Systems Neuroscience 2019 Brain Anatomy and Ascending and Descending Pathways

Daniel J. Felleman, Ph.D. Professor Dept. of Neurobiology and Anatomy MSB 7.168 713-500-5629 [email protected] Objectives

• Organization of the nervous system: central vs. peripheral, autonomics, axes • Spinal cord • Meninges • Overview: organization of cortex: functional divisions of lobes • Architectonics • Blood supply • Brain stem and cranial nerves • Diencephalon: thalamic and hypothalamic nuclei • Gustatory/Olfactory systems: ascending pathways and cortical targets • Visual system: eye and primary retinal pathways • Vestibular system: ascending pathways and cortical targets • Auditory system: ascending pathways and cortical targets • Somatosensory system: ascending pathways and cortical targets • Motor system(s): descending pathways and cortical/subcortical origins • Limbic system: organization and basic pathways Figure A1 (A) Anatomical terminology of the brain and brainstem; (B) Major planes of section Figure A1 (A) Anatomical terminology of the brain and brainstem (Part 1) Figure A1 (B) Major planes of section of the brain (Part 2) Axis Conventions in Human Neuroanatomy Figure A2 The subdivisions and components of the central nervous system Figure A4 Relationship of the spinal cord and spinal nerves to the vertebral column Figure A5 Internal structure of the spinal cord Figure A6 The internal histology of the human spinal cord in a lumbar segment

Introduction to Spinal Cord Organization Meninges, Dural Sinuses and CSF Circulation

Meninges, superficial veins, diploic vessels and arachnoid granulations Dural sinuses

Figure A21 The ventricular system of the human brain (Part 3) FIGURE A10 Embryological derivation of internal structure in the brainstem (Part 1)

Figure A3 Surface anatomy of the cerebral hemisphere Figure A10 Lateral view of the human brain Figure A11 Views of the human brain Figure A12 Midsagittal view of the human brain Figure A13 Major internal structures of the brain Organization of Cerebral Cortex: Lobes and Gyri V Frontal lobe major sulci and gyri Organization of Cerebral Cortex: Lobes and Gyri IV Frontal lobe major sulci and gyri Organization of Cerebral Cortex: Lobes and Gyri III Parietal lobe major sulci and gyri Organization of Cerebral Cortex: Lobes and Gyri II Temporal lobe major sulci and gyri Hemispheric Lateralization Cortical Activations During Different “Language” Tasks Aphasia

Basic Language Areas, Circuits, and Networks Cerebral artery distribution Middle and Anterior Cerebral Artery Distribution Visual System: Occipital Lobe Medial Wall and Corpus Callosum Human Head MRI Figure A14 Internal structures of the brain seen in coronal section Figure A16 The major arteries of the brain Arterial Supply including the Circle of Willis Figure A17 Blood supply of the three subdivisions of the brainstem Cranial Nerves and Nuclei in Brainstem

Figure A7 The locations of the cranial nerves as they enter or exit the midbrain, pons, and medulla TABLE A3 Classification and Location of the Cranial Nerve Nucleia Brainstem Cranial Nerves: Components, Functions, and Cross-sections Figure A8 Brainstem cranial nerve nuclei locations that are the target or source of cranial nerves Cranial Nerve Nuclei Figure A9 Internal organization along the rostral–caudal axis Diencephalon: Thalamic and Hypothalamic Nuclei General ‘geographic’ parcellation of cerebral cortex Olfactory and Gustatory Pathways Visual System II: Optic Nerve Afferents and Efferents

Macaque Monkey Visual Areas and their Interconnections:

Felleman and Van Essen 1991 Cerebral Cortex 1:1-47. Diffusion Tensor Imaging: Diffusion Tensor Imaging: DTI

Organization of Cerebral Cortex: Architectonics circa 1900 190+ multi-modally defined areas vs. Brodmann (44) and other architectonic maps The Human Connectome: Multi-modal Parcellation of Human Cortex

Partially inflated cortical surface to aid the visualization of cortex within sulci

Full unfolded, 2D cortical maps Human Connectome Project 190 areas on partially inflated cortical hemisphere- Left Human Connectome Project 190 areas on partially inflated cortical hemisphere- Medial –ventral surface=Left Unfolded Cortical Hemisphere- Left The HCP’s multi-modal parcellation, version 1.0 (HCP_MMP1.0)

The 180 areas delineated and identified in both left and right hemispheres are displayed on inflated and flattened cortical surfaces. Black outlines indicate areal borders. Colours indicate the extent to which the areas are associated in the resting state with auditory (red), somatosensory (green), visual (blue), task positive (towards white), or task negative (towards black) groups of areas (see Supplementary Methods 5.4). The legend on the bottom right illustrates the 3D colour space used in the figure. Data at http://balsa.wustl.edu/WN56. M F Glasser et al. Nature 1–8 (2016) doi:10.1038/nature18933 Visual System IV: Modern Architectonics

Nissl, myelin, pigments

Cytochrome oxidase SMI-32 antibody Visual System V: Monkey Visual Areas and their Interconnections Vestibular Ascending and Descending Pathways Auditory Ascending Pathway Somatosensory Pathways Somatosensory Pathways II Motor System I: Cortico-spinal Motor System II: vestibulo-spinal and rubro-spinal pathways Motor System III: reticulo-spinal pathways Limbic System I

Limbic System II Plate 1 Surface features of a human brain specimen (Part 1) Plate 1 Surface features of a human brain specimen (Part 2) Plate 1 Surface features of a human brain specimen (Part 3) Plate 1 Surface features of a human brain specimen (Part 4) Plate 2 Coronal section demonstrating internal forebrain structures, MRI (Part 1) Plate 2 Coronal section demonstrating internal forebrain structures, MRI (Part 2) Plate 2 Coronal section demonstrating internal forebrain structures, MRI (Part 3) Plate 2 Coronal section demonstrating internal forebrain structures, MRI (Part 4) Plate 3 Axial section demonstrating internal forebrain structures, T1-weighted MRI (Part 1) Plate 3 Axial section demonstrating internal forebrain structures, T1-weighted MRI (Part 2) Plate 3 Axial section demonstrating internal forebrain structures, T1-weighted MRI (Part 3) Plate 3 Axial section demonstrating internal forebrain structures, T1-weighted MRI (Part 4) Plate 3 Axial section demonstrating internal forebrain structures, T1-weighted MRI (Part 5) Plate 3 Axial section demonstrating internal forebrain structures, T1-weighted MRI (Part 6) Plate 3 Axial section demonstrating internal forebrain structures, T1-weighted MRI (Part 7) Plate 3 Axial section demonstrating internal forebrain structures, T1-weighted MRI (Part 8) Plate 4 Sagittal section demonstrating internal forebrain structures, T1-weighted MRI (Part 1) Plate 4 Sagittal section demonstrating internal forebrain structures, T1-weighted MRI (Part 2) Plate 4 Sagittal section demonstrating internal forebrain structures, T1-weighted MRI (Part 3) Plate 4 Sagittal section demonstrating internal forebrain structures, T1-weighted MRI (Part 4) Plate 5 Transverse section acquired and prepared to simulate myelin staining (Part 1) Plate 5 Transverse section acquired and prepared to simulate myelin staining (Part 2) Plate 5 Transverse section acquired and prepared to simulate myelin staining (Part 3) Plate 5 Transverse section acquired and prepared to simulate myelin staining (Part 4) Plate 6 Transverse section acquired and prepared to simulate myelin staining (Part 1) Plate 6 Transverse section acquired and prepared to simulate myelin staining (Part 2) Plate 6 Transverse section acquired and prepared to simulate myelin staining (Part 3) Plate 6 Transverse section acquired and prepared to simulate myelin staining (Part 4) Spinal Cord Gross Anatomy and Meninges PLATE 6 (1) Brainstem Atlas PLATE 6 (2) Brainstem Atlas PLATE 6 (3) Brainstem Atlas PLATE 6 (4) Brainstem Atlas PLATE 7 (1) Spinal Cord Atlas PLATE 7 (2) Spinal Cord Atlas PLATE 7 (3) Spinal Cord Atlas PLATE 7 (4) Spinal Cord Atlas BOX A Thalamus and Thalamocortical Relations (Part 1) BOX A Thalamus and Thalamocortical Relations (Part 2) Consistency of fine spatial details in independent group averages

Relative myelin content maps (left hemisphere) and task fMRI contrast beta maps from the LANGUAGE story contrast (right hemisphere) on inflated (columns 1 and 3) and flattened surfaces (columns 2 and 4). Rows 1 and 2 are the group averages of the 210P and 210V data sets, respectively. White and black arrows indicate consistent variations in myelin content within primary somatosensory cortex that are correlated with somatotopy (see Supplementary Neuroanatomical Results 6 and Supplementary Neuroanatomical Results Fig. 8). The white oval indicates a small, sharp, and reproducible feature in the right hemisphere of the LANGUAGE story contrast. Relative myelin content will hereafter be referred to as myelin (see legend of Supplementary Fig. 1 in Supplementary Results and Discussion 1.1). Data at http://balsa.wustl.edu/WDpX

M F Glasser et al. Nature 1–8 (2016) doi:10.1038/nature18933 Parcellation of exemplar area 55b using multi-modal information

The border of 55b is indicated by a white or black outline. a, Myelin map. b, Group average beta map from the LANGUAGE Story versus Baseline task contrast. c, d, Functional connectivity correlation maps from a seed in area PSL (white sphere, arrow) (c) and a seed in area LIPv (white sphere, arrow) (d). e, Gradient magnitude of the myelin map shown in a. f, Gradient magnitude of the LANGUAGE Story versus Baseline task contrast shown in b. g, Mean gradient magnitude of the functional connectivity dense connectome (see section on modalities for parcellation in the Methods). h, A dorsal schematic view of the prefrontal cortex as parcellated in ref. 22, in which shading indicates the amount of myelin found using histological stains of cortical grey matter. Data at http://balsa.wustl.edu/Qv4P.

M F Glasser et al. Nature 1–8 (2016) doi:10.1038/nature18933 The HCP’s multi-modal parcellation, version 1.0 (HCP_MMP1.0)

The 180 areas delineated and identified in both left and right hemispheres are displayed on inflated and flattened cortical surfaces. Black outlines indicate areal borders. Colours indicate the extent to which the areas are associated in the resting state with auditory (red), somatosensory (green), visual (blue), task positive (towards white), or task negative (towards black) groups of areas (see Supplementary Methods 5.4). The legend on the bottom right illustrates the 3D colour space used in the figure. Data at http://balsa.wustl.edu/WN56.

M F Glasser et al. Nature 1–8 (2016) doi:10.1038/nature18933 Example parcellated analyses using the HCP’s multi-modal cortical parcellation

a, Dense myelin maps on lateral (top) and medial (bottom) views of inflated left hemisphere. b, c, Example dense (b) and parcellated (c) task fMRI analysis (LANGUAGE story versus baseline) expressed as Z statistic values. d, The entire HCP task fMRI battery’s Z statistics for 86 contrasts (47 unique, see section on modalities for parcellation in the Methods) analyzed in parcellated form and displayed as a matrix (rows are parcels, columns are contrasts, white outline indicates the map in c). e, A major improvement in Z statistics from fitting task designs on parcellated time series instead of fitting them on dense time series and then parcellating afterwards (blue points are 360 parcels × 86 task contrasts; note the upward tilting deviation from the red line). f, Parcellated myelin maps. g, A parcellated folding-corrected cortical thickness map (in mm). h, i, Parcellated functional connectivity maps on the brain (seeded from area PGi, black dot). These parcellated connectomes are computed using either full or partial correlation (see Supplementary Methods 7.1). In both cases, the task negative (default mode) network is apparent. j, A parcellated connectome matrix view with the full correlation connectome below and the partial correlation connectome above the diagonal (white line shows the displayed partial correlation brain map). Data at http://balsa.wustl.edu/RG0x. PLATE 5 (1) Diffusion Tensor Imaging PLATE 5 (2) Diffusion Tensor Imaging PLATE 5 (3) Diffusion Tensor Imaging