Transcript Introduction
Slicer Tutorial
The SPL-PNL Brain Atlas
Ion-Florin Talos, M.D.
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Acknowledgments
NIH P41RR013218 (Neuroimage Analysis Center) NIH R01MH050740
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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.
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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
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Learning Objectives
Manipulating the data: • Loading the atlas data • Creating, displaying and annotating customized 3D views Neuroanatomy: • The Motor System and Basal Ganglia • The Visual System • The Limbic System
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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
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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
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Loading the Brain Atlas Data
Slicer can load: • Anatomic grayscale data (CT, MRI) …………………….
• Label maps…………………………… • 3D-Models……………………………… • XML Scenes ……………………….
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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”
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Loading the Brain Atlas Data
3D-models
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MRI with overlaid label maps
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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
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3D-Model Hierarchy
Select the
“Models”
module, in order to display the
3D-model hierarchy
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The 3D-model hierarchy reflects the organization plan of the nervous system into major anatomical sub divisions
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Selective 3D-Model Display
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The 3D-model hierarchy allows for selective display of individual 3D-models or 3D-model groups
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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
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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
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Customized 3D-Views
Motor system
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Creating Customized 3D-Views
Example: teaching file
“Brainstem”
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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
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Creating Customized 3D-Views
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Annotating Structures
Step 1:
From the
“More”
menu, select the
“Fiducials”
module
Step 2:
Enter a name for your fiducials list here
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NEXT STEP
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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
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Annotating Structures
Step 4:
Enter the name of the anatomic structure here
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Annotating Structures
The name of the annotated anatomic structure appears in the 3D-view window
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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
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Displaying Customized 3D-Views
Click on the
“Select” “Views”
button in the menu, then select one of the customized views from the list
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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
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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.
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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
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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
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The Primary Motor Cortex
Precentral gyrus Paracentral lobule Central sulcus
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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)
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Leg area
The Primary Motor Cortex
Face area Hand area
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The Corticospinal Tract
Precentral gyrus (primary motor cortex) Corticospinal tract Internal capsule
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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 cord
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
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The Basal Ganglia
Caudate nucleus (head) Putamen Globus pallidus Thalamus
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Body of caudate nucleus Head of caudate nucleus
The Basal Ganglia
- left basal ganglia - dorsal view Tail of caudate nucleus Putamen Internal capsule
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Head of caudate nucleus Body of caudate nucleus
The Basal Ganglia
- left basal ganglia - ventral view Putamen Globus pallidus Tail of caudate nucleus
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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
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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
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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
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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
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The Basal Ganglia
• The
Pallidum (Globus pallidus)
consists of two functionally distinct subdivisions: the
external (GP e )
and
internal (GP i ) pallidal segment
• The
internal pallidal segment
one of the
major output nuclei
(GP i ) represents of the basal ganglia
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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
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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
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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 GP i .The direct pathway facilitates movement by directly inhibiting the GP i , and thus disinhibiting the thalamus (ventral anterior nucleus).The indirect pathway inhibits movement, by inhibiting the GP e . This results in a decreased inhibition of the GP i and of the subtalamic nucleus, which, in turn results in an increased inhibition on the thalamocortical projections.
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The Visual System
Components: • Retina • Optic nerve • Optic tract • Lateral geniculate nucleus • Optic radiation • Primary visual cortex
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Eyeball Optic nerve Optic chiasm
The Visual System
Optic tract
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The Visual System
Optic radiation Lateral geniculate nucleus Optic chiasm Eyeball
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Optic tract Optic nerve
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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
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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
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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
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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
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Corpus callosum
The Limbic System
Cingulate gyrus Fornix Lateral ventricle (occipital horn) Hypothalamus Amygdaloid complex
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Hippocampus
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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
striatum) (part of ventral
7. Orbitofrontal cortex
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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)
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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 sub structures:
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
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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
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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 Dorsomedial thalamic nucleus
via the • 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
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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
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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
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