FEAT: Make multi-step registration optional

Author: mgxd

nibabies/cli/parser.py

@@ -758,6 +758,12 @@ def _str_none(val):
         action='store_true',
         help='Replace low intensity voxels in CSF mask with average',
     )
+    g_baby.add_argument(
+        '--multi-step-reg',
+        action='store_true',
+        help='For certain adult templates (MNI152NLin6Asym), perform two step '
+        'registrations (native -> MNIInfant -> template) and concatenate into a single xfm',
+    )
     return parser
 
 

nibabies/config.py

@@ -578,6 +578,9 @@ class workflow(_Config):
     """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
     medial_surface_nan = None
     """Fill medial surface with :abbr:`NaNs (not-a-number)` when sampling."""
+    multi_step_reg = False
+    """Perform multiple registrations (native -> MNIInfant -> template) and concatenate into a
+    single transform"""
     norm_csf = False
     """Replace low intensity voxels in CSF mask with average."""
     project_goodvoxels = False

nibabies/workflows/anatomical/fit.py

@@ -889,9 +889,13 @@ def init_infant_anat_fit_wf(
     concat_xfms = []
     found_xfms = {}
     intermediate = None  # The intermediate space when concatenating xfms - includes cohort
-    intermediate_targets = {
-        'MNI152NLin6Asym',
-    }  # TODO: 'MNI152NLin2009cAsym'
+    intermediate_targets = (
+        {
+            'MNI152NLin6Asym',  # TODO: 'MNI152NLin2009cAsym'
+        }
+        if config.workflow.multi_step_reg
+        else set()
+    )
 
     for template in spaces.get_spaces(nonstandard=False, dim=(3,)):
         # resolution / spec will not differentiate here