LONI: Laboratory of Neuro Imaging

Software

  • AIR(Automated Image Registration) - AIR allows for automated registration of 3D (and 2D) images within and across subjects and across imaging modalities. More AIR
  • ANIMAL (Automated Non-linear Image Matching and Anatomical Labeling) - The ANIMAL algorithm performs labeling of brain voxels in 3D by deforming one MRI to match another, previously labeled, MRI volume.  It builds up the 3D non-linear deformation field in a piecewise linear fashion, fitting cubical neighborhoods in sequence. The algorithm is applied iteratively in a multi-scale hierarchy. At each step, image volumes are convolved with a 3D Gaussian blurring kernel of successively smaller width. Anatomical labels are defined in the new volume by interpolation from the original labels, via the spatial mapping of the 3D deformation field. More ANIMAL
  • BrainSuite2 - Brain Suite is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.
  • CH (Convex Hull) - A fully automated application for UNIX platforms (Sun Solaris 2.5 and greater) for global spatial normalization.  This software can perform an entire spatial normalization operation on PET images in less than 20 seconds. More Convex Hull
  • Display - Display is a tool to view, segment, and analyze MNC format image volumes. More Display
  • ICBMview - ICBMview is an internet browser Java Script application for entry, review, and report generation of subject data for the ICBM project. It includes all of the information acquired during the NeuroCog computer screening, as well as physical exam, and personal history and other statistical data. More ICBMview
  • Image Toolkit - Image Toolkit an X-window/Motif application used to co-register image data when motion is detected during imaging or to simplify spatial normalization of images from the same subject acquired on different imaging systems (e.g., MRI and PET).  More Image Toolkit
  • INSECT - INSECT is a series of algorithms used for tissue classification. These have been implemented as part of a pipeline for automatically processing multi-spectral (T1-,T2-, proton density(PD)-weighted) datasets from large numbers of subjects, known as INSECT(Intensity-Normalized Stereotaxic Environment for Classification of Tissues).
  • jViewbox -jViewBox is a flexible framework in Java for developing portable and high-performance biomedical imaging applications. It consists of a set of Java classes, organized under a simple and yet extensive API, that provides the core functionality of 2-D image presentation needed by most imaging applications. More jViewbox
  • LONI Pipeline - The LONI Pipeline is a simple graphical environment for constructing complex scientific analyses of data. It provides a visually intuitive interface to data analysis while also allowing for diverse programs to interact seamlessly. The Pipeline allows researchers to share their methods of analysis with each other easily and provides a simple platform for distributing new programs, as well as program updates, to the desired community. More LONI Pipeline
  • LOVE - LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. More LOVE
  • MIPS - The MIPS analysis software uses a modification of the Change Distribution Analysis routines to extract coordinates in the Talairach format that relate to the centroid of extrema sites within activated brain regions. It is highly integrated with the SN application and uses the same coordinate transforms to guarantee spatial normalization of images prior to analysis. More MIPS
  • MSD (Multiple Surface Deformation) - MSD is a completely automated procedure for unfolding the entire human cortex, using an algorithm which automatically fits a 3D mesh model to the cortical surface extracted from MRI.
  • MultiTracer - MultiTracer is a java-based tool that is useful for manual editing of MRI images in a variety of formats. Such editing is a prerequisite for most intersubject registration tools that can be used to create volume deformation parameters. In addition, the tool also allows manually delineated contours to be traced as used by the surface parameterization project. This tool is being used for landmark delineation in a variety of projects.
  • NeuroCog - Neurocog is a fully computerized Neurocognitive assessment software application. It incorporates a battery of tests that provide an overview of a subject's health, psychological state, laterality, and cognitive status. More NeuroCog
  • Register - Register is an interactive tool for 3D display and analysis of image volumes. It is used for combined display of any two MINC files, e.g. MRI and PET or MRI and SP_AM), and also is used for registration of data sets by manual specifications of corresponding landmarks in each volume. More Register
  • SEAL (Surface Extraction and Labeling) - SEAL calculates the mean curvature at every voxel on the MSD isosurface. Voxels with negative mean curvature, belonging to sulci, are extracted and pruned to obtain a set of sulcal traces on the cortical surface. More SEAL
  • SVT (Sub-Volume Thresholding) - SVT is a tool for determining the statistically significant regions of activation in single or multi-subject human brain functional studies and for analyzing development, dementia and other anatomical changes to structural brain data over time. More SVT
  • WAIR - The WAIR software is a tool for quantitative analysis of various n-dimensional (n-D) image registration techniques. In particular, its applications include analyzing warp performance for stereotactic Human Brain anatomical and functional data. Using the Discrete Wavelet Transform (WT), several image registration (warp) classification schemes including the "triangle", "cluster-group" and "spread-group" have been developed. More WAIR