LONI encourages dialogue between the user community and laboratory personnel. This section serves as a forum for general questions and comments about LONI.

This thread is for all other software that are not listed below.

A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs.

Brain Parser software segments regions of interest based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

BrainSuite is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head. We have written the software to require minimal user interaction and with the goal of extracting a topologically spherical cortical surface from a raw MR volume within a matter of minutes.

The LONI Debabeler enables researchers to manage the conversion of imaging data from one file format to another using a graphical user interface. Many file formats and a variety of translations are already supported, but the advantage of the visual programming environment is to make it easy to alter existing translations of the data.

A simple to use Java application for removing patient-identifying information (e.g., patient name and id) from medical image files. Removal of this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner.

The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files.

iTools offers a graphical interface for perusing meta-data information about software tools, databases and material resources freely provided by NCBC funded institutions. iTools is built upon the XML framework prescribed by biositemaps.org, for generating and disseminating resource descriptions.

The MiND framework enables data sharing and software interoperability for diffusion-weighted MRI.

Multitracer is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision.

The LONI Pipeline is a free workflow application primarily aimed at Neuroimaging Researchers. With the LONI Pipeline, users can create workflows that take advantage of all the greatest Neuroimaging tools available, quickly.

Provenance, the description of the history of a set of data, has grown more important with the proliferation of research consortia-related efforts in neuroimaging. Knowledge about the origin and history of an image is crucial for establishing data and results quality; detailed information about how it was processed, including the specific software routines and operating systems that were used, is necessary for proper interpretation, high fidelity replication and re-use. We have drafted a mechanism for describing provenance in a simple and easy to use environment, alleviating the burden of documentation from the user while still providing a rich description of an image’s provenance. This combination of ease of use and highly descriptive metadata should greatly facilitate the collection of provenance and subsequent sharing of data.

This web resource provides an online framework for evaluating the results of skull-stripping algorithms. Users may browse the results produced by others, or they may download the test data, segment it with their own algorithm, and upload it to have it evaluated.

The ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines.

The Synchronized Histological Image Viewing Architecture (SHIVA) is a Java-based visualization and analysis application. SHIVA can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets.

LONI offers its users and collaborators access to its Linux HPC resources for data processing and storage.