LONIR provides meaningful, instructional and interesting content that is regularly updated to reflect the current state of our research and other activities of our Resource. We provide users with the ability to download software, atlases and protocols that have been developed in our lab. In addition, a web-based database containing images, animations and other samples is available for browsing and media requests.


The LONI Neuroimaging Quality Control System (LONI QC) is an imaging data review and assessment system for human neuroimaging research studies involving one or more centers. LONI QC allows users to anonymously download imaging data from the LONI IDA and run a standardized quality control check via an automated pre-processing system specifically designed to generate a range of vector statistics and derived images.

View the LONI QC

Research Protocols

LONI Resource provides investigators access to the LONI research protocols. The protocols provide collaborators and researchers with a validated set of methods that will enable them to analyze their brain imaging data. The methods have been implemented to facilitate communications and provide a well-defined standard for scientific investigation.

Research protocols

Software & Tools

We have created several open-source Software & Tools that service a wide variety of laboratories, nationally and internationally. Browse our list of Software & Tools below. Click on any item for more information or if you are interested in downloading the free software.

This is a collection of software tools for the computational analysis of brain anatomy with MRI data. It includes automated software tools from surface reconstruction to their mapping via metric optimization in the Laplace-Beltrami embedding space. It is general and can be applied to a wide range of anatomical structures including cortical, sub-cortical, and fiber bundle surfaces.

Click Offerings to sort:

Data Management
Shape Analysis
Image Processing
Statistical Analysis


This booklet gives an introduction to LONI Pipeline, and provides installation instructions. It has several concrete and complete neuroimaging processing examples from designing modules to executing workflows to viewing results.

LONI Pipeline Handbook