Fiberfox: facilitating the creation of realistic white matter software phantoms

Abstract

Purpose: Phantom-based validation of diffusion-weighted image processing techniques is an important key to innovation in the field and is widely used. Openly available and user friendly tools for the flexible generation of tailor-made datasets for the specific tasks at hand can greatly facilitate the work of researchers around the world.

Methods: We present an open-source framework, Fiberfox, that enables (1) the intuitive definition of arbitrary artificial white matter fiber tracts, (2) signal generation from those fibers by means of the most recent multi-compartment modeling techniques, and (3) simulation of the actual MR acquisition that allows for the introduction of realistic MRI-related effects into the final image.

Results: We show that real acquisitions can be closely approximated by simulating the acquisition of the well-known FiberCup phantom. We further demonstrate the advantages of our framework by evaluating the effects of imaging artifacts and acquisition settings on the outcome of 12 tractography algorithms.

Conclusion: Our findings suggest that experiments on a realistic software phantom might change the conclusions drawn from earlier hardware phantom experiments. Fiberfox may find application in validating and further developing methods such as tractography, super-resolution, diffusion modeling or artifact correction.

Keywords: artifact simulation; diffusion-weighted imaging; open-source software; software phantoms; synthetic white matter fibers.