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The command epi_reg (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide#epi_reg) produces a segmentation map. In the current version of nipype, only the white-matter segmentation can be accessed, the white-matter, gray-matter, csf segmentation map is included in the output specs.
I would suggest adding this segmentation map to the output specs. May I open a pull request for this?