FIX: Purge --ants-affine-init

Author: mgxd

README.md

@@ -289,17 +289,11 @@ Other options:
                         (default: False)
 
 NiBabies specific options:
-  --anat-modality {t1w,t2w}
-                        Preferred modality to use for anatomical processing
-                        (default: t1w)
   --age-months AGE_MONTHS
                         Age in months (default: None)
   --segmentation-atlases-dir SEGMENTATION_ATLASES_DIR
                         Directory containing precalculated segmentations to
                         use for JointLabelFusion. (default: None)
-  --ants-affine-init {random,search}
-                        TESTING: Customize parameters for ants AI
-                        initialization. (default: None)
 ```
 
 </details>

nibabies/cli/parser.py

@@ -594,11 +594,6 @@ def _bids_filter(value):
         "--segmentation-atlases-dir",
         help="Directory containing precalculated segmentations to use for JointLabelFusion."
     )
-    g_baby.add_argument(
-        "--ants-affine-init",
-        choices=("random", "search"),
-        help="TESTING: Customize parameters for ants AI initialization."
-    )
     return parser
 
 

nibabies/config.py

@@ -491,10 +491,6 @@ class workflow(_Config):
     """Age (in months)"""
     anat_only = False
     """Execute the anatomical preprocessing only."""
-    anat_modality = "t1w"
-    """Structural MRI modality"""
-    ants_affine_init = None
-    """Customize ants affine initialization"""
     aroma_err_on_warn = None
     """Cast AROMA warnings to errors."""
     aroma_melodic_dim = None

nibabies/workflows/anatomical/brain_extraction.py

@@ -257,11 +257,6 @@ def init_infant_brain_extraction_wf(
             verbose=True,
         )
 
-        if ants_affine_init == "random":
-            ants_kwargs["metric"] = ("Mattes", 32, "Random", 0.2)
-        if ants_affine_init == "search":
-            ants_kwargs["search_grid"] = (20, (20, 40, 40))
-
         init_aff = pe.Node(
             AI(**ants_kwargs),
             name="init_aff",

nibabies/workflows/base.py

@@ -286,7 +286,7 @@ def init_single_subject_wf(subject_id):
 
     # Preprocessing of anatomical (includes registration to UNCInfant)
     anat_preproc_wf = init_infant_anat_wf(
-        ants_affine_init=config.workflow.ants_affine_init or True,
+        ants_affine_init=True,
         age_months=config.workflow.age_months,
         anat_modality=anat_modality,
         t1w=subject_data["t1w"],