC. In the current atlas, and in contrast to \cite{mai_atlas_2008}, we include the ventral putamen in the main Pu label, rather than as a separate anatomical label. ### Globus Pallidus (GP): In T1w templates both segments of the GP are hypointense, with clear contrast against the surrounding myelinated white matter, including the internal capsule. The GPe encloses the GPi laterally and rostrally and both lie medial to the Putamen. The anterior commissure (ac) provides a convenient ventral limit for the GPe, separating the latter from the ventral pallidum (VeP). ### Subthalamic Nucleus (STH): The STH is a relatively well-defined hyperintense structure in T1w templates and lies caudal and lateral to the hypothalamus. The ventromedial boundary of the STH with SNr and PBP is indistinct in the T2w templates, because all are hypointense. The segmentation of the STH therefore relies on combined evaluation of the T1w and T2w contrast in coronal and sagittal sections. ### Substantia Nigra, pars reticulata (SNr): The SNr appears as a hypointense band, ventrolateral to the SNc in coronal T1w sections. ### Hypothalamus (HTH): The hypothalamus is internally heterogeneous in both T1w and T2w templates and is most easily delineated in coronal sections using the anterior commissure, mammillary nucleus, extended amygdala, sublenticular fascicle and thalamus as landmarks and boundaries. The caudal boundary of the HTH corresponds approximately with the appearance of the RN in coronal sections. ### Habenular Nuclei (HN): The HN have a relatively high myelin content and are hyperintense in T1w and hypointense in the T2w sections with clear boundaries with neighboring tissue and CSF spaces in all directions. ### Ventral Pallidum (VeP): The ventral pallidum is internally heterogenous in both T1w and T2w templates, partially due to its relatively small size, and edge effects with surrounding tissue introduced during midspace template construction. However, it is not entirely indistinct, and can be well localized because of surrounding nuclei. Rostrally, it borders with the nucleus accumbens. Ventrally, it borders with the hypothalamus and substantia innominata. Dorsally, it is separated from the ventral GPe by the anterior commissure. ### Nucleus Accumbens (NAC): The boundaries between the nucleus accumbens and the caudate and putamen respectively are indistinct, but not entirely invisible and are best delineated using a combination of coronal and axial sections from both T1w and T2w templates. The caudal limit of the NAC coincides with the appearance of the anterior commissure in coronal sections. ### Substantia Nigra, pars compacta (SNc): The SNc is visible in coronal T1w sections as a semi-continguous, irregularly-shaped, hyperintense band between the PBP and SNr. The rostral limit of the SNc coincides approximately with the caudal limit of the hypothalamus. ### Parabrachial Pigmented Nucleus (PBP): The PBP is visible as a hypointense band in T2w coronal sections, running ventromedially to dorsolaterally between the red nucleus and the SNc. The PBP has a high contrast, explicit boundary with the hypointense red nucleus dorsomedially and a lower contrast boundary with the SNc ventrolaterally in T2w templates. Rostrocaudally, the PBP extends from the caudal limit of the hypothalamus to the caudal limit of the red nucleus, medial to the subthalamic nucleus. ### Ventral Tegmental Area (VTA): In coronal sections, the VTA lies ventral to the RN at the ventromedial limit of the PBP. Rostrocaudally, the VTA extends from the approximate rostrocaudal midpoint of the RN to just beyond the caudal limit of the RN as seen in coronal sections. The boundary with the RN is a well defined and explicit, but the transition from PBP to VTA, and both rostral and caudal limits are poorly defined and therefore implicit in both T1w and T2w templates. ### Extended Amygdala (EXA): The extended amygdala consists of the bed nuclei of the stria terminalis (BNST), the sublenticular extended amygdala (SLEA) and the interstitial nucleus of the posterior limb of the anterior commissure, though this last region cannot be identified in either the T1w or T2w templates and is consequently omitted from the atlas. In coronal sections, the EXA extends ventrally from the ventromedial edge of the caudate nucleus to the anterior commissure, lying between the columns of the forix and the internal capsule. The SLEA extends laterally from the main body of the BNST, immediately caudal to the anterior commissure and dorsolateral to the hypothalamus. ### Red Nucleus (RN): The red nucleus is hypointense in the T2w template with clear, high-contrast boundaries with the surrounding midbrain but has very low contrast in the T1w templates. It is an important landmark for the PBP, SNr, SNc and VTA labels. ### Mammillary Nucleus (MN): The mammillary nucleus is well defined in both T1w and T2w templates with a distinct, more heavily myelinated capsule (comprised mainly of fibers of the mammillary peduncle, fornix and mammillothalamic tract) which appears hyperintense in T1w and hypointense in T2w templates. The MN is readily located at the ventral terminations of the fornix and mammillothalamic tract. ## References **Release preprint:** Pauli, W. M., Nili, A. N. & Tyszka, J. M. A High-Resolution Probabilistic In Vivo Atlas of Human Subcortical Brain Nuclei. bioRxiv 211201 (2017). [doi:10.1101/211201][3] **Primary Anatomical Reference:** Allen Adult Human (Gyral) Reference Atlas. [http://atlas.brain-map.org/][4] [1]: https://osf.io/r2hvk/wiki/home/ [2]: https://neurovault.org/collections/3145/ [3]: https://www.biorxiv.org/content/early/2017/10/30/211201 [4]: http://atlas.brain-map.org/