Problem neural structures

From NeuroLex

These structural terms have been identified as problemmatic for information systems because they are not defined consistently. Some may require further clarification from experts or a panel of experts that can recommend a reasonable definition. Builders of databases and other electronic resources should provide a clear computable definition when using these terms. To see the issues, click on the category and view the discussion tab or the comments field (under the advanced tab).

Below is a list of all brain parts that have editorial notes, suggesting that they require further review.

This table is also available in CSV

Overview

A

B

C

D

F

G

H

I

I cont.

K

Kolliker-Fuse nucleus

L

M

N

O

P

P cont.

R

S

T

V

Detail

	Id	Synonym	Definition	EditorialNote
Accessory abducens nucleus	nlx_144454		A small cluster of neurons in the pontine reticular formation in some mammals, containing the majority of motoneurons innervating the retractor bulbi muscles of the eye	According to Brain Info, Crosby-1962 questioned whether, in the human, it exists independently of the accessory facial nucleus.
Accessory nerve fiber bundle	birnlex_916	accessory nerve fibers	Fibers of the accessory nerve (11th cranial nerve) contained within the medulla	NeuroNames uses the preferred term "accessory nerve fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym.
Ansa lenticularis	nlx_87326		White matter bundle containing part of the projection of the globus pallidus to the thalamus, forming a compact, conspicuous bundle running beneath the internal capsule and hooking around its medial edge (Nolte, The Human Brain, 6th ed., 2009, pg 659)	Brainmaps.org lists the ansa lenticularis as an avian and primate term.
Anterior perforated substance	birnlex_1096	substantia perforata anterior	Regional part of telencephalon lying on the basal surface and bounded by the olfactory trigone rostrally, the diagonal band medially and caudally and the prepiriform cortex laterally. It is characterized by many perforations caused by small blood vessels entering the gray matter (Meyer et al., J. Comp. Neurol 284: 405, 1989).	Should consider whether this is a superficial feature or not
Area X	birnlex_1379	superior part nucleus ventrooralis internus nucleus ventralis oralis pars posterior (Dewulf) nucleus ventrooralis internus (Hassler) area X of Olszewski nucleus lateralis intermedius mediodorsalis situs ventralis medialis anteromedial part of ventral lateral posterior nucleus (Jones)		Synonyms derived both from UMLS and from NN, with NN given precedence (BB: 2007-03-03).
Basal ganglia	birnlex_826		Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum.	Note that the term basal ganglia is also used to refer to subcortical nuclei of telencephalic origin. We have listed this definition under "Basal nuclear complex" and listed basal ganglia as a synonym.
Bed nucleus of stria terminalis	birnlex_724	bed nucleus stria terminalis (Johnson) interstitial nucleus of stria terminalis intercalate nucleus of stria terminalis bed nucleus of the stria terminalis nucleus of the stria terminalis bed nuclei of the stria terminalis	Nucleus defined on the basis of Nissl stain whose cells are embedded in, and surround the stria terminalis at its rostral extreme, where it splits into multiple bundles directed ventrally toward different parts of the hypothalamus. The nucleus wraps around the anterior commissure. It is bounded laterally by the internal capsule, medially by the lateral septal nucleus and the anterior column of the fornix, and dorsally by the head of the caudate nucleus and the frontal horn of the lateral ventricle. Some authors have expanded the definition on the basis of other stains and connectivity studies to include cell groups distributed through the dorsal part of substantia innominata between the classical nucleus and the amygdala. The extended nucleus of stria terminalis by that definition is classified as part of the extended amygdala ( Olmos-2004 ). The nucleus is found in the human, the macaque, the rat and the mouse. Adapted from Brain Info.	Neuronames lists this nucleus as a regional part of the septal nuclear complex and so we have followed that convention here; however, it may also be considered to be part of the basal forebrain. All of these structural part of relationships will have to be reviewed carefully.
Brainstem	birnlex_1565	brain stem	The lower portion of the brain through which the forebrain sends information to, and receives information from, the spinal cord and peripheral nerves. Major functions located in the brainstem include those necessary for survival, e.g., breathing, heart rate, blood pressure, and arousal. (NIDA Media Guide Glossary). Note that the definition of brainstem varies in different nomenclatures, for example, some definitions include the diencephalon.	As this aggregate structure includes portions of the forebrain, the midbrain, and the hindbrain, it must be kept here at the base of the brain region hierarchy in order to avoid multiple inheritance (BB).
Caudal part of ventral lateral nucleus	birnlex_1144	pars caudalis ventral lateral nucleus dorsal part of ventral lateral posterior nucleus (Jones) caudal part ventral lateral thalamic nucleus nucleus ventralis lateralis nucleus lateralis intermedius mediodorsalis situs dorsalis nucleus dorsooralis (Van Buren)		Synonyms derived both from UMLS and from NN, with NN given precedence (BB: 2007-03-03).
Central medial nucleus	birnlex_971	nucleus centralis medialis thalami central medial thalamic nucleus central medial nucleus thalamus (Rioch 1928) central medial nucleus of thalamus nucleus centralis medialis		Note that this BAMS ID assignment should be vetted further, but I do think this is the ID for the BAMS equivalent of this structural region (BB: 2007-03-05).
Cerebellar penducular complex	birnlex_970	cerebellar peduncles and decussations cerebellar peduncles		UMLS uses the preferred term "cerebellar peduncles and decussations", NeuroNames uses the preferred term "cerebellar peduncles", but I'm trying to avoid plurals. NN & UMLS preferred terms included as a synonym.
Cerebral peduncle	birnlex_1202			Cerebral peduncle seems to be used differently in different nomenclatures. In the rodent (and other non-human species), it seems to refer to the crus cerebri, while in human, it's the entire ventral midbrain. Need to reconcile/clarify
Cerebrum	birnlex_1042		Gross division of the brain. The term cerebrum has several definitions ranging in generality from equivalence to the term "brain" to the sum of the left cerebral hemisphere and right hemisphere, to a composite structure consisting of the cerebral cortex and adjacent cerebral white matter. A thorough discussion of the nature and history of the different definitions is presented in Anthoney-94 (NeuroNames).	It is definitely correct to sub-class Cerebrum as a Regional_part_of_forebrain. It isn't clear all would agree Cerebrum and Telencephalon are equivalent. Is this what we want to declare for BIRNLex? (BB). Nolte (The Human Brain: An Introduction to its Functional Neuroanatomy, 6th ed pg 72, presents a hierarchy where the cerebrum consists of the cerebral hemispheres (plus subcortical structures) and the diencephalon. This is not a term that has much scientific validity, nor, in my opinion, is it worth declaring a definition one way or the other (MM)
Cingulate cortex	birnlex_934			The only elements labelled "cingulate cortex" in neuronames related to mouse brain parcellations both from Swanson and from Paxinos. No "cingulate cortex" is listed for primates. There are the many cortical areas defined by Brodmann's parcellation scheme present in NeuroNames, and they are obviously the mans by which cortical parenchyma regions are accessed. (BB).
Cingulate gyrus	birnlex_798	cingulate region cingulate area	One of the convolutions on the medial surface of the cerebral hemisphere. It surrounds the rostral part of the brain and interhemispheric commissure and forms part of the limbic system. (MSH) One of three essential structures comprising the limbic lobe, the other two being the hippocampus and parahippocampal gyrus. (CSP)	Will keep the NN "gyri" distinct from the BIRN "cortex" regions. Should we later decide the intended meanings are the same, we can set the corresponding classes to be equivalent. In the end, any such correspondence really would depend on how the various cortical areas defined by Brodmann or some other parcellation scheme as defined for the NN gyri relate to those cortical areas assigned to the BIRN coritical regions (BB)., UMLS includes a CUI for "Cingulate cortex" (C0598179) separate from this other for "Cingulate gyrus"., Note that in BrainMap.org, they mere list LimbicLobe.AnteriorCingulate.GrayMatter under which they included Brodmann areas 10, 24, 25, 32, & 33 and LimbicLobe.CingulateGyrus.GrayMatter under which they include Brodmann areas 23, 24, 31, and 32. This indicates not all gray matter contained within the cingulate cortex lies within the cingulate gyrus - at least it doesn't according to BrainMap.org's parcellation., Now I see where my confusion derives from. It relates to the fact this distinction between surface and volumetric, parenchymal structures is a bit unclear in NeuroNames. There sulci are clearly listed as "superficial" (i.e., defining surfaces), whereas gyri as listed as "volumetric structures". The organization of the parenchyma within the lobes of the cerebral cortex are largely given according to complex structures lumped into the "ancillary terms" - e.g., all of the Brodmann areas. The implication for listing "gyri" as volumetric is that the cortical parenchyma lying underneath the gyral surface are also included in these gyral regions. Therefore, it may in fact be correct to set the BIRN "cingulate cortex" == NN "cingulate gyrus". It should also be possible to declare which of the various Brodmann areas are associated with the BIRN defined cortical regions such as "caudal anterior cingulate cortex" (BB)., Was going to assume cingulate cortex for BIRN is equivalent to what is listed as cingulate gyrus in NeuroNames, but clearly that assumption is invalid. In the strictest since, "gyrus" is a description of the surface protuberance between invaginated sulci, while "cortex" typically refers to brain parenchyma with defined cytoarchitectural layers. This is the gross anatomical description of brain tissue. Given this representation is intended to follow the anatomical bases for describing brain structure, it is best we keep cortex and gyri distinct (BB).
Cochlear nuclear complex	birnlex_1151	Cochlear nucleus Cochlear nuclei		BFO includes a "snap:ObjectAggregate". That would probably be more appropriate for these sort of aggregate structures (BB).
Composite part spanning multiple base regional parts of brain	birnlex_1304			Note that many of these composite structures could be created by simply defining them as the union of their constituent parts - e.g., Medial_lemniscus = UNION(Medial_lemniscus_of_midbrain, Medial_lemniscus_of_pons, Medial_lemniscus_of_medulla). I've hard-coded these examples using class equivalency to show there are more than a single means to bring classes together. The cerebellar peduncular complex was constructed using equivalency relations to demonstrate another alternative. Each of these mechanisms has its own set of pros and cons (BB)., It will be necessary to create a composite class set at a higher level than this, should we seek to assemble classes whose constituents lie both inside and outside the brain. For instance, to construct the entirety of the cuneate or gracile fasciculi, you'd need to included the components residing in the spinal cord as well.
Cuneus cortex	birnlex_1396	cuneate lobule cuneus gyrus cuneus of hemisphere cuneus	Component of the occipital lobe. The rostral boundary was the first coronal slice above the calcarine sulcus where the cuneus cortex becomes visible whereas the caudal boundary was the last slice where the calcarine sulcus was visualized. The medial boundary was the most medial portion of the occipital and parietal cortices. The superio-lateral boundary was the parieto-occipital fissure whereas the inferolateral boundary was the pericalcarine cortex (Christine Fennema-Notestine).	UMLS and NeuroNames use the preferred name "cuneus".
Deep cerebellar nuclear complex	birnlex_1568	intracerebellar nuclei deep cerebellar nuclei Cerebellar nuclei		BFO includes a "snap:ObjectAggregate". That would probably be more appropriate for these sort of aggregate structures (BB).
Dentatothalamic tract	birnlex_1104			Needs review
Dorsal external arcuate fiber bundle	birnlex_1250	external arcuate fibers dorsal external arcuate fibers dorsal superficial arcuate fibers		NeuroNames uses the preferred term "dorsal external arcuate fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym.
Dorsal longitudinal fasciculus	birnlex_986		A fiber bundle containing fibers from nuclei of the hypothalamus that project to the dorsal tegmental nucleus and other regions of the midbrain and the pons, as well as fibers originating in the pontine reticular formation and the medullary reticular formation that project to the thalamus and other regions of the forebrain (Carpenter-83). In NeuroNames it is a composite structure consisting of the dorsal longitudinal fasciculus of hypothalamus, the dorsal longitudinal fasciculus of midbrain, the dorsal longitudinal fasciculus of pons and the dorsal longitudinal fasciculus of medulla. (NeuroNames)	This is another example of how the class UNION axion can be used to construct more complex structures.
Fasciola cinerea	nlx_144464	fasciolar gyrus gyrus fasciolaris		Different nomenclatures place this structure as part of the hippocampus, dentate gyrus, hippocampal formation or archicortex, according to BAMS and Brain Info. I have tentatively put it as part of the hippocampal formation, as that is consistent with all but Brain Info. But needs attention.
Fimbria of hippocampus	birnlex_1502	fimbria of the fornix fimbria fimbria-fornix	Part of fornix lying closest to the hippocampal formation continuos with the alveus.	NeuroNames uses the preferred term "fimbria of hippocampus". That is included here as a synonym (BB). Note that many consider the fimbria to be separate from the fornix, but as they are continuous, I see no reason to keep them separate except for historical reasons (MM).
Frontal pole	birnlex_1716		Component of the frontal lobe. The rostral and caudal boundaries of the frontal pole are the superior frontal gyrus and the rostral division of the middle frontal gyrus respectively (Christine Fennama-Notestine).	Don't know whether this term holds in all mammals. I would suspect so, but need to confirm.
Fundus striati	nlx_144261	fundus of the striatum striatal fundus	The ventral portion of the dorsal striatum, linking the caudate nucleus and the putamen anteriorly (adapted from Wikipedia)	Need to check on this definition. May also include the nucleus accumbens in some definitions.
Globus pallidus external segment	birnlex_1610	external part of globus pallidus lateral segment of globus pallidus lateral globus pallidus lateral pallidum external pallidum	The more lateral of the two segments of the globus pallidus, abutting the putamen in species which have both a caudate and putamen; the caudoputamen in other species.	NN uses the preferred term "external part of globus pallidus".
Globus pallidus internal segment	birnlex_1555	internal part of globus pallidus Internal pallidum medial segment of globus pallidus globus pallidus internus	The more medial segment of the globus pallidus.	NN used "internal part of globus pallidus" as the preferred term.
Glossopharyngeal nerve fiber bundle	birnlex_1274	glossopharyngeal nerve fibers ninth cranial nerve fibers central part of glossopharyngeal nerve		NeuroNames uses the preferred term "glossopharyngeal nerve fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym.
Hypoglossal nerve fiber bundle	birnlex_1288	root of hypoglossal nerve central part of hypoglossal nerve hypoglossal nerve fibers		NeuroNames uses the preferred term "hypoglossal nerve fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym.
Hypophysis	birnlex_1353	Pituitary gland Pituitary		Need to check on this. Brainmaps has the hypohysis as part of the hypothalamus, as does Brain Info (http://braininfo.rprc.washington.edu/whereisit.aspx?language=0&requestID=ID399&parentID=ID392&originalID=ID399)
Inferior parietal cortex	birnlex_1194	inferior parietal lobule	Component of the parietal lobe. The inferior parietal cortex label includes the inferior parietal gyrus and the angular gyrus and lies inferior to the superior parietal gyrus. The rostral and caudal boundaries were the supramarginal gyrus and the parieto-occipital incisure respectively. The medial and lateral boundaries were the superior parietal gyrus and the middle temporal gyrus respectively (Christine Fennema-Notestine).	Both NeuroNames and UMLS use "inferior parietal lobule" as the preferred term.
Inferior pulvinar nucleus	birnlex_830	nucleus pulvinaris thalami nucleus pulvinaris inferior nucleus pulvinar pars inferior nucleus pulvinaris inferior thalami	One of four subdivisions recognized in the primate pulvinar based on initially on topography, located ventrally between the medial and lateral geniculate bodies (Carpenter, A core text of neuroanatomy, 3rd ed., 1985, pg 238)	A few papers mention this nucleus in the cat. Needs review
Insula	birnlex_1117	Insular cortex central lobe insular gyrus insular lobe insular region insulary cortex island of Reil Lobus insularis	Gray matter of the insular region of the neocortex. In gyrencephalic animals, it is part of the insular lobe and lies in the depths of the lateral fissure and covered by portions of the frontal, parietal and temporal lobes. It includes Brodmann areas 13-16.	I added the synonyms from Brain Info, but I'm still debating whether insular gyrus is a synonym for insular cortex. I think so, but perhaps needs review.
Interanterodorsal nucleus of the thalamus	nlx_144468	interanterodorsal nucleus of thalamus	a group of nerve cells that bridges the midline of the thalamus between the anterodorsal nucleus of the thalamus of the left and right sides. According to Crosby (1962), it is more developed and consistently present in rodents than in primates (adapted from Brain Info).	Not sure whether this is equivalent to the massa intermedia. Needs review.
Intercalated amygdaloid nuclei	birnlex_2683	Massa intercalata Massa intercalata of amygdala intercalated nucleus of the amygdala intercalated nuclei of amygdala intercalated masses of nucleus amygdaloideus	Discrete clusters of cells intercalated among the major amygdaloid nuclei. They stain darkly in Nissl stains and have been identified in all mammals. The main groups lie between the lateral-basolateral nuclear coplex and the central and medial nuclei. Additional cell groups have been described by some in other locations (Millhouse, O. E. The intercalated cells of the amygdala. J Comp Neurol 247: 246-271, 1986)., Groups of cells located between the lateral basolateral amygaloid nuclear complex and the central nucleus of the amygdala. They stain darkly in Nissl stains and have been identified in all mammals. (Millhouse, O. E. The intercalated cells of the amygdala. J Comp Neurol 247: 246-271, 1986)	The intercalated amygdaloid nuclei may be better characterized as a cell group (NIF class) rather than a nucleus, because we describe them in terms of groupings of individual cells rather than masses of gray matter.
Internal arcuate fiber bundle	birnlex_1091	arcuate fibers medial lemniscus internal arcuate fibers		NeuroNames uses the preferred term "internal arcuate fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym.
Islands of Calleja	birnlex_1113	Islets of Calleja	Small clusters of granule cells located in the olfactory tubercle and also within the Island of Calleja magna that lies between the septum and the nucleus accumbens	According to Millhouse (1987), the term "Islands of Calleja" has not been applied consistently and there is confusion about the features to which Calleja was referring in his 1893 paper. The term has come to be identified with the clusters of granule cells found in the olfactory tubercle but the original paper may have been pointing to the dense cell layer. He recommended that it be dropped (Millhouse, J Comp Neurol., 265: 1-24, 1987). Meyer et al. prefer that only those aggregates within the olfactory tubercle be called Islands of Calleja and that the term "clusters of granule cells" be adopted elsewhere. However, others use Islands of Calleja to refer to all granule cell clusters.
Islands of Calleja of olfactory tubercle	nlx_50741	Islets of Calleja	Part of olfactory tubercle defined by dense aggregations of granule cells	According to Millhouse (1987), the term "Islands of Calleja" has not been applied consistently and there is confusion about the features to which Calleja was referring in his 1893 paper. The term has come to be identified with the clusters of granule cells found in the olfactory tubercle but the original paper may have been pointing to the dense cell layer. He recommended that it be dropped (Millhouse, J Comp Neurol., 265: 1-24, 1987). Meyer et al. prefer that only those aggregates within the olfactory tubercle be called Islands of Calleja and that the term "clusters of granule cells" be adopted elsewhere.
Kolliker-Fuse nucleus	birnlex_2641	diffuse reticular nucleus		Brain Info lists the KF nucleus as part of the medulla, but atlases and other hierarchies in BAMS show it to be part of the pons
Lateral lemniscus (birnlex 976)	birnlex_976		A fiber bundle that runs through the medulla, pons and midbrain that arises in the cochlear nucleus and projects to various brainstem nuclei and ultimately the contralateral inferior colliculus of the midbrain. The brainstem nuclei include the superior olive, the medial nucleus of the trapezoid body, and the dorsal nucleus of the lateral lemniscus. Fibers leaving these brainstem nuclei ascending to the inferior colliculus rejoin the lateral lemniscus. In that sense, this is not a 'lemniscus' in the true sense of the word (second order, decussated sensory axons), as there is third (and out of the lateral superior olive, fourth) order information coming out of some of these brainstem nuclei. Adapted from Wikipedia.org (MM).	The definition for Lateral_lemniscus implies portions of this fiber bundle clearly lie outside the pons, and yet all atlases and nomenclatures I've checked only list a single lateral lemniscus located in the pons (BB).
Lateral occipital cortex	birnlex_735	lateral occipital gyrus	Component of the occipital lobe. The rostral and caudal boundaries of the lateral occipital cortex were the superior parietal gyrus and as the last visible portion of occipital cortex respectively. The medial and lateral boundaries were the cuneus/pericalcarine cortex and the inferior temporal/inferior parietal gyri respectively (Christine Fennema-Notestine).	UMLS and NeuroNames use the preferred name "lateral occipital gyrus".
Limbic lobe	birnlex_1128		Part of cerebral hemisphere located on the medial surface, forming a ring around the brain stem	According to T.R. Anthoney, who compared uses of the term in 23 different sources, the limbic lobe, or Gyrus fornicatus, is defined variously even by authors who cite Broca as their original source. Most definitions include the cingulate gyrus, the parahippocampal gyrus and parts or all of the archicortex, the three structures that comprise the limbic lobe in NeuroNames. The major differences in definition have to do with whether the CA fields, supracallosal gyrus, paraterminal gyrus and olfactory structures, such as the olfactory bulb, olfactory tract and olfactory tubercle are included. A discussion of the many definitions, including Broca's, is presented in Anthoney-1994. (adapted from Neuronames)
Lissauer's tract of spinal cord	nlx_143967	dorsolateral fasciculus of spinal cord	White matter tract in spinal cord laying between the substantia gelatinosa and the surface of the spinal cord.	Neuronames uses the name "dorsolateral fasciculus" as the preferred name. However, Nolte recommends that Lissauer's tract be used (Nolte, The Human Brain, 6th ed, page 235 footnote)
Mammillary body	birnlex_865		One of two hemispherical bulges on the base of the posterior hypothalamus (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 455).	Brain Info/Neuronames lists the mammillary body as a superficial feature of the posterior hypothalamus. However, the MSH definition clearly indicates that it is the nuclei that it refers to. Needs review.
Mammillary peduncle	birnlex_1486	Peduncle of mammillary body	White matter bundle in the posterior hypothalamus containing ascending afferent fibers to the mammillary bodies from the ventral and dorsal tegmental nuclei (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 671).	The description in Butler and Hodos (pg. 460) describes this as originating int he dorsal and ventral tegmental nuclei and terminating in the mammillary body. The reciprocal connection is the mammillotegmental tract. It seems like this should be classifed as a tract according to the definition.
Medial part of ventral lateral nucleus	birnlex_1159	ventral lateral nucleus pars medialis medial part nucleus ventrooralis medialis (Hassler) nucleus ventralis lateralis thalami ventral medial nucleus of thalamus ventral medial nucleus		Synonyms derived both from UMLS and from NN, with NN given precedence (BB: 2007-03-03).
Medial pes lemniscus	birnlex_1310			Having a little trouble tracking down this structure. Does not seem to appear in the literature, but Neuronames has it referenced to Carpenter 1983.
Medial septal nucleus	birnlex_1668	Medial septum	Cells lying generally in front of Regional_part_of_septal_nuclei, lying ventral to and slightly medial to the lateral septal nucleus. Neurons in this nucleus give rise to the bulk of efferents from the septal nuclei. A major projection from the medial septal nucleus terminates in the hippocampal formation (Adapted from Brodal, 1981).	Definition needs to be fixed
Medial superior olivary nucleus	birnlex_1682		One of two subnuclei of the superior olive located within the caudal pontine tegmentum. Appears as a parasagittal row of transversely oriented bipolar neurons in transverse sections of human, with elongated somata in humans and other primates and large caliber dendrites.	Someone had inserted nucleus laminaris as a synonym. As that is in the avian brain, I hesitate to equate the two without further information. I also don't believe that synonyms should be used to assert homology
Medullary anterior horn	birnlex_2649			Cannot find reference to this structure in the literature
Medullary raphe nuclear complex	birnlex_1420	raphe nuclei of medulla		BFO includes a "snap:ObjectAggregate". That would probably be more appropriate for these sort of aggregate structures (BB).
Metencephalon	birnlex_965		Anterior part of the hindbrain ventral to the cerebellum.	I took this division out of the primary hierarchy of adult brain regions as I don't think it is helpful; unlike forebrain, midbrain and hindbrain, it is not used very much in referrential adult neuroanatomy.
Midbrain tegmentum	birnlex_1200			I'm not sure that the cerebral peduncle and midbrain tegmentum are defined similarly in all species; we'll need to look into that.
Neocortex	birnlex_2547	neopallium homotypical cortex isocortex	Part of cerebral cortex defined on the basis of cytoarchitecture that has six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83) (NN) * The largest portion of the CEREBRAL CORTEX. It is composed of NEURONS arranged in six layers. (MSH) * the newer, 6 layered portion of the cerebral cortex showing stratification and organization characteristic of the most highly evolved type of cerebral tissue. (CSP)	The term neocortex is somewhat controversial (see notes below) but I am in agreement with Butler and Hodos (ISBN-13: 978-0471210054; pg 58) that even though the term is not correct in an evolutionary sense, it is the preferred term for the regions of cerebral cortex that it refers, compared to others like isocortex. So I am recommending it as a preferred label for now.
Nucleus of anterior commissure	birnlex_712	bed nucleus of anterior commissure bed nucleus of the anterior commissure Nucleus commissurae anterioris		Neuronames has this nucleus as a part of the septal nuclear complex and so we have followed that convention.
Nucleus of diagonal band	birnlex_719			Neuronames has this nucleus listed as part of the septal nuclear complex and so we have followed that convention here; however, it also may be considered part of the basal forebrain by some. We will need to carefully review all of these structures.
Nucleus of medial eminence	birnlex_870			I am having trouble tracking down any reference to this nucleus other than Brain Info
Nucleus of the stria medullaris	nlx_144458		Small nucleus in the thalamus lying between the fornix and the stria medullaris.	According to Risold and Swanson (1995), this nucleus was likely first described by Cajal in newborn mice, but has been described by other authors as well.
Oral part of ventral lateral nucleus	birnlex_817	ventral lateral nucleus pars oralis nucleus lateralis oralis situs principalis ventral lateral thalamic nucleus nucleus ventralis lateralis oral part nucleus ventrooralis externus ventral lateral anterior nucleus anterior part (Van Buren) subnucleus rostralis		Synonyms derived both from UMLS and from NN, with NN given precedence (BB: 2007-03-03).
Orbital frontal cortex	birnlex_1049	orbitofrontal cortex	Component of the prefontal cortex, frontal lobe, inferior region (Christine Fennema-Notestine).	UMLS clearly has obscured this distinction between cortex and gyri here, as they include the following under this CUI: orbital gyrus, orbital area, orbital cortex, gyri orbitales, orbitofrontal gyrus, orbitofrontal gyri, gyrus orbitofrontalis. Clearly, this would equate this volumetric structure defined as Orbital Frontal Cortex and the "volumetric" structure defined in NN as "Orbital gyrus".
Pars postrema of ventral lateral nucleus	birnlex_1170	ventral lateral nucleus (pars postrema) pars postrema nucleus ventralis lateralis thalami nucleus lateralis intermedius mediodorsalis situs postremus posterodorsal part of ventral lateral posterior nucleus (Jones) nucleus dorsointermedius externus magnocellularis (Hassler)		Synonyms derived both from UMLS and from NN, with NN given precedence (BB: 2007-03-03).
Parvocellular oculomotor nucleus	birnlex_822	Edinger-Westphal nucleus	Nucleus that is part of the oculomotor nerve complex consisting of preganglionic parasympathetic neurons situated close to the midline at the level of the superior colliculus (Heimer, the Human Brain and Spinal Cord, 1994, pg 244)	Neuronames has the parvocellular oculomotor nucleus as the preferred label but I think Edinger Westphal is more common.
Periamygdaloid area	birnlex_1291	periamygdaloid region semilunar gyrus periamygdaloid cortex ventral cortical nucleus of amygdala cortical amygdaloid nucleus		Brain Info has the periamygdaloid area as part of the parahippocampal gyrus. As the parahippocampal gyrus is a human structure, I placed it as part of telencephalon. Needs review
Periamygdaloid cortex	nlx_144210	periamygdaloid area	Is located ventral to the basal nucleus and has three subdivisions: the periamygdaloid cortex, the medial division, and the sulcal division.	Both Brain Info and BrainMaps list the periamygdaloid area as a substructure of cortex (parahippocampal gyrus for Brain Info). Needs review
Pericalcarine cortex	birnlex_1059		Component of the parietal lobe. The rostral boundary of the pericalcarine cortex was the first appearance of the calcarine sulcus whereas the caudal boundary was the most posterior coronal slice where the calcarine sulcus was visualized. The medial and lateral boundaries were the medial portion of the temporal and occipital cortices and the inferomedial end of the calcarine sulcus respectively (Christine Fennema-Notestine).	Neither UMLS nor NeuroNames specifically defines this predominantly gray parenchymal region of the parietal lobe but do obviously contain the superficial boundary structures.
Pontine nuclear complex	birnlex_1516	pontine gray pontine nuclei pontine nucleus	Nuclei in the basal pons, intermingled among the descending axons from the cortex, that receive neocrotcial input and give rise to many axons that cross the midline to enter the contralateral cerebellum (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 135)	BFO includes a "snap:ObjectAggregate". That would probably be more appropriate for these sort of aggregate structures (BB).
Posterior horn lateral ventricle	birnlex_1297	occipital horn posterior horn of the lateral ventricle	Part of the lateral ventricle that extends posteriorly into the occipital lobe.	This term is misclassified in UMLS as a body part rather than a body space or junction.
Posterior nuclear complex	birnlex_1467	posterior thalamic nuclear group nuclei posteriores thalami posterior nuclear complex of thalamus posterior complex of thalamus	Part of thalamus comprising ill defined cellular groups in the caudal thalamus at the meso-diencephalic junction. It is not a homogeneous structure but consists of several distinct cellular groups, including the suprageniculate and limitans nuclei, the magnocellular division of the medial geniculate body, portions of the pulvinar nucleus and an area of mixed cell types intercalated between the ventroposterior nucleus and the nucleus lateral posterior (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 97)	According to Brodal, the term was first introduced by M. Rose (1935) and J. E. Rose (1942)
Posterior thalamic region	nlx_15105	Posterior thalamus		Not sure what this refers to; needs review
Postsubiculum	nlx_144245	Postsubicular cortex	Division of subicular cortex characterized by projections from the anterodorsal thalamic nucleus and to a lesser extent the anteroventral nucleus, bordered ventrally and laterally by the presubiculum and dorsally and medially by the retrosplenial granular a cortex.. The border is characterized by an abrupt change in the cyto- and chemoarchitecture	The post subiculum is not recognized by all anatomists.
Precentral gyrus	birnlex_1455		Component of the frontal lobe. The appearance and disappearance of the central sulcus is the rostral and caudal boundaries of the precentral gyrus respectively. The medial boundary is specific frontal gyri (superior, middle and inferior) whereas the lateral boundary is the medial bank of the central sulcus (Christine Fennema-Notestine).	UMLS has a seperate CUI for the distinct structure "precentral gyrus of insula (human only)" (C0694588).
Precerebellar nucleus	nlx_151901	precerebellar nuclei	Neuron population that send all or nearly all of its efferents to the cerebellum, including cell populations in the spinal cord, the funicular nuclei, the nucleus solitarius, the principal nucleus of the trigeminal nerve, the locus coeruleus, the inferior olive and the pontine nucleus in mammals (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg. 256.)	According to Brain Info, Carpenter includes only the nuclei of the hindbrain (http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1244). See also Altman and Bayer (1997): "It is not common to speak of spinal precerebellar nuclei, since the term "precerebellar" is usually reserved to edullary and pontine structures that send fibers principally, if not exclusively, to the cerebellum. But, in fact, etensive portions of the spinal gray matter, including some discrete nuclei , are dedicated to the relay of mesages to the cerebellum..." (Altman and Bayer, Development of the Cerebellar System, 1997, pg 45).
Precuneus cortex	birnlex_1446	precuneus quadrate lobule precuneate lobule	Component of the parietal lobe. The rostral boundary was the posterior extent of the paracentral lobule whereas the caudal boundary was the lingual gyrus. The medial and lateral boundaries were the parieto-occipital fissure and the superior parietal gyrus respectively (Christine Fennema-Notestine).	UMLS and NeuroNames use precuneus alone as the preferred term.
Pretectum	nlx_59721	pretectal region	Region of brain lying between the midbrain tectum and the thalamus (Sefton and Dreher, in Paxinos, G The rat central nervous system, 1995, pg 859), Situated at the level of poterior commissure and just rostral to the superior colliculus (Brodal, Neurological Anatomy, 3rd ed, 1981, pg 542)	According to Brodal, it is divided up into subnuclei, but anatomists differ on the nomenclature and the nuclei ((Brodal, Neurological Anatomy, 3rd ed, 1981, pg 542). The parts of the pretectum are currently derived from NeuroNames.
Primate neocortex	nlx_144184			This is a test class for the INCF PONS program. Do not add to NIFSTD/
Pyramid	nlx_21189	medullary pyramid pyramis	White matter structure at the base of the medulla containing the axons of the corticospinal tract (MM)	Not sure whether this should be classified as a superficial feature or a part of brain
Rostral linear nucleus	nlx_144319		Nucleus of the medial ventral tegmental area, originally identified in the rat but also in cat, monkey and human, comprising an average of 7% volume of the VTA across the different species, with the largest being present in the cat.	Brain Info does not list the linear nuclei as part of the ventral tegmental area but as a co-area of the midbrain tegmentum. Am assuming the rostral linear nucleus of the raphe is synonymous, but needs further review.
Rostral superior temporal gyrus	nlx_14855	anterior superior temporal cortex anterior superior temporal gyrus		Still needs clarification as to whether this is a recognized brain area; I see 11 article in Pub Med and SUMS DB using the term, so I have classified it as a brain region for now
Secondary olfactory cortex	birnlex_2709	secondary olfactory cortical area (Carpenter) area 28 of Brodmann (Crosby) secondary olfactory areas	Brodmann's area 28; major gateway for neocortical input to the hippocampus; origin of the perforant pathway; a component of the medial temporal lobe memory system. (CSP) * The cytoarchitecturally well-defined area of multilaminate cerebral cortex on the medial aspect of the parahippocampal gyrus, immediately caudal to the olfactory cortex of the uncus. The entorhinal cortex is the origin of the major neural fiber system afferent to the hippocampus, the so-called PERFORANT PATHWAY. (Stedman, 25th ed) (MSH)	The relationships between this definition which is human centric and that for other species needs some review
Septal nuclear complex	birnlex_1313	Septal nuclei	Collection of nerve cells in the medial forebrain lying generally in front of the anterior commissure (Maryann Martone).	BFO includes a "snap:ObjectAggregate". That would probably be more appropriate for these sort of aggregate structures (BB).
Sexually dimorphic nucleus of the preoptic area	nlx_152051		Nucleus in the medial preoptic area that shows marked sexual dimorphism, being much larger in the male than the female.	Not sure whether this belongs as part of the medial preoptic region
Submedial nucleus	birnlex_946	submedial nucleus thalamus submedial nucleus of thalamus nucleus submedius thalami gelatinosus thalamic nucleus submedial thalamic nucleus	Thalamic nucleus separated from the ventromedial part of the mediodorsal nucleus of the thalamus by the internal medullary lamina (Paxinos The rat nervous system 2nd ed, Academic Press, 1995).	Brain Info has this nucleus as part of the posterior nuclear group. Based on the description in Paxinos, I thought it needed review.
Substantia innominata	birnlex_915		A predominantly gray matter structure of the basal telencephalon defined on the basis of Nissl stain. Caudal to the anterior commissure it lies deep to the globus pallidus and dorsal to the amygdala. Rostral to the anterior commissure it lies deep to the striatum. The more rostral portion contains the basal forebrain nucleus ( Anthoney-1994 ). In the late twentieth century the region containing the substantia innominata was resegmented on the basis of neurochemistry and connectivity to constitute the striatopallidal system ( Heimer-1995 ). In this scheme the caudal portion of substantia innominata is located largely in the ventral pallidum and the rostral portion in the ventral striatum. (from Brain Info)	UMLS includes the following synonyms not listed in NeuroNames: substantia innominata of meynert, substantia innominata of reichert, substantia innominata of reil
Substantia nigra pars compacta	birnlex_990	pars compacta Substantia nigra compact part Substantia nigra compacta	Regional part of substantia nigra consisting of a densely packed region of cells, more or less dorsal to the pars reticulata, but extending into the pars reticulata in some species. The dominant neurotransmitter used by pars compacta neurons is dopamine. Pars compacta neurons are pigmented in many species (MM).	NeuroNames uses the preferred label "pars compacta."
Substantia nigra pars lateralis	birnlex_866	pars lateralis	Part of the pars reticulata of substantia nigra. It is the lateral, 'most fibrous' part (Poirier-83), which is regarded to be the phylogenetically oldest part of the substantia nigra and the only part found in nonmammalian vertebrates (Crosby-62) (Adapted from Brain Info: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2159)	NeuroNames uses the preferred label "pars lateralis of substantia nigra."
Substantia nigra pars reticulata	birnlex_968	pars reticulata Substantia nigra reticulata	Regional part of substantia nigra consisting of loosely packed cells, generally located ventral and lateral to the pars compacta. Many cells in this region use GABA as a neurotransmitter (MM).	NeuroNames uses the preferred label "pars reticulata."
Superior parietal cortex	birnlex_1450	superior portion of parietal gyrus superior parietal gyrus superior parietal lobule	Component of the parietal lobe. The rostral and caudal boundaries of the superior parietal cortex were the precentral gyrus and lateral occipital cortex respectively. The medial and lateral boundaries were the precuneus and/or cuneus cortex and the infererior parietal cortex respectively (Christine Fennema-Notestine).	UMLS and NeuroNames both use the preferred term "superior parietal lobule."
Superior salivatory nucleus	birnlex_1131		Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703).	Brodal has the SSN in the medulla (Fig. 11-2, pg 703); Brain Info in the pontine tegmentum. It looks to be at the pontomedullary junction, so I suppose that it's just where you'd like to put it, but needs review.
Tectobulbar tract	birnlex_750			I'm having trouble tracking down information on this tract in mammals. Do not add to hierarchy until more information is found.
Thalamus	birnlex_954		Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH).	maybe propose nucleus (part of same functional system) vs region (= groups of nuclei like the thalamus)
Third ventricle	birnlex_714	3rd ventricle	Part of the ventricular system of the brain, forming a single large cavity in the midline of the diencephalon; it is continuous with the lateral ventricles through the interventricular foramen and the fourth ventricle through the cerebral aqueduct. (Maryann Martone. It is bounded anteriorly by the lamina terminalis; much of the medial surface is formed by the thalamus and hypothalamus; part of the hypothalamus forms its floor (Nolte, the Human Brain, 6th ed., 2009, pg 101).	There is a separate entry for "Entire third ventricle" in UMLS. This ID is for "third ventricle".
Trapezoid nuclear complex	birnlex_745	trapezoid gray trapezoid nuclei nucleus of the trapezoid body		Brain Info uses the term "trapezoid nuclear complex" but I am wondering whether this is equivalent to the nucleus of the trapezoid body? For now, I am listing it as a synonym
Trigeminal nerve fibers	birnlex_974			This term and hierarchy was taken from Brain Info, which lists both the motor root of the trigeminal and trigeminal nerve fibers as part of the pontine tegmentum. Needs clarification.
Tuber cinereum	birnlex_1189		Layer of gray matter in the hypothalamus that also forms part of the floor of the third ventricle and merges anteriorly into the infundibulum. (MSH)	Brain Info lists this as a superficial part of brain, but from the MESH definition, it seems like they are describing something of substance. Needs review.
Vagal nerve fiber bundle	birnlex_765	vagal nerve fibers central part of vagus nerve tenth cranial nerve fibers		NeuroNames uses the preferred term "vagal nerve fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym.
Ventral external arcuate fiber bundle	birnlex_1628	ventral external arcuate fibers		NeuroNames uses the preferred term "ventral external arcuate fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym.
Vestibular nuclear complex	birnlex_1337	vestibular nuclei vestibular nucleus		Used this preferred term from Carpenter-83, as opposed to the NeuroNames preferred term, because we're trying to avoid plurals (BB)., BFO includes a "snap:ObjectAggregate". That would probably be more appropriate for these sort of aggregate structures (BB).
Vestibulocochlear nerve fiber bundle	birnlex_1636	vestibular root of vestibulocochlear nerve statoacoustic nerve fibers vestibulocochlear nerve roots central part of vestibulocochlear nerve vestibulocochlear nerve fibers cochlear-vestibular nerve		NeuroNames uses the preferred term "vestibulocochlear nerve fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym.
Visual cortex primary	nlx_143552	V1 striate cortex primary visual cortex	Region of visual cortex that receives visual input from the eyes through the lateral geniculate nuclei (Sadato et al., 1996, PMID: 8606771).	Need to determine what relates a functional area to a regional part of

Contributors

Akash, Memartone