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Quick Start: Register and Label a Brain

The surface and volume registration process requires many of the files created by the Cortical Surface Extraction Sequence, so either run this module as a continuation of that sequence or make sure you have the necessary files before proceeding.
Due to factors such as machine differences, software versions, and the physical placement of subjects in MRI scanners, one MRI image’s space is often quite different from another (e.g., coordinates that in one image point to a subject’s chin could easily point to the left temporal lobe of another subject in a different scan). It is thus necessary to register MRI images to a common space before analyzing them, even if the scans are of the same subject on the same machine (e.g., longitudinal studies). Registering images to a common space also allows for automatic labeling of cortical and subcortical structures, allowing for analysis of ROIs to be automated. BrainSuite includes SVReg, a program that registers the surfaces and volumes generated by the Cortical Surface Extraction Sequence to a brain atlas manually labeled by an expert neuroanatomist. Future versions will allow you to create and use your own atlases.

More detailed information about SVReg can be found in the Processing area on this site, but the information below can get you started with registration.

Running SVReg from the BrainSuite GUI

The easiest way to use SVReg is as a continuation of CSE. Simply check the box next to “Register and label brain” on the Cortical Surface Extraction Sequence dialog and then click “Run All”. The registration process is computationally intensive, so you may experience a slowdown in other programs while it is running. It takes about 1—1.5 hours to run, and will open several dialog boxes to inform you of its progress.

Alternatively, if you have already run CSE previously, you can access SVReg from the Cortex menu. Just make sure that the original T1-weighted volume, located in the directory that contains the outputs from the CSE run, is already loaded in BrainSuite.


Click “Apply” in the dialog that opens and SVReg will automatically register and label the surface and volume files generated by CSE. Once it is finished, the labeled mid cortical surface will be displayed in the surface viewer. Use BrainSuite to check the other surfaces and label volumes generated by SVReg.