ENH: Set MNI Infant as the default output space

Author: mgxd

nibabies/config.py

@@ -684,6 +684,12 @@ def init_spaces(checkpoint=True):
     if checkpoint and not spaces.is_cached():
         spaces.checkpoint()
 
+    if workflow.age_months is not None:
+        from .utils.misc import cohort_by_months
+
+        if "MNIInfant" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
+            cohort = cohort_by_months("MNIInfant", workflow.age_months)
+            spaces.add(Reference("MNIInfant", {"cohort": cohort}))
     # # Add the default standard space if not already present (required by several sub-workflows)
     # if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
     #     spaces.add(Reference("MNI152NLin2009cAsym", {}))
@@ -695,10 +701,9 @@ def init_spaces(checkpoint=True):
     #     # Make sure there's a normalization to FSL for AROMA to use.
     #     spaces.add(Reference("MNI152NLin6Asym", {"res": "2"}))
 
-    cifti_output = workflow.cifti_output
     if workflow.cifti_output:
         # CIFTI grayordinates to corresponding FSL-MNI resolutions.
-        vol_res = "2" if cifti_output == "91k" else "1"
+        vol_res = "2" if workflow.cifti_output == "91k" else "1"
         spaces.add(Reference("fsaverage", {"den": "164k"}))
         spaces.add(Reference("MNI152NLin6Asym", {"res": vol_res}))
 

nibabies/utils/misc.py

@@ -41,9 +41,29 @@ def check_deps(workflow):
 
 
 def cohort_by_months(template, months):
+    """
+    Produce a recommended cohort based on partipants age
+    """
     cohort_key = {
-        'MNIInfant': (2, 5, 8, 11, 14, 17, 21, 27, 33, 44, 60),
-        'UNCInfant': (8, 12, 24),
+        'MNIInfant': (
+            # upper bound of template | cohort
+            2,  # 1
+            5,  # 2
+            8,  # 3
+            11,  # 4
+            14,  # 5
+            17,  # 6
+            21,  # 7
+            27,  # 8
+            33,  # 9
+            44,  # 10
+            60,  # 11
+        ),
+        'UNCInfant': (
+            8,  # 1
+            12,  # 2
+            24,  # 3
+        ),
     }
     ages = cohort_key.get(template)
     if ages is None:
@@ -52,7 +72,6 @@ def cohort_by_months(template, months):
     for cohort, age in enumerate(ages, 1):
         if months <= age:
             return cohort
-
     raise KeyError("Age exceeds all cohorts!")