Revisit segmentation directory structure

[mgxd]

Current implementation:

nibabies/nibabies/workflows/anatomical/segmentation.py

Lines 156 to 178 in bfe9bcb

	def _parse_segmentation_atlases(anat_modality, template_dir):
	"""
	Parse segmentation templates directory for anatomical and segmentation files.
	This is currently hardcoded to match DCAN lab templates.
	Will need to rethink standardization for more general cases.
	"""
	from pathlib import Path
	anats, segs = [], []
	for f in Path(template_dir).glob("**/*.nii*"):
	if "Segmentation" in f.name:
	segs.append(str(f.absolute()))
	elif anat_modality in f.name:
	anats.append(str(f.absolute()))
	assert anats
	assert segs
	# there should matching files per template
	assert len(anats) == len(segs)
	return sorted(anats), sorted(segs)

• The validity of the segmentation directory should happen as soon as inputs are processed.
• We should implement a more BIDS-like structure.