The pyAFQ Mapping API

pyAFQ has a system for users to specify how to register an image from each subject to a given template, called the mapping. The mapping API is similar to our Mask API.

In the AFQ.definitions.mapping module, there are four mapping classes one can use to specify the mapping. As a user, one should initialize mapping classes and pass them to the AFQ.api objects, or write out the initialization as a string inside of one’s configuration file for use with the CLI.

• AFQ.definitions.mapping.SynMap: The default mapping class is to use Symmetric Diffeomorphic Image Registration (SyN). This is done with an optional linear pre-alignment by default. The parameters of the pre-alginment can be specified when initializing the SynMap.

• AFQ.definitions.mapping.SlrMap: Use this class to tell pyAFQ to use Streamline-based Linear Registration (SLR) for registration. Note that the reg_template and reg_subject parameters passed to AFQ.api.group.GroupAFQ should be streamlines when using this registration.

• AFQ.definitions.mapping.AffMap: This will only perform a linear alignment for registration.

• AFQ.definitions.mapping.FnirtMap: If you have an existing mapping calculated using Fnirt, you can pass bids filters to AFQ.definitions.mapping.FnirtMap and pyAFQ will find and use that mapping.