I am trying to use nipype’s pipelines fro dmri artifact correction (those in nipype.workflows.dmri.fsl.artifacts), but am confused about how to concatenate them.
In particular I want to run head motion correction (hmc_pipeline) followed by eddy current correction (ecc_pipeline). (I wan to skip susceptibility artifact correction for now).
I see that ecc_pipeline has an in_xfms input that can come from the output of hmc_pipeline. If I do this, should I provide as input to ecc the diffusion images corrected for head motion of those before motion correction (which assumes that ecc_pipeline will concatenate on its own the transformations from hmc and the one ecc computes)?