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Slicer Tutorial The SPL-PNL Brain Atlas Ion-Florin Talos, M.D. Surgical Planning Laboratory -1- http://www.slicer.org Brigham and Women’s Hospital Acknowledgments NIH P41RR013218 (Neuroimage Analysis Center) NIH R01MH050740 Surgical Planning Laboratory -2- http://www.slicer.org Brigham and Women’s Hospital Disclaimer It is the responsibility of the user of 3DSlicer to comply with both the terms of the license and with the applicable laws, regulations and rules. Surgical Planning Laboratory -3- http://www.slicer.org Brigham and Women’s Hospital Material • Slicer 2.6 http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started • Atlas data set http://wiki.na-mic.org/Wiki/index.php/BrainAtlas • • • • MRI Labels 3D-models Model hierarchy http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Surgical Planning Laboratory -4- http://www.slicer.org Brigham and Women’s Hospital Learning Objectives Manipulating the data: • Loading the atlas data • Creating, displaying and annotating customized 3Dviews Neuroanatomy: • The Motor System and Basal Ganglia • The Visual System • The Limbic System Surgical Planning Laboratory -5- http://www.slicer.org Brigham and Women’s Hospital Prerequisites • Slicer Training Slicer Training 1: Loading and Viewing Data Slicer Training 2: Segmentation http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Surgical Planning Laboratory -6- http://www.slicer.org Brigham and Women’s Hospital Overview • Part 1: Loading the Brain Atlas Data • Part 2: 3D-Model Hierarchy and Selective Model Display • Part 3: Creating, Annotating, Saving and Displaying Customized 3D-Views • Part 4: Neuroanatomy Teaching Files Surgical Planning Laboratory -7- http://www.slicer.org Brigham and Women’s Hospital Loading the Brain Atlas Data Slicer can load: • Anatomic grayscale data (CT, MRI) ……………………. • Label maps…………………………… • 3D-Models……………………………… • XML Scenes ………………………. Surgical Planning Laboratory -8- http://www.slicer.org Brigham and Women’s Hospital Loading the Brain Atlas Data Select “File” -> “Open Scene” In the pop-up window,click on the “Browse”-button; go to the directory with the atlas data, select the file “atlas2007.xml” and then click “Open” Surgical Planning Laboratory -9- http://www.slicer.org Brigham and Women’s Hospital Loading the Brain Atlas Data 3D-models MRI with overlaid label maps Surgical Planning Laboratory -10- http://www.slicer.org Brigham and Women’s Hospital Overview • Part 1: Loading the Brain Atlas Data • Part 2: 3D-Model Hierarchy and Selective Model Display • Part 3: Creating, Annotating, Saving and Displaying Customized 3D-Views • Part 4: Neuroanatomy Teaching Files Surgical Planning Laboratory -11- http://www.slicer.org Brigham and Women’s Hospital 3D-Model Hierarchy Select the “Models” module, in order to display the 3D-model hierarchy The 3D-model hierarchy reflects the organization plan of the nervous system into major anatomical subdivisions Surgical Planning Laboratory -12- http://www.slicer.org Brigham and Women’s Hospital Selective 3D-Model Display The 3D-model hierarchy allows for selective display of individual 3D-models or 3D-model groups Surgical Planning Laboratory -13- http://www.slicer.org Brigham and Women’s Hospital Overview • Part 1: Loading the Brain Atlas Data • Part 2: 3D-Model Hierarchy and Selective Model Display • Part 3: Creating, Annotating, Saving and Displaying Customized 3D-Views • Part 4: Neuroanatomy Teaching Files Surgical Planning Laboratory -14- http://www.slicer.org Brigham and Women’s Hospital Customized 3D-Views By taking advantage of the ability to selectively display 3D-models, customized 3D-views for neuroanatomy teaching can be created - e.g. functional systems, anatomic regions. The structures displayed in the 3D-view can be annotated, using fiducial markers Surgical Planning Laboratory -15- http://www.slicer.org Brigham and Women’s Hospital Customized 3D-Views Motor system Surgical Planning Laboratory -16- http://www.slicer.org Brigham and Women’s Hospital Creating Customized 3D-Views Example: teaching file “Brainstem” Surgical Planning Laboratory -17- http://www.slicer.org Brigham and Women’s Hospital Creating Customized 3D-Views Step 1: In the “Models” module, Select “Show none”; all models will be removed from the 3D-view Step 2: In the model hierarchy, click on the “Brainstem” group; Only the 3D-models grouped under “Brainstem” will be displayed in the 3D-view Surgical Planning Laboratory -18- http://www.slicer.org Brigham and Women’s Hospital Creating Customized 3D-Views Surgical Planning Laboratory -19- http://www.slicer.org Brigham and Women’s Hospital Annotating Structures Step 1: From the “More” menu, select the “Fiducials” module Step 2: Enter a name for your fiducials list here NEXT STEP Surgical Planning Laboratory -20- http://www.slicer.org Brigham and Women’s Hospital Annotating Structures Step 3: In the 3D-view window, place your mouse over the structure to be annotated and press “p” on your keyboard NEXT STEP Surgical Planning Laboratory -21- http://www.slicer.org Brigham and Women’s Hospital Annotating Structures Step 4: Enter the name of the anatomic structure here Surgical Planning Laboratory -22- http://www.slicer.org Brigham and Women’s Hospital Annotating Structures The name of the annotated anatomic structure appears in the 3D-view window Surgical Planning Laboratory -23- http://www.slicer.org Brigham and Women’s Hospital Saving Customized 3D-Views Right-click on the “Select” button in the “Views” menu In the pop-up window, enter a Name for your customized view, then click OK Surgical Planning Laboratory -24- http://www.slicer.org Brigham and Women’s Hospital Displaying Customized 3D-Views Click on the “Select” button in the “Views” menu, then select one of the customized views from the list Surgical Planning Laboratory -25- http://www.slicer.org Brigham and Women’s Hospital Overview • Part 1: Loading the Brain Atlas Data • Part 2: 3D-Model Hierarchy and Selective Model Display • Part 3: Creating, Saving, Annotating and Displaying Customized 3D-Views • Part 4: Neuroanatomy Teaching Files Surgical Planning Laboratory -26- http://www.slicer.org Brigham and Women’s Hospital Teaching Files The following slides are intended as a companion to the customized neuroanatomy views provided with the SPL-PNL Brain Atlas (“neuroanatomy teaching files”). They are meant to facilitate the user interaction with the visual material, and not as comprehensive, text-book-like descriptions of neuroanatomy. A list of recommended neuroanatomy and neuroscience reference works is provided at the end of this presentation. Surgical Planning Laboratory -27- http://www.slicer.org Brigham and Women’s Hospital The Motor System • The motor system is organized hierarchically: the spinal cord, brainstem and forebrain contain successively more complex motor circuits • The primary motor cortex controls voluntary movement; it projects to the brainstem and spinal cord motor neurons (lower motor neurons) via the corticobulbar and corticospinal tract respectively • The activity of the motor cortex and brainstem is influenced by the basal ganglia and cerebellum Surgical Planning Laboratory -28- http://www.slicer.org Brigham and Women’s Hospital The Primary Motor Cortex • Located in the precentral gyrus of the frontal lobe • Posterior limit: central sulcus, which separates the precentral gyrus from the postcentral gyrus (primary somatosensory cortex) • Anterior limit: precentral sulcus • Inferior limit: lateral sulcus (Sylvius) • Contiguous with the paracentral lobule on the medial aspect of the cerebral hemisphere Surgical Planning Laboratory -29- http://www.slicer.org Brigham and Women’s Hospital The Primary Motor Cortex Precentral gyrus Paracentral lobule Central sulcus Surgical Planning Laboratory -30- http://www.slicer.org Brigham and Women’s Hospital The Primary Motor Cortex • There is a precise somatotopic representation of the different body parts in the primary motor cortex, with the foot and leg areas located close to the midline, and the head and face areas located laterally on the convexity of the cerebral hemisphere (motor homunculus) • The size of the cortical representation for a specific body part is proportional to the complexity of the movements performed by that particular body part (e.g. the surface of the hand area is significantly larger than that of the foot area) Surgical Planning Laboratory -31- http://www.slicer.org Brigham and Women’s Hospital The Primary Motor Cortex Face area Leg area Surgical Planning Laboratory -32- http://www.slicer.org Hand area Brigham and Women’s Hospital The Corticospinal Tract Corticospinal tract Precentral gyrus (primary motor cortex) Internal capsule Surgical Planning Laboratory -33- http://www.slicer.org Brigham and Women’s Hospital The Corticospinal Tract • • • • • • The corticospinal tract (CST) is a massive collection of axons originating in the giant pyramidal cells (Betz), in the layer V of the primary motor cortex The axons of the CST converge in the posterior limb of the internal capsule At the level of the midbrain, the CST occupies the ventral aspect of the cerebral peduncle; the fibers continue their descent through the ventral pons and ventral medulla oblongata The axons that synapse with motor neurons in the (mostly) contralateral cranial nerve nuclei (III, IV, VII, IX, X, XI, XII) form the corticobulbar tract At the level of the lower medulla oblongata, most (ca. 80%) of the corticospinal axons cross over to the contralateral side (pyramidal decussation), and then continue their descent through the brainstem and spinal cord as the lateral corticospinal tract The CST axons that do not cross at the medulla level continue their travel down the spinal cord as the ventral corticospinal tract; most of these fibers cross over to the contralateral side shortly before reaching their target, the lower motor neurons, located in the anterior horn of the spinal cord Surgical Planning Laboratory -34- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia Caudate nucleus (head) Putamen Globus pallidus Thalamus Surgical Planning Laboratory -35- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia - left basal ganglia - dorsal view - Body of caudate nucleus Head of caudate nucleus Tail of caudate nucleus Putamen Internal capsule Surgical Planning Laboratory -36- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia - left basal ganglia - ventral view Head of caudate nucleus Putamen Body of caudate nucleus Globus pallidus Tail of caudate nucleus Surgical Planning Laboratory -37- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia • The basal ganglia (BG) are the principal component of a family of subcortical circuits linking the thalamus with the cerebral cortex • BG play a major role in the initiation of voluntary movement, and they also participate in cognitive functions, mood and non-motor behavior Surgical Planning Laboratory -38- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia • The main subdivisions of the basal ganglia are: 1. Striatum 2. Putamen 3. Globus pallidus (with two functionally distinct parts: external and internal pallidal segment) 4. Substantia nigra 5. Subthalamic nucleus Surgical Planning Laboratory -39- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia • • The Striatum is composed of: 1. Caudate nucleus 2. Putamen 3. Ventral striatum (including Nucleus accumbens) The Striatum is the major input nucleus to the basal ganglia Surgical Planning Laboratory -40- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia • The C-shaped Caudate nucleus is located medially and forms part of the wall of the lateral ventricle • The head of the caudate nucleus is located above the anterior Substantia perforata and it is separated from the Putamen by the anterior limb of the internal capsule • The Putamen lies laterally to the Caudate nucleus and medially to the Insula Surgical Planning Laboratory -41- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia • The Pallidum (Globus pallidus) consists of two functionally distinct subdivisions: the external (GPe) and internal (GPi) pallidal segment • The internal pallidal segment (GPi) represents one of the major output nuclei of the basal ganglia Surgical Planning Laboratory -42- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia • The Subthalamic nucleus (STN) is located between the thalamus (cranially) and the anterior part of the Substantia nigra (caudally) • The STN is the only component of the basal ganglia sending excitatory output Surgical Planning Laboratory -43- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia • • The Substantia nigra (SN) is located in the rostral midbrain SN has two histologically and functionally distinct components: 1. Pars compacta (dorsally) - contains dopaminergic neurons 2. Pars reticularis (ventrally) - contains GABA-ergic neurons Surgical Planning Laboratory -44- http://www.slicer.org Brigham and Women’s Hospital The Basal Ganglia - Function GPi sends inhibitory projections to the thalamus (ventral anterior nucleus). The thalamus, in turn, sends excitatory projections to the cortex. The subthalamic nucleus sends excitatory output to GPi.The direct pathway facilitates movement by directly inhibiting the GPi, and thus disinhibiting the thalamus (ventral anterior nucleus).The indirect pathway inhibits movement, by inhibiting the GPe. This results in a decreased inhibition of the GPi and of the subtalamic nucleus, which, in turn results in an increased inhibition on the thalamocortical projections. Surgical Planning Laboratory -45- http://www.slicer.org Brigham and Women’s Hospital The Visual System Components: • • • • • • Retina Optic nerve Optic tract Lateral geniculate nucleus Optic radiation Primary visual cortex Surgical Planning Laboratory -46- http://www.slicer.org Brigham and Women’s Hospital The Visual System Eyeball Optic nerve Optic tract Optic chiasm Surgical Planning Laboratory -47- http://www.slicer.org Brigham and Women’s Hospital The Visual System Optic radiation Optic tract Lateral geniculate nucleus Optic nerve Optic chiasm Eyeball Surgical Planning Laboratory -48- http://www.slicer.org Brigham and Women’s Hospital The Visual System • The retina contains photoreceptor cells (rods and cones) • The rods are responsible for the detection of dim light, whereas the cones mediate color vision • The retina output originates in the ganglion cells • The visual stimulus is transmitted from photoreceptor cells to the ganglion cells via an intricate network of interneurons Surgical Planning Laboratory -49- http://www.slicer.org Brigham and Women’s Hospital The Visual System • The retinal image is inversed • Via the Optic nerves, the retina projects to the Lateral geniculate nucleus of the thalamus, as well as to the Pretectal area of the midbrain (responsible for pupillary reflexes) and the Superior colliculus (responsible for saccadic eye movements) • In the Optic chiasm, the optic nerve fibers originating in the nasal hemiretinae cross over to the contralateral Optic tract, whereas the fibers originating in the temporal hemiretinae do not cross over Surgical Planning Laboratory -50- http://www.slicer.org Brigham and Women’s Hospital The Visual System • From the Lateral geniculate nucleus, the visual information is projected to the primary visual cortex via the Optic radiation • The neurons in the primary visual cortex are organized in columns, which in turn are connected via horizontal links • A column contains neurons with neighboring receptive fields Surgical Planning Laboratory -51- http://www.slicer.org Brigham and Women’s Hospital The Visual System • Lesions of specific segments of the visual system produce typical visual field defects - see illustration at http://www.brown.edu/Research/Memlab/py47/di agrams/visual-field-defects.jpg Surgical Planning Laboratory -52- http://www.slicer.org Brigham and Women’s Hospital The Limbic System Corpus callosum Cingulate gyrus Lateral ventricle (occipital horn) Fornix Hypothalamus Amygdaloid complex Surgical Planning Laboratory -53- http://www.slicer.org Hippocampus Brigham and Women’s Hospital The Limbic System The limbic system (aka the limbic lobe) comprises several phylogenetically older structures centered around the brainstem: 1. Cingulate gyrus 2. Parahippocampal gyrus 3. Hippocampus (hippocampal formation) 4. Amygdaloid complex 5. Parts of Hypothalamus 6. Nucleus accumbens (part of ventral striatum) 7. Orbitofrontal cortex Surgical Planning Laboratory -54- http://www.slicer.org Brigham and Women’s Hospital The Limbic System • The Cingulate gyrus (CG) lies on the medial aspect of the cerebral hemisphere, above the Corpus callosum, from which it is separated by the Sulcus of corpus callosum • CG is limited superiorly by the Cingulate sulcus; inferiorly, it is contiguous with Indusium griseum (a thin layer of primitive cortex covering the Corpus callosum) Surgical Planning Laboratory -55- http://www.slicer.org Brigham and Women’s Hospital The Limbic System • The Hippocampus is located in the depth of the temporal lobe; on coronal sections, its shape resembles that of a sea horse, and this is where it derives its name from • The Hippocampus is consists of the following substructures: Dentate gyrus, Hippocampus proper (Amon’s horn), Subiculum and Entorhinal cortex • The Uncus is the anterior, enlarged portion of the Hippocampus; the tail of the Dentate gyrus separates the inferior portion of the Uncus into the Uncinate gyrus (anterior) and Intralimbic gyri (posterior) • Note: the Hippocampus plays a major role in encoding of long-term memory, and contrary to earlier views, does not appear to participate significantly in the processing of emotions Surgical Planning Laboratory -56- http://www.slicer.org Brigham and Women’s Hospital The Limbic System • The Amygdaloid complex (AC) represents a group of subcortical nuclei located just in front of the Hippocampus • The AC receives input from subcortical areas concerned with the somatic expression of emotions (Hypothalamus and brain stem nuclei), via the Basolateral nucleus, and sends output to cortical areas concerned with the cognitive aspects of emotion via the Central nucleus Surgical Planning Laboratory -57- http://www.slicer.org Brigham and Women’s Hospital The Limbic System • The Nucleus accumbens (NACC) is located at the convergence between the head of the Caudate nucleus and Putamen, just lateral to Septum pellucidum • The histology and connectivity pattern of the NACC is very similar to that of the other components of the Striatum • The majority of the NACC neurons are GABA-ergic medium spiny neurons • Major input to the NACC originates in the Ventral tegmental area (Dopaminergic), prefrontal cortex, Amygaloid complex and Hippocampus • The NACC projects back to the prefrontal cortex via the Dorsomedial thalamic nucleus • The NACC is thought to play a major role in reward and addiction; the state of activity in the NACC appears to be regulated by the dopaminergic projections from the Ventral tegmental area Surgical Planning Laboratory -58- http://www.slicer.org Brigham and Women’s Hospital The Limbic System • The Orbitofrontal cortex (OFC) lies just above the orbital roof, at the base of the frontal lobe • The olfactory and the orbital sulci divide the surface of the OFC into four gyri: Gyrus rectus, Medial orbital gyrus, Anterior orbital gyrus, Posterior orbital gyrus and Lateral orbital gyrus (Note: there are many antomical variants of the OFC, which may substantially differ from the above description) Surgical Planning Laboratory -59- http://www.slicer.org Brigham and Women’s Hospital Further Reading Nieuwenhuys, R., Voogd, J., and Van Huizen, C., The Human Nervous System. Springer, 1980 Martin, J.H., Neuroanatomy: Text and Atlas. Third Edition, McGrawHill, 2003 Kandel, E.R., Schwartz, J.H., Jessell, T.M. (eds.), Principles of Neural Science, Fourth Edition, McGraw Hill, 2000 Surgical Planning Laboratory -60- http://www.slicer.org Brigham and Women’s Hospital
