A description of the manual segmentation of the structures follows from the anatomical definitions (Wang et al., 2007, Qiu et al., 2010, Qiu et al., 2009) with the assistance of an atlas (Mai et al., 1997).
The amygdala is a complex structure that is located in the medial temporal lobe, inferior to the putamen and the globus pallidus and anterior to the hippocampus. The first anterior slice of the amygdala appears as an ovoid shape when the temporal lobe already connects to the frontal lobe by a visible limen insulae. The superior boundary of the amygdala is the endorhinal sulcus while its inferior boundary is the white matter which separates it from the parahippocampal gyrus. Its lateral boundary is the white matter of the temporal lobe and its medial boundary is marked distinctively by CSF and the semiannular sulcus. Moving posteriorly, the inferior boundary of the amygdala is the uncal recess of the temporal horn of lateral ventricle and the alvear white matter of the hippocampus. The amygdala subsequently becomes smaller and is replaced by the hippocampus. In caudal slices, the amygdala appears as a thin gray matter stripe superior to hippocampus and inferior to the globus pallidus and then gradually disappears.
The caudate nucleus is a large C-shaped deep gray matter mass located medial to the internal capsule and related throughout its length to the surface of the lateral ventricle. It has an expanded rostral component (head) that bulges into the lateral wall of the frontal horn of the lateral ventricle, and tapers to form the tail located along the lateral wall of the lateral ventricle, and then becomes further attenuated as it courses along the roof of the temporal horn of the lateral ventricle. The tail terminates at the amygdaloid nucleus. The head forms a convexity into the anterior horn of the lateral ventricle. The tail forms the lateral wall of the body of the lateral ventricle and occupies a position in the roof of the inferior (i.e., temporal) horn of the lateral ventricle. In essence, the caudate nucleus follows the curvature of the lateral ventricle.
The entorhinal cortex is a structure with boundaries that are challenging to define reliably in MRI, with there being considerable variation among protocols in the definition of the lateral border (Feczko et al., 2009, Honeycutt et al., 1998, Insausti et al., 1998) and with the protocols varying in the extent of inclusion of the trans-entorhinal cortex corresponding to the part of the entorhinal cortex that lies within the collateral sulcus. Our approach follows the procedure of Feczko et al (2009) defining the lateral extent of the entorhinal cortex at the shoulder of the medial bank of the collateral sulcus, including the maximal extent of the entorhinal cortex as can be defined in MRI over the entire length of the hippocampal head. The medial boundary is chosen by locating the most medial aspect of white matter of the parahippocampal gyrus, and moving medially through grey matter to the dura boundary. The medial bank of the collateral sulcus (on the coronal slice 4mm rostral to the most rostral extent of the hippocampus) is identified, with the tail identified at the white matter/grey matter boundary at the medial bank of the collateral sulcus (on the coronal slice 2mm posterior to the most caudal extent of the gyrus intralimbicus). Sections are segmented uniformly along the head-tail principal axis on parallel sections, two at the medial bank of the collateral sulcus (one at the grey/white matter boundary, one at grey matter/dura boundary), and two at the most medial extent of the entorhinal cortex (gray/white matter and gray matter/dura boundary). In caudal sections, the medial boundary is defined by subiculum where hippocampal fissure is evident. The procedure excludes dura/tentorium.
The globus pallidus is a wedge-shaped deep GM mass located between the putamen and posterior limb of the internal capsule. The base (larger end) of the wedge lies against the medial aspect of the putamen and the tapering end lies against the internal capsule. The putamen and the globus pallidus are separated by a thin lamina of myelinated fibers called the external medullary lamina. A similar lamina (internal medullary lamina) divides the GP into a lateral or external division (GPe) and a medial or internal (GPi) division. The globus pallidus is traversed by numerous myelinated fibers, which provide its characteristic pale appearance in T1-weighted MR images.
The hippocampus is a seahorse shaped structure with interfolded layers that plays a central role in the lymbic system. It is located within the temporal lobe, posterior to the amygdala. The first anterior slice of the hippocampus head appears as a thin stripe inferior to the amygdala and superior to the entorhinal cortex with its alvear white matter as a well-defined boundary with the amygdala. The superior boundary of the hippocampus is the amygdala while its inferior boundary is the white matter of the the parahippocampal gyrus that separates it from the entorhinal cortex. Its lateral boundary is the temporal horn of the lateral ventricle and the medial boundary is the well-contrasted CSF. Moving posteriorly, the hippocampus gradually replaces the amygdala. It is then surrounded by the white matter of the temporal lobe and the crus of the fornix. The hippocampus disappears when the splenium of the corpus callosum stops connecting the two brain hemispheres.
Following Djamanakova et al. (2013), at each axial slice a seeded region-growing algorithm was applied which delineated voxels that were connected and had a value below a specified threshold. This step was followed by a manual correction step, in which the third ventricle and any brain matter were explicitly excluded.
The nucleus accumbens is situated adjacent to the medial and ventral parts of the caudate/putamen. The nucleus accumbens is the GM mass connecting the inferior aspects of the anterior ends of the putamen and the head of the caudate nucleus. The putamen and the globus pallidus together constitute the main bulk of the lentiform nucleus (excluding the claustrum). The anterior part of the putamen and the caudate head are interconnected by gray matter bands (or striae), giving rise to the term corpus striatum. The caudate nucleus and the lentiform nucleus constitute the basal ganglia. The nucleus accumbens borders the inferior component of the caudate head, which is continuous laterally with the inferior aspect of the anterior end of the putamen.
The putamen is a wedge-shaped deep GM mass located lateral to the caudate nucleus, with the base (larger end) of the wedge anteriorly and its tapering end posterior. It is incompletely separated from the caudate by the anterior limb of the internal capsule. In their most rostral extents, the caudate nucleus and the putamen are continuous around the anterior limb of the internal capsule, and ventrally are poorly differentiated from the nucleus accumbens.
The first anterior slice of the thalamus is taken to be immediately posterior to the descending column of the fornix, although there may be some thalamus in the last slice where fornix is seen. In the medio-lateral dimension, the thalamus extends from the third ventricle or the midline to the internal capsule. Dorsally, it is bounded by the lateral ventricle and, dorsolaterally, by the caudate nucleus. The inferior edge of the thalamus is taken to be a horizontal line extending from the ventromedial part of the internal capsule to the bulge in the third ventricle (the hypothalamic sulcus). This boundary separates the thalamus from the hypothalamus. In its posterior half, the thalamus enlarges laterally as the internal capsule also moves laterally. The inferior edge of the thalamus extends across the internal capsule ventrolaterally to include the lateral geniculate nucleus, which can be distinguished lateral and posterior to the internal capsule, and superior and medial to the hippocampus. The medial geniculate nucleus is inserted between the posterior part of the lateral geniculate and the rest of the thalamus, dorsal to cerebral peduncle. At this posterior level, where the posterior commissure becomes distinguishable, the thalamus is pushed laterally by the pretectal nuclei, and then by the periaqueductal gray and the superior colliculus, and no longer extends to the edge of the third ventricle.
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