Library
The theory: structures, diagnoses, systems
The atlas's knowledge as readable pages. Search for a structure, diagnosis, system or network, or jump to one of the sections below. Every item is referenced and marked with its level of evidence.
Brain regions
43 main regions and 22 substructures; each one's anatomy, functions, development, clinical relevance and treatment on its own page.
Frontal Lobe
- Dorsolateral Prefrontal Cortex
- Orbitofrontal Cortex
- Medial & Frontopolar Prefrontal Cortex
- Broca’s Area (Inferior Frontal Gyrus)
- Premotor Cortex & SMA
- Primary Motor Cortex
Parietal Lobe
- Primary Somatosensory Cortex
- Superior Parietal Lobule
- Inferior Parietal Lobule
- Temporoparietal Junction
Temporal Lobe
Occipital Lobe
Limbic Cortex & Insula
Limbic Structures
Basal Ganglia
- Caudate Nucleus
- Putamen
- Globus Pallidus
- Subthalamic Nucleus
- Substantia Nigra
- Nucleus Accumbens
- Ventral Pallidum
Diencephalon
Commissures
Brainstem
- Mesencephalon (Midbrain)
- Periaqueductal Gray
- Ventral Tegmental Area
- Red Nucleus
- Reticular Formation (Mesencephalic and Pontine)
- Pedunculopontine and Laterodorsal Tegmental Nuclei
- Raphe Nuclei (Dorsal and Median)
- Pons
- Locus Coeruleus
- Parabrachial Complex
- Medulla Oblongata
- Vagal Nuclei
Cerebellum
Psychopathology
Ten diagnoses, each with its brain circuits, findings from large studies, networks, neurotransmitters and treatment. In the atlas they open with four lenses.
- Attention-Deficit/Hyperactivity DisorderAttention, impulse control and reward circuits; frontostriatal and frontoparietal networks, dopamine and noradrenaline.ADHD
- Autism Spectrum DisorderSocial perception, theory of mind, sensory processing and interoception circuits; imaging differences are small and group-level.ASD
- Obsessive-Compulsive DisorderLoops through the orbitofrontal cortex, cingulate cortex, striatum and thalamus that "get stuck".OCD
- DepressionReward, stress response and emotion regulation circuits; irritability and anhedonia can come first in adolescence.Depression
- Generalized Anxiety DisorderThreat perception (amygdala), sustained anxiety about uncertain threat (BNST), bodily sensation (insula) and prefrontal regulation.GAD
- Post-Traumatic Stress DisorderFear learning and extinction circuit: an overactive amygdala, with weak ventromedial PFC braking and weak contextual input from the hippocampus.PTSD
- Bipolar DisorderEmotion regulation (amygdala, ventrolateral PFC) and reward circuits; swings between mania and depressive episodes.Bipolar
- SchizophreniaIncreased striatal dopamine, the hippocampus and prefrontal cortex; positive, negative and cognitive symptoms.Schizophrenia
- Borderline Personality DisorderEmotion regulation circuit: an overactive amygdala and an underactive DLPFC in response to negative emotion; mentalizing and social pain.Borderline
- Tic Disorders and Tourette SyndromeSensorimotor cortico-striato-thalamo-cortical loop; the premonitory urge before tics is linked to the insula and supplementary motor area.Tics
Emotional systems
Panksepp's seven primary emotional systems: their circuits, chemistry and clinical links; they open in the atlas with their live circuits.
Neurotransmitter pathways
The source nuclei, pathways and receptors of six neurotransmitters, and the targets of medication. The book's main pathways are in the atlas's Pathways section too.
- Dopamine PathwaysThe signal of motivation, learning and movement: spreads along four main pathways; the shared target of stimulants and antipsychotics.3B
- Serotonin PathwaysA modulator spreading from the raphe nuclei to the whole brain: mood, impulse control, sleep and pain; the target of SSRIs.3B
- Noradrenaline PathwaysA wakefulness and attention signal spreading from the locus coeruleus; it launches the stress response and has an inverted-U relationship with…3B
- Acetylcholine PathwaysThe cholinergic signal of attention, learning and wakefulness: from the basal forebrain to the cortex, from the septum to the hippocampus…3B
- Histamine PathwaysOne of the chemical switches of wakefulness: from the tuberomammillary nucleus of the posterior hypothalamus to the whole brain.3B
- Orexin (Hypocretin) PathwaysThe wakefulness stabilizer of the lateral hypothalamus: keeps the other wakefulness nuclei on together; its loss causes narcolepsy.3B
Brain networks
Large-scale brain networks: default mode, salience, executive control, attention and the rest; what changes in which diagnosis is on their cards.
- Seven Networks TogetherYeo 2011: every point of the cortex in its network's color3B
- Default Mode NetworkThe network that switches on when we withdraw from the outside world: thinking about oneself, memories, imagining the future and understanding other…3B
- Frontoparietal Control NetworkThe hub of flexible cognitive control: changes its connections with the other networks according to the task and regulates goal-directed behavior.3B
- Multiple-Demand (MD) CoreA “general-purpose” core that activates together in almost any difficult task: the infrastructure of fluid intelligence and problem solving.3B
- Salience / Ventral Attention NetworkThe network that notices what matters and turns attention to it: initiates switching between the other networks according to salient signals from the…3B
- Dorsal Attention NetworkThe network that directs goal-driven attention: selects top-down what and where to look, and guides eye movements.3B
- Somatomotor NetworkThe network that moves and feels the body; in the Yeo atlas it also includes auditory cortex. One of the most mature networks at birth.3B
- Visual NetworkThe visual areas of the occipital lobe: the first steps from analyzing the image to perceiving objects and motion.3B
- Limbic Network (Yeo)In the Yeo atlas, a network made of the orbitofrontal cortex and temporal pole; despite its name, it does not include the amygdala or hippocampus.3B
Data sources and licenses
The atlas is built from open data, with its limits stated openly.
- MNI ICBM152 2009c nonlinear symmetric template (Fonov et al., 2011)free, with notice
- CerebrA cortical gyri and deep nuclei (Manera et al., 2020)CC0
- HCP-MMP1.0 cortical parcellation (Glasser et al., 2016)CC BY 4.0
- CIT168 subcortical atlas (Pauli et al., 2018)CC BY 4.0
- Harvard AAN v2.0 brainstem arousal network (Edlow and Kinney, 2023)CC0
- Najdenovska thalamic atlas seven nuclear groups (2018)CC BY-SA 4.0
- SUIT cerebellar lobules and deep nuclei (Diedrichsen et al., 2009)CC BY-NC 3.0
- Yeo 2011 seven-network atlas (Yeo et al., 2011)MIT
MNI template copyright notice
Copyright (C) 1993–2004 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies. The authors and McGill University make no representations about the suitability of this software for any purpose. It is provided “as is” without express or implied warranty.
All sources and license details are in the atlas’s opening card, under “Data sources and licenses”.