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FIX: Clean up default output space handling #196

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Merged
merged 1 commit into from
Mar 24, 2022
Merged

FIX: Clean up default output space handling #196

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17 changes: 9 additions & 8 deletions nibabies/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -697,16 +697,17 @@ def init_spaces(checkpoint=True):
if checkpoint and not spaces.is_cached():
spaces.checkpoint()

if workflow.age_months is not None:
# NiBabies' default volumetric space is MNIInfant
# However, if age is not provided, do not add a default template as we cannot
# make an assumption about cohort.
if (
not any(s.space == 'MNIInfant' for s in spaces.references)
and workflow.age_months is not None
):
from .utils.misc import cohort_by_months

# cohort workaround
if any(
"MNIInfant" in space.split(":")[0]
for space in spaces.get_spaces(nonstandard=False, dim=(3,))
):
cohort = cohort_by_months("MNIInfant", workflow.age_months)
spaces.add(Reference("MNIInfant", {"cohort": cohort}))
cohort = cohort_by_months("MNIInfant", workflow.age_months)
spaces.add(Reference, {"cohort": cohort})

# Ensure user-defined spatial references for outputs are correctly parsed.
# Certain options require normalization to a space not explicitly defined by users.
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