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LONI Software Training

LONI develops a diverse array of modeling, analysis and visualization software and provides user guides, forums and training workshops demonstrating the use of these computational resources to solve specific biomedical imaging problems. Software training is available for researchers who use LONI software. Visit our calendar on the News and Events page for information about upcoming scheduled training. On-site trainings are held in the LONI DIVE theatre. Off-site trainings can be arranged at your institution.

LONI Pipeline Training

The LONI Pipeline provides a graphical framework for development, maintenance and dissemination of neuroimaging data-analysis protocols. The Pipeline environment offers a scalable infrastructure for graphical integration of diverse, complex and heterogeneous software. The training course covers how to employ any of the available Pipeline library modules and workflows. Attendees will get acquainted with the Pipeline interface and learn how to describe their own modules and create processing workflows, including a hands-on demonstration of segmentation, shape analysis and cortical thickness workflows.

LONI Pipeline

LONI Research Protocols

LONI provides trainees with access to a diverse array of neuroimaging research protocols. These protocols illustrate the functionality and utilization of heterogeneous datasets, a number of validated methods and tools for data analysis, as well as web-services for managing brain imaging data.

LONI Resource (LONIR) supports neuroimaging researchers investigating brain structure, function and physiology in health and disease using comprehensive imaging analysis. The goal of the Resource is to develop a collaborative environment equipped with the necessary tools for discovery in brain imaging research. The algorithms and tools developed by LONIR are made available to the neuroscience research community. In doing so, LONIR hopes to foster research relationships that will disseminate new information and train investigators in the use of new techniques. LONI Resource is operated by the Laboratory of Neuro Imaging (LONI) at USC and funded by the P41 Biomedical Technology Resource Center award. This NIH grant is governed by the National Institute of Biomedical Imaging and Bioengineering (NIBIB).

LONI Resource

LONI Instructional Web

The LONI Instructional Web illustrates concepts behind different research methods and neuroimaging techniques. This online tutorial was developed to train medical students and neuroanatomists. It is accessible to the public.
Techniques
Ventricles
Telencephalon
Diencephalon
Brainstem
Cerebellum
Techniques Review

Techniques in Neuroimaging

Information about CT, MRI and SPECT/PET image types along with tabluation of tissue image characteristics.

CT (Roentgen-Ray Computed Tomography)
A beam of x-rays passes through the brain and is detected according to the density of the tissue encountered. Detectors positioned around the circumference of the scanner collect attenuation readings from multiple angles. A computerized algorithm reconstructs an image of each slice.
MRI (Magnetic Resonance Imaging)
When protons are placed in a magnetic field, they become capable of receiving and then transmitting electromagnetic energy. The strength of the transmitted energy is proportional to the number of protons in the tissue. Signal strength is modified by properties of each proton's microenvironment, such as its mobility and the local homogeneity of the magnetic field. MR signal can be "weighted" to accentuate some properties and not others. When an additional magnetic field is superimposed, one which is carefully varied in strength at different points in space, each point in space has a unique radio frequency at which the signal is received and transmitted. This makes constructing an image possible. It represents the spatial encoding of frequency, just like a piano.
Read more about MRI physics
MRI Physics

PRINCIPLE

To understand the fMRI method, investigators should be familiar with the physical principles of magnetic resonance that determine its signal characteristics, and through which it is possible to form images. In overview the process is as follows:
  • The subject is first placed into a strong and homogeneous magnetic field. Various atomic nuclei, particularly the proton nucleus of the hydrogen atom (from here, we will consider only the proton), align themselves with this field and reach a thermal equilibrium. The subject is thereby “magnetized.”
  • The proton nuclei precess about the applied field at a characteristic frequency, but at a random phase (or orientation) with respect to one another.
  • Application of a brief radio frequency (RF) electromagnetic pulse disturbs the equilibrium and introduces a transient phase coherence to the nuclear magnetization that can, in turn, be detected as a radio signal and formed into an image.

MR SIGNAL FORMATION

The proton nuclei of the hydrogen atom possess a small magnetic moment. When placed within a magnetic field, a torque will be exerted upon them, resulting in a slight energetic advantage of one orientation (parallel to the field) over another (the anti-parallel orientation). Over time, random atomic collisions and other perturbations allow the complete system to reach a magnetic and thermal equilibrium with an excess of protons aligned with the magnetic field. The combined alignment of all of these protons results in a net magnetic moment; a subject placed within a magnetic field thus becomes “magnetized.”

Figure 1

Figure 2

Figure 3
Figure 1: Magnetic Properties of the proton nucleus of the Hydrogen Atom.
(Left) The hydrogen proton possesses the quantum property of “spin” or angular momentum, and has a small magnetic dipole moment. When placed in a magnetic field, a torque is exerted on the particle, causing it to precess about the applied field.

Figure 2: Vector description of proton magnetization
The rotating magnetic moment of the proton can be decomposed into a longitudinal component, along the applied magnetic field, and a transverse component orthogonal to it and rotating (precessing) about it.

Figure 3: Spontaneous Decay of Transverse Magnetization (Signal)
SPECT/PET (Single Photon/ Positron Emission Computed Tomography)
When radiolabeled compounds are injected in tracer amounts, their photon emissions can be detected much like x-rays in CT. The images made represent the accumulation of the labeled compound. The compound may reflect, for example, blood flow, oxygen or glucose metabolism, or dopamine transporter concentration. Often these images are shown with a color scale.
Simplified Tabulation of Tissue Image Characteristics
Normal Tissue
MR-T1 MR-T2 Xray-CT2
Dense bone dark dark bright
Air dark dark dark
Fat bright bright dark
Water dark bright dark
Brain "anatomic"3 intermediate intermediate
  1. Bright means high signal intensity, dark means low, and interm. means intermediate.
  2. Bright means high density/high attenuation of x-rays, dark means low.
  3. Grey matter appears grey, white matter white.
Abnormal Tissue
MR-T1 MR-T2 Xray-CT2 Enhancement1
Infarct dark bright dark sub-acute
Bleed bright2 bright2 bright no
Tumor dark bright dark3 yes
MS plaque dark bright dark4 acute
  1. Blood brain barrier leak. For MR, gadolinium; for CT, iodinated contrast material.
  2. Unless very fresh or very old.
  3. Unless calcified.
  4. Often isodense.

Ventricles and Cisterns

Can you identify the ventricles and cisterns that appear in this image?
Hydrocephalus: coronal, gross. This is a post-mortem coronal section through a brain of a patient with hydrocephalus. Notice that the lateral and the 3rd ventricles are greatly enlarged. An obstruction at what point could give this pathology?
Hydrocephalus: horizontal, CT. This is a CT of a patient with hydrocephalus similar to that observed in the gross coronal section above. Notice the greatly enlarged lateral ventricles.
Left Ventricle Hydrocephalus horizontal MRI. This is an MRI of a patient with an obstruction of the left foramen of Monroe, causing left ventricular hydrocephalus. Compare the relative size of the left and right lateral ventricles.
Cerebral Aqueduct Hydrocephalus: horizontal MRI. This is an MRI of a patient at the level of the cerebellum. The patient has hydrocephalus of the Cerebral aqueduct caused by a mass in the cerebellum.
Forebrain structures. as seen from surface models. This is a cut-away 3D surface madel of the basal ganglia and adjacent structures. Can you identify the structures? (from the Digital Anatomist site)
Uncal Herniation When the flow of CSF through the ventricles is obstructed, intracerebral pressure (ICP) may increase. In this example, an increase in ICP caused the uncus and hippocampus to herniate through the tentorium, making the groove indicated by the arrow.
MRI and MR Angiograpy This image contains an MR angiogram, which uses a pulse sequence to enhance blood flowing through vessels, and the corresponding T1 MRI. Can you identify the vessels and corresponding neuroanatomy? Labels are available. (Image from the Digital Anatomist site [J.S. Tsuruda]) Figure legend available.
Angiogram movie This is a mini-movie of an angiogram, lateral view through the cranium. A radio-opaque dye is injected into a cerebral vessel (in this case the left corotid) in order to visualize flow (and look for pathology). Given that this is a lateral view, what vessel is this?
Optical Imaging movie This is a mini-movie of an optical intrinsic signal produced by a sustained stimulation in rodent cortex. Large branches seen are from the rodent middle cerebral artery. Note that blood delivery to cortex is not static, rather it is dynamic, increasing in response to cortical stimulation. For reference of OIS mpeg sequences.
Supplement Woods et al Woods, R.P., Iacoboni, M., Mazziota, J.C. (1994) "Bilateral spreading cerebral hypoperfusion during spontaneous migraine headache" NEJM 331:1689-1692. This PET imaging study of a migraine headache in progress indicates the pattern and alteration of cerebral blood flow caused by the migraine. Notice that the spreading hypoperfusion is not restricted to a single cerebral vascular zone, suggesting a primiary cortical process.

Telencephalon

Uncal Herniation When cerebral edema occurs as a result from injury, lower structures may be displaced by the accumulating fluid. In the Cerebellum session we saw an example of tonsilar herniation. Here we see a gross specimen of uncal herniation. Due to cerebral edema, the uncus and hippocampus have herniated over the tentorium, making the groove indicated by the arrow. (from CNS Pathology)
Alzheimer's Disease, gross specimen When cerebral edema occurs as a result from injury, lower structures may be displaced by the accumulating fluid. In the Cerebellum session we saw an example of tonsilar herniation. Here we see a gross specimen of uncal herniation. Due to cerebral edema, the uncus and hippocampus have herniated over the tentorium, making the groove indicated by the arrow. (from CNS Pathology)
Pick's Disease, gross specimen Pick's disease is also a degenerative disease of the cortex which presents as progressive dementia. However, the pattern of degeneration is different. Notice from the gross specimen that in contras to Alzheimer's, the degeneration is confined to the frontal and temporal lobes. Furthermore, note that the superior temporal gyrus is spared (characteristic for Pick's disease). (from CNS Pathology)
The corpus callosum interconects the cerebral cortex. A general trend exists such that more anterior cortex crosses in the more anterior portions of the corpus callosum. As seen from the figure this is quite complex, however the trend still exists. The data presented here is from intraoperative mapping studies indicating the location of cortical fibers decussating in the corpus callosum.
Optical imaging of somatosensory cortex These are images produced by a technique called optical intrinsic signal imaging. These are maps of somatosensory cortex in humans obtained intraoperatively. The upper left panel indicates cortical response to median transcutaneous stimulation. The upper right panel is ulnar nerve stimulation. The lower right panel is a simultaneous median and ulnar stimulation. For comparison purposes, the medain only and ulnar only responses were added and indicated in the lower left panel. Notice that the simultaneous response (lower right panel) is much greater than the sums of separate stimulations (lower left panel). Anterior is left.
PET Actication in language cortex These are images indicating activation in language associated cortices during specific language tasks. Compare the magnitude and spatial distributions of responses during each of the tasks.
Word Generation in language cortex This is a PET study using word generation tasks. In study 1, objects were named (red). In study 2, words were named (yellow). Areas activated in both studies are indicated in black. Compare the spatial distributions of responses during eachof the tasks.
Visual cortex activation This is a PET study showing activation in the occipital lobe in response to visual stimulation. Both blood flow and glucose utilization are indicated.
Visual cortex mapped retinotopically fMRI was used to map the retinotopic representation in area 17 of the cortex. Visual fields were stimulated using the patterns indicated. (a)indicates that the right visual field maps to left striate cortex (and vice versa). (b)indicates that upper visual filed maps to inferior striate cortex (below the calcrine fissue), and vice versa. (c) indicates a complex visual field stimulation. The upper right hand corner indicates the orientation of the MR slice (coronal).
Visual movement fMRI studies have revealed the cortical area activated by object moving in the visual field. This area is referred to as MT and is postulated to be responsible for the perception of movement in the visual field.
Epilepsy This is a PET study of a single patient indicating the pre-, ictal, and post-seizure activity. Pre-ictal (interictal) activity is normal (left pannel) as indicated by the arrow. The middle panel indicates the hypermetabolism associated with the ictal event. After the seizure (postictal, right panel) there is a marked hypometabolism in the cortex near the foci of the event (straight arrows). The curved arrow indicates a hypermetabolism of the area underneath the area associated with the ictal event.
Alzheimer's Disease Brains of Alzheimer's disease patients develop profound atrophy of the parietal and temporal cortex (see above).This atropy is a functional loss and can be visualized before the huge cellular loss associated with the specimen seen above. These images are PET studies of the same patient, about 5 years between scans. The scan on the left is beginning stage, on the right is mid-stage disease.

Diencephalon and Basal Ganglia

This is a multiple slice tour of the Diencephalon as seen by T2 weighted MRI's. (adopted from Harvard's whole brain atlas) On the following sections identify the mamillary bodies, red nucleus, substantia nigra, pineal gland, pituitary gland, sphenoid sinus, infundibulum, suprasellar cistern, cerebral peduncle, hypothalamus, posterior commisure, thalamus and fornix.
Pituitary Adenoma This gross specimen illustrates a circumscribed mass lesion present in the sella turcica. Though pituitary adenomas are benign, they can produce problems either from a mass effect (usually visual problems from pressing on the optic chiasm and/or headaches) or from production of hormones such as prolactin or ACTH. (from the CNS pathology site)
Horizontal MRI This is a horizontal T2 weighted MRI at the level of the basal ganglia. Can you identify the structures with the pointers? (from Harvard's Whole Brain Atlas)
Gross coronal section through the forebrain from a frozen specimen. The section is take at the level where connections can be seen between the head of the caudate and the putamen. (from the Laboratory of Neuro Imaging)
Mini Movie of the Ventricles, hippocampus, striatum, and cerebellum. Given your recent study of the diencephalon can you identify the rest of the structures on the mini-movie from last week?
Forebrain structures. as seen from surface models. This is a cut-away 3D surface madel of the basal ganglia and adjacent structures. Can you identify the structures? (from the Digital Anatomist site)
The corpus callosum interconects the cerebral cortex. A general trend exists such that more anterior cortex crosses in the more anterior portions of the corpus callosum. As seen from the figure this is quite complex, however the trend still exists. The data presented here is from intraoperative mapping studies indicating the location of cortical fibers decussating in the corpus callosum.
Huntingtons Disease, Gross Huntingtons disease is a degeneration of specific cells in the head of the caudate. Notice in this gross specimen, coronal cut, that the ventricle appear enlarged due to the mass cell loss in the head of the caudate. (from CNS Pathology site)
Parkinson's Disease on T2 MRI Last week you learned that a loss of connectivity in the cortex can lead to an increase of iron in the area of loss. This presents on MRI as a dark area (a loss of signal). This was demonstrated by a T2 weighted MRI of a Parkinson's patient's brainstem with signal loss in the substantia nigra and the red nucleus. This is the same patient. What structure is unusually dark, implying a loss of neuronal connections? A potential treatment for Parkinson's disease is the implantation of fetal substantia nigra tissue into the putamen. This patient has undergone this procedure but only on the right putamen. The image is a PET scan of this patient before implantation and in the following months. Notice the continued loss of function in the left putamen and the recovery of function in the right putamen.

Brainstem

For multiple brainstem models and diagrams please see the Digital Anatomist site at Washington University.

Horizontal MRI of Low Brainstem This is a T1 weighted MRI at the level of the low brainstem. Can you identify the structures with the pointers? (from Harvard's Whole Brain Atlas)
Horizontal MRI of Mid Brainstem This is a T1 weighted MRI at the level of the low brainstem. Can you identify the structures with the pointers? (from Harvard's Whole Brain Atlas)
Mini Movie of the diencephalon, globus pallidus with the pyramidal tracts and the substantia nigra. Post-mortem cryo-section anatomy was used to construct these surface models. (from the Laboratory of Neuro Imaging)
Horizontal MRI of Upper Brainstem with Aneurysm This is a T2 weighted MRI showing an aneurysm in the interpeduncular cistern of the brainstem. Which vessel is located in this cistern? Need a hint, see the angiogram. (anterior to posterior orientation)
Horizontal MRI of a Parkinson's Disease Brainstem This is a T2 weighted MRI of a patient with Parkinson's disease. Notice that the substantia nigra in the brainstem is unusually dark. It has been postulated that this darkening of the substantia nigra results from the accumulation of iron. Iron accumulation is thought to occur when normal pathways are interupted. Such an MRI in an asymptomatic patient should raise the suspicion of Parkinson's disease.
Coronal MRI of an acoustic schwannoma This is a coronal T1 weighted MRI with contrast of a patient with a very common cranial neoplasm. Notice the displacement of the pons due to the growth surrounding the 8th nerve. Name the common location of this neoplasm.
Normal VII Nerve This is a sagittal oblique T1 weighted MRI indicating a normal facial nerve (arrows). Can you name the bony structure though which the nerve is seen to travel?
Facial Schwannoma This is also a sagittal oblique T1 weighted MRI. A schwannoma of the facial nerve is indicated by the arrow. This could be easily confused with which other nerve? Why?

Cerebellum

What is the function of the cerebellum? The cerebellum is involved in motor pathways, and is often associated with coordinated movement. The Gao et. al. article indicates that the cerebellum also is involved in sensory pathways. What else? There does exists evidence for the involvement of the cerebellum in higher cognitive function. Middleton, F.A., and Strick, P.L. (1994) "Anatomical evidence for Cerebellar and Basal Ganglia Involvement in Higher Cognitive Function" Science 266:458-461. Abstract available.


Abstract

The possibility that neurons in the basal ganglia and cerebellum innervate areasof the cerebral cortex that are invloved in cognitive function has been a controversial subject. Here, retrograde tansneuronal transport of herpes simplex virus type 1(HSV1) was used to identify subcortical neurons that project via the thalamus to area 46 of the primate prefrontal cortex. This cortical area is known to be involved in spatial working memory. Many neurons in restricted regions of the dentate nucleus of the cerebellum and in the internal segment of the globus pallidus were labeled by transneuronal transport of virus from area 46. The location of these neurons was different from those labeled after HSV1 transport from motor areas of the cerebral cortex. These observations define an anatomical substrate for the involvement of basal ganglia and cerebellar output in higher cognitive function.

Mid-Sagittal Cryosection This is a post-mortem sagittal cryosection at the midline. The cerebellum is seen along the midline axis. A mini-movie cutting through the brain in the sagital plane also is provided. Can you see any of the cerebellar nuclei in the movie? (provided by the Laboratory of Neuro Imaging)
Mid-Sagittal Cryosection This is a T2 weighted horizontal MRI of the cerebellum. A sagittal section indicating the section level is included. Can you identify the structures with the pointers? (from Harvard's Whole Brain Atlas)
Cerebellar tonsil herniation Acute cerebral swelling can often produce herniation of the cerebellar tonsils into the foramen magnum. Note the con shape of the tonsils around the medulla in this cerbellum. What fatal problem can this cause? (from CNS Pathology)
Cerebellar function, PET This is a Positron Emission Tomographic (PET) image of cerbellar function. The top figure indicates cerebellar activation during a motor control task (finger movement). Do you know your pathways? Is the response ipsilateral or contralateral to the finger movement? Why? The bottom figure indicates cerbellar activation during a timing task. Note that the response is bilateral and superior with correcponding activation in the vermis. (from Jueptner, M., Rijntjes, M., Weiller, C., Faiss, J.H., Timmann, D., Mueller, S.P., Diener, H.C. (1995) "Localization of a cerebellar timing process using PET" Neurology 45:1540-1545) Figure legend

Top Figure

The possibility that neurons in the basal ganglia and cerebellum innervate areasof the cerebral cortex that are invloved in cognitive function has been a controversial subject. Here, retrograde tansneuronal transport of herpes simplex virus type 1(HSV1) was used to identify subcortical neurons that project via the thalamus to area 46 of the primate prefrontal cortex. This cortical area is known to be involved in spatial working memory. Many neurons in restricted regions of the dentate nucleus of the cerebellum and in the internal segment of the globus pallidus were labeled by transneuronal transport of virus from area 46. The location of these neurons was different from those labeled after HSV1 transport from motor areas of the cerebral cortex. These observations define an anatomical substrate for the involvement of basal ganglia and cerebellar output in higher cognitive function.


Bottom Figure

Increases of regional cerebral blood flow in the timing task (timing versus control). Subjects had to estimate time differences by comparing a test interval with a standard interval. The increases of blood flow occurred in the superior part of the cerebellar hemispheres bilaterally and the cerebellar vermis. The left sides of planes C and D correspond to the left side of the brain.

Cerebellar function, fMRI This is a functional MRI image of cerebellar function. Magnetic Resonance imaging of the lateral cerebellar output nucleus (dentate) was used to determine the relative roles of the cerebellum in sensory and motor systems. Activation occurred durring motor and sensory tasks. Gao, J.H., Parsons, L.M., Bower, J.M., Xiong, J., Li, J., and Fox, P.T. "The Role of the Cerebellum in Sensory Discrimination: A Functional Magnetic Resonance Imaging Study" Science 1996 Apr 26, 272(5261):545-7. Figure legend

Functional MRI (color) superimposed on the anatomical MRI (gray) showing dentate activations (18) for each task: (A) Grasp Objects, (B) Grasped Objects Discrimination, (C) Cutaneous Stimulation, and (D) Cutaneous Discrimination. The dentate nuclei are the two dark crescent-shaped structures symmetrically-opposed about the midline of the cerebellum. Both functional and anatomical images were co-registered for each task by performing rotation, translation, and scaling on each individual subject's images and then averaging the coregistered images across subjects. A Student's group t-test was performed on these coregistered images for each task comparing task-induced changes relative to rest. Brain activation was detected by use of a threshold defined by both a t-value of 2.5 and a cluster of 5 adjacent pixels. The above-threshold sites represent activations statistically significant to P < 0.05 relative to the whole cerebellar plane sampled. The activations are displayed on a color scale ranging from a t-value of 2.5 (green) to 10.0 (red). R and L are right and left sides of the brain respectively.

Neuroimaging Techniques Review

Review the Neuro Imaging Techniques. In particular, since MRI has become such an important tool used in medicine review the tissue image characteristics as seen by T1 and T2 scans. Can you identify a T2 scan when you see one?

Left Ventricle Hydrocephalus: horizontal MRI This is an MRI of a patient with an obstruction of the left foramen of Monroe, causing left ventricular hydrocephalus. Compare the relative size of the left and right lateral ventricles.
MRI and MR Angiograpy This image contains an MR angiogram, which uses a pulse sequence to enhance blood flowing through vessels, and the corresponding T1 MRI. Can you identify the vessels and corresponding neuroanatomy? Labels are available. (Image from the Digital Anatomist site [J.S. Tsuruda]) Figure legend available.
Mid-Sagittal Cryosection This is a T2 weighted horizontal MRI of the cerebellum. A sagittal section indicating the section level is included. Can you identify the structures with the pointers? (from Harvard's Whole Brain Atlas)
Horizontal MRI of Low Brainstem This is a T1 weighted MRI at the level of the low brainstem. Can you identify the structures with the pointers? (from Harvard's Whole Brain Atlas)
Horizontal MRI of Mid Brainstem This is a T1 weighted MRI at the level of the low brainstem. Can you identify the structures with the pointers? (from Harvard's Whole Brain Atlas)

This is a multiple slice tour of the Diencephalon as seen by T2 weighted MRI's. (adopted from Harvard's whole brain atlas) On the following sections identify the mamillary bodies, red nucleus, substantia nigra, pineal gland, pituitary gland, sphenoid sinus, infundibulum, suprasellar cistern, cerebral peduncle, hypothalamus, posterior commisure, thalamus and fornix.


Horizontal MRI This is a horizontal T2 weighted MRI at the level of the basal ganglia. Can you identify the structures with the pointers? (from Harvard's Whole Brain Atlas)

Brain Trivia