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 AFQ/definitions/mapping.py, 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.