Morphometry BIRN Tools Primer
The Morphometry BIRN (mBIRN) testbed provides tools to aid researchers over the entire course of an experiment, with an emphasis on the particular challenges of multi-site studies. The goal of a brain morphometry experiment is to use magnetic resonance imaging (MRI) to visualize and find quantitative measures for brain structures. The types of MRI included in this domain include conventional structural (T1-weighted) MRI as well as diffusion tensor imaging (DTI).
A standard experimental flow follows in the example question and answer sequence below:
Imaging Protocols – What should my imaging parameters be to ensure that I acquire data that will answer the scientific questions that I am interested in? How can I ensure that all images in my study meet minimum quality standards?
The mBIRN has developed imaging protocols for both T1-weighted and diffusion tensor imaging. These protocols cover scanners from the three major manufacturers (Siemens, GE, and Philips). Browse and overview of these protocols.
Distortion Correction Tools – Do I need to correct my images for distortions, and if so, how?
Image distortions can arise from variations in the main magnetic field (B0), from imaging gradient non-linearity, and from the eddy currents induced by the application of large diffusion-weighting gradient used in DTI. The mBIRN has developed a set of software tools that can correct the distortions arising from these sources. View an overview of these tools.
Database Solutions – Once I’ve acquired data, how can I store, organize and query my data?
The ability to store, organize and query data becomes increasingly important as the size of a study increases or when a study is conducted over a number of sites. mBIRN researchers have developed the eXtensible Neuroimaging Archive Toolkit (XNAT) which is a platform designed to facilitate data management. XNAT includes a secure database that is accessed through a web-based user interface. The database is easily modifiable to accommodate a wide range of data and is written with open-source code to facilitate further customization. View an overview of XNAT.
Workflows – How can I process, in an automated fashion, the large amount of data that I have acquired?
The ability to send data through a succession of software programs is critical for the successful analysis of complex images. Two groups within mBIRN have developed data pipeline managers to handle the processing of images in an easily customizable way. Browse and overview of the available workflows.
Analysis Tools – What tools can I use to perform morphometric analysis on my data? How can I perform group analyses on my data?
The mBIRN has produced a rich set of analysis tools for both morphometric (FreeSurfer) and DTI analysis (DTI Studio and AVID). Browse an overview of analysis tools.
Visualization Tools – How can I see the results of my study?
Morphometric data can be visualized using 3D Slicer. The current version (Slicer 3) is open source and has the ability to work together with FreeSurfer. Visualization of DTI data can be done using DTI Studio, AVID, or Slicer 3. Click here for an overview of the visualization tools.
Data Sharing Tools – How can I share the raw and derived data from this study with others?
The mBIRN contributes data to the BIRN Data Repository from which it can be shared. XNAT can also be used to share data. Examine an overview of how to share data using BIRN tools.