WIP: Add atlas support #129
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This PR adds support for using atlases existing on templateflow. It extends the CLI with the --atlas flag, and has a config file in /data/atlas/config.json providing the necessary mappings between templateflow and the files needed for PETPrep. The workflow estimates the transform from anatomical space to the template space, or collects previously estimated transform derivatives. If the transforms cannot be collected, it adds the template to the --output-spaces. When the transform from template space to anatomical space has been estimated, if will register the corresponding dseg.nii.gz file to anatomical space, from where it can be used in a similar way as the segmentations used with the --seg, providing subject-specific segmentations in anatomical space.
The output of the atlas workflow is the segmentation/atlas dseg file in anatomical space, along with a morph file containing the volumes of each region.