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Neuroimaging Analysis Center

Ron Kikinis, Ph.D.
P41EB015902
Active

Center Overview

The Neuroimage Analysis Center (NAC) is an NIH-sponsored National Resource Center dedicated to the development of imaging, algorithms, and software tools that improve our understanding of brain diseases and enable innovative treatments.

The center is organized around four research cores. The White Matter Architecture from Diffusion Tensor Images Core focuses on algorithms to elucidate and quantify white matter in individuals and populations. The fMRI Informatics Core extracts information on brain function by developing statistical technologies for the analysis of fMRI in populations. The Clinical Computational Anatomy Core uses symbolic descriptions of neural systems to augment high-resolution structural brain images. The Engineering Core develops the software environment that enables interactions between cores and makes their scientific advances usable by biomedical scientists.

To help the NIH fulfill its mission of advancing the health of the nation, the NAC maintains a close collaboration with many clinician-scientists who are working to understand the brain and treat brain disorders. This teamwork drives research innovation, informs the implementation of new software tools and techniques, and validates the work by addressing real-world medical needs.

Impact on Human Health

The mission of the Surgical Planning Laboratory (SPL) is to improve understanding of the human body in health and disease. SPL is a leader in developing advanced computational algorithms and scientific approaches for the comprehensive and quantitative analysis of structure and function derived from medical image data. It is also a leader in designing and implementing projects that use these capabilities to enable novel treatments.

SPL is a key partner in many national and international collaborations. One important ongoing collaboration is its role in coordinating the efforts of a number of NIH-funded centers, including NA-MIC, the National Alliance for Medical Image Computing, and NCIGT, the National Center for Image Guided Therapy.

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
3D Slicer
Neuroimaging Analysis Center
NIBIB

3D Slicer (Slicer) is a free, open source software package for image analysis and scientific visualization. Slicer is used in a variety of medical applications, including autism, multiple sclerosis, systemic lupus erythematosus, prostate cancer, schizophrenia, orthopedic biomechanics, COPD, cardiovascular disease and neurosurgery.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer Annotations
Neuroimaging Analysis Center
NIBIB

This is a core module for 3D Slicer and is used to create and edit annotations, use rulers to measure tumor diameters.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer Change Tracker Wizard
Neuroimaging Analysis Center
NIBIB

ChangeTracker is a 3D Slicer module for quantification of the subtle changes in 3D images of pathology. It has been tuned specifically for

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer DICOM
Neuroimaging Analysis Center
NIBIB

This is a core module for 3D Slicer that provides support for a subset of the DICOM standard including query/retrieve, store, and a local database.

Linux, Mac OSX, Windows DICOM N/A N/A
3D Slicer DTI Import/Export
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module imports and exports tensor datasets from various formats, including the NifTi file format.

Linux, Mac OSX, Windows NifTI (.nia), NifTI (.nii,...(more) N/A N/A
3D Slicer DWI to DTI Estimation
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module performs a tensor model estimation from diffusion weighted images.

Linux, Mac OSX, Windows DICOM, MetaImage (.mha), MetaImage...(more) N/A N/A
3D Slicer Editor
Neuroimaging Analysis Center
NIBIB

This is a core module for 3D slicer for manual segmentation of volumes. Some of the tools mimic a painting interface like photoshop or gimp, but work on 3D arrays of voxels rather than on 2D pixels.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer EM Segmentation with Atlas
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer module for atlas-based Expectation-Maximization segmentation of volume data.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer Image Registration
Neuroimaging Analysis Center
NIBIB

This is an introduction to using the various image registration algorithms in 3D Slicer, and how to select the most suitable one.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer Joint Rician LMMSE DWI Image Filter
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module reduces Rician noise (or unwanted detail) on a set of diffusion weighted images

Linux, Windows DICOM, MetaImage (.mha), MetaImage...(more) N/A N/A
3D Slicer LongitudinalPETCT
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer extension module that provides standardized uptake value (SUV) based on bodyweight for different regions of interest and for different timepoints.

Linux, Mac OSX, Windows DICOM, DICOM PET/CT N/A N/A
3D Slicer N4ITK Bias Field Correction
Neuroimaging Analysis Center
NIBIB

This is one of the many ITK filters provided in 3D Slicer. It performs MRI bias correction using N4 algorithm

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer Region Growing Segmentation
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer module for region growing segmentation based on intensity statistics.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer Resample Images
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer module for changing the resolution and spacing of an image.

Linux, Mac OSX, Web-Based Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer Robust Statistics Segmentation
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module is a general purpose segmenter that evolves an contour model to extract the desired boundary of the object.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer TubeTK
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer extension module that provides a toolkit for the segmentation, registration, and analysis of tubes and surfaces in images.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer UKFTractography
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer extension module for performing a particular style of diffusion image tractography that uses an unscented Kalman filter.

Linux, Mac OSX, Windows DICOM, MetaImage (.mha), MetaImage...(more) N/A N/A
3D Slicer Volume Rendering
Neuroimaging Analysis Center
NIBIB

This is a core module for 3D Slicer and is used for interactive volume rendering of 3D image data.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer Volume Statistics
Neuroimaging Analysis Center
NIBIB

This 3D Slicer module calculates image and volume properties using and label map and a grayscale image.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
3D Slicer XNATSlicer
Neuroimaging Analysis Center
NIBIB

This is a 3D Slicer extension module that provides secure graphical-user interface based input/output exchange betwen 3D Slicer and any XNAT Server.

Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
CT Atlas of the Abdomen
Neuroimaging Analysis Center
NIBIB

The abdomen atlas was derived from a computed tomography (CT) scan.

CT 0 - 500MB
Head and Neck Atlas
Neuroimaging Analysis Center
NIBIB

The head and neck atlas was derived from a reduced resolution (256x256) CT MANIX data set from the OSIRIX data sets.

CT 0 - 500MB
Multi-modality MRI-based Atlas of the Brain
Neuroimaging Analysis Center
NIBIB

The brain atlas is based on a MRI scan of a single individual.

MRI 0 - 500MB
NA-MIC HD Traveling Human Phantom
Neuroimaging Analysis Center
NIBIB

Traveling Human Phantom: 5 human subjects with >7 MRI scans from different institutions and scanners as well as a ball phantom. (Fill out the form File:NAMIC DATA SHARING.doc to request access.)

MRI N/A
NA-MIC Huntingtons Disease Data
Neuroimaging Analysis Center
NIBIB

A longitudinal collection of MRI scans for Huntingtons subjects. (Fill out the form File:NAMIC DATA SHARING.doc to request access.)

MRI N/A
Registration Image Library
Neuroimaging Analysis Center
NIBIB

Contains example cases of image registration using the Slicer registration tools. Includes multiple modalities (MRI, MR DTI, CT, PET), multiple anatomic structures (brain, thoracic, abdominal), multiple approaches (manual, automated, affine, non-rigid, masking) Includes for each case suggested processing pipeline with stepwise instructions.

Linux, Mac OSX, Windows NRRD (.nhdr), NRRD (.nrrd) MRI 0 - 500MB
SPL Automated Segmentation of Brain Tumors Image Datasets
Neuroimaging Analysis Center
NIBIB

A repository of 10 automated and manual segmentations of meningiomas and low-grade gliomas.

MRI N/A
SPL Knee Atlas
Neuroimaging Analysis Center
NIBIB

The knee atlas was derived from a MRI scan, using semi-automated image segmentation and three-dimensional reconstruction techniques.

MRI N/A