Co-registration step in BrainSuite Diffusion Pipeline (BDP) can be sub-divided into two steps — (1) Rigid registration of MPRAGE and diffusion image and (2) Distortion correction of diffusion images. Depending on the mode of co-registration, these two steps are executed in different fashion. BDP offers three different modes of distortion correction and co-registration:
- Registration based distortion correction: This method uses information from MPRAGE image to ‘un-distort’ diffusion data and hence does not requires any additional data collection (like fieldmap). In this method, rigid registration of MPRAGE and diffusion image is performed first, followed by distortion correction. Distortion correction involves a constrained non-rigid registration and requires more computational resources. The details of the algorithm can be found in Bhushan et al., 2012. This method is the default option in BDP (and does not require any flags to invoke it).
- Fieldmap based correction: This method uses fieldmap, which should be collected during diffusion MRI session, for distortion correction. In this method, diffusion images are corrected for distortion first, followed by rigid registration of MPRAGE and diffusion image. This method is computationally cheaper than registration based correction and can be run on machines with lower memory. BDP requires the input fieldmap in units of radian/second. Users may need to first process the collected fieldmap to convert it in the required units (check additional tools for some limited support). This method can be invoked by using flag
--fieldmap-correctionand requires echo-spacing of the diffusion EPI scan in units of seconds via flag
--echo-spacing=<t>. Please go through all “Fieldmap Flags” on BDP Flag page for important note about field of view of diffusion and fieldmap scans.
- No distortion correction: This mode can be useful if in some situation users need not perform distortion correction. In this mode only rigid registration of MPRAGE and diffusion images are performed. This mode can be invoked by use of
Note that all other BDP functionalities, like statistics computation and volume transformation to-and-fro from diffusion and MPRAGE coordinate, works as expected with all the three co-registration modes described above.
Please visit BDP Usage page for usage instructions and BDP Flags page for detailed flag description.