Current Projects

Cortical Parcellation	Automated Cortical Parcellation	Parcellation of the Cerebellum	Definition of the Thalamus and Subnuclei	Definition of the globus pallidus
Definition of the hippocampus	Enhancing visualization of subcortical structures	BRAINS2	BIRN Project	MIND Project

Cortical Parcellation

We have developed a cortical parcellation scheme of the cerebral cortex which divides each hemisphere into 40+ regions. These regions have been defined based on functional as well as cytoarchiture differences between the regions. Since these definitions are applied based on MR images, the divisions had to occur based on anatomical structures which the raters could see in the images. Tracing took place using the three co-planar views and the intersection of the cortical surface with the planar view was also visible. The raters could simply inclose the portion of the cortical surface which would define the current region by generating traces where the rater was only concerned about the location where the ROI clips the surface. This method was a rapid and reliable way for the rater to define each ROI. Papers describing the Frontal and Temporal lobe parcellation schemes have been published in NeuroImage. The methods for parcellating the parietal and occipital lobes have been submitted. In addition a patient control comparison of surface area and the volume of the cortical grey matter ribbon has been published in Biological Psychiatry.

Automated Cortical Parcellation

Because the number of regions that define the cerebral cortex are numerous the method for manual parcellation of the cerebral cortex is quite labor intensive. We are currently developing an automated way to parcellate the cortex. The method warps an atlas of the parcellation map onto the scan of an individual using non-linear morphing techniques. This is based on several homologous points which are picked by a trained rater. Software for implementing this technique is currently being developed along with some additional post processing software to simplify the editing of the automated labelling that occurs. An initial automated parcelation method is described in the abstracts for Human Brain Mapping 2000 conference which are published in NeuroImage.

Parcellation of the Cerebellum

We have establish reliable methods for parcellation of the cerebellum into four regions (anterior, superior posterior, inferior posterior and corpus medullary) per side. In addition, reliable methods for defining the cerebellar vermis in 3D have been developed. The artificial neural network used by the lab for definition of structures like the caudate and putamen is being trained to identify these regions as well. Two papers are currently in progress which describe these methods.

Definition of the Thalamus and Subnuclei

The gross thalamus and the medial dorsal nucleus of the thalamus have been traced using reliable methods for structure identification. The Gross thalamus traces have been completed on a sample of 25 subjects with schizophrenia and 25 normal controls. The artificial neural network is being trained to identify these structures. In addition further definition of the thalamic subnuclei is being undertaken.

An novel MR sequence, CAIR, has been developed to enhance visualization of the thalamic subnulei. Cortex attenuated inversion recovery (CAIR) uses and inversion time which nulls grey matter. This enhaces the differences between the grey matter and white matter within the thalamus. Since a limited FOV can be obtained with the current pulse sequence implementation, we are trying to reliably fit these images to the T1 structural scans which were obtained.

Definition of the globus pallidus

Methods have been developed by the IPL to identify the globus pallidus both internal and external portions using the RGB "super-image" display cabailities of BRAINS2. These methods have been applied to as sample to study reliability. A sample of 30 has been completed and we will soon start training the neural network to determine the ability of the neural network define these regions.

Definition of the hippocampus

We have developed tracing guidelines for the hippocampus and the have completed a reliability study and neural network training. The methods paper describing the tracing guidliens used in this study are currently in press in Hippocampus.

Enhancing visualization of subcortical structures

We are working to develop novel methods which enhance the visualization of subcortical regions of the brain. These include the use of an red, green, blue (RGB) image which display information from the coregistered T1, T2 and proton density images simultaneously. Since the images are weighted differently the combination of the images allows for enhanced visualization of certain structures because they appear in there own unique color. In addition displaying information presented to the rater in this way enhances visualization because of the amount of information presented.

Additional methods for enhancing using various techniques are being studied to allow for smaller structures like the subnuclei of the thalamus and the nucleus accumbens to be identified reliably.

BRAINS2

BIRN Project

"Although brain imaging techniques have generated remarkable progress in understanding how mental and neurological disorders develop, it has been nearly impossible for one laboratory to share and compare data with other labs. A lack of coordinated data networks, plus limitations in compatible computer hardware and software, have isolated scientists, excluding them from collaborative efforts that could provide a sufficient number of subjects for a comprehensive look at brain dysfunction.

The Function BIRN is enabling these researchers to exploit large existing databases of functional imaging data at the participating sites, to design and execute new cooperative functional neuroimaging studies across sites, and to use the techniques developed by the BIRN-CC to create grid-based workflows from their current analysis tools. The scientific goals of the project are to determine if frontal and temporal lobe dysfunction contribute to schizophrenia, and to assess the impact of treatments on functional brain abnormalities."

- http://www.nbirn.net/TestBeds/Function/index.htm

MIND Project

"The institute is based in Albuquerque, New Mexico and is closely linked with partner sites at Harvard University, the University of Minnesota, the University of New Mexico, and Los Alamos National Laboratory. It also collaborates with other imaging centers around the United States, such as The University of Iowa and the National Institutes of Health.

The MIND Institute is a unique scientific consortium. Its investigators are leaders in developing cutting edge neuroimaging technologies. They share their advances and pool their resources with one another, making the whole greater than its parts. Many different brain imaging techniques can be used to study the mind and brain, such as structural magnetic resonance (sMR), functional magnetic resonance (fMR), magnetoencephalography (MEG), magnetic resonance spectroscopy (MRS), and optical imaging. Each alone has limitations. Therefore, The MIND institute has launched an initiative to combine these multiple tools to create a "virtual" image of the workings of the mind and brain. This integrative strategy-sharing techniques and expertise across sites and combining multiple approaches to understanding the mind and brain-positions them well to apply their advances to crucial questions about the mechanisms and treatment of mental illness."

- http://www.themindinstitute.org/index.htm

Latest update May 7, 2005 Webpages maintained by Hans J. Johnson. E-mail the webmaster

MB March 9, 2005