FIX: Purge --anat-modality

Author: mgxd

README.md

@@ -61,7 +61,7 @@ usage: nibabies [-h] [--version] [--skip_bids_validation]
                 [--reports-only] [--config-file FILE] [--write-graph]
                 [--stop-on-first-crash] [--notrack]
                 [--debug {compcor,registration,fieldmaps,all} [{compcor,registration,fieldmaps,all} ...]]
-                [--sloppy] [--anat-modality {t1w,t2w}]
+                [--sloppy]
                 [--age-months AGE_MONTHS]
                 [--segmentation-atlases-dir SEGMENTATION_ATLASES_DIR]
                 [--ants-affine-init {random,search}]

nibabies/cli/parser.py

@@ -584,12 +584,6 @@ def _bids_filter(value):
 
     # Add new options
     g_baby = parser.add_argument_group("NiBabies specific options")
-    g_baby.add_argument(
-        "--anat-modality",
-        default="t1w",
-        choices=("t1w", "t2w"),
-        help="Preferred modality to use for anatomical processing",
-    )
     g_baby.add_argument(
         "--age-months",
         dest="age_months",

nibabies/workflows/base.py

@@ -152,7 +152,7 @@ def init_single_subject_wf(subject_id):
 
     anat_only = config.workflow.anat_only
     anat_derivatives = config.execution.anat_derivatives
-    anat_modality = config.workflow.anat_modality
+    anat_modality = "t1w" if subject_data["t1w"] else "t2w"
     spaces = config.workflow.spaces
     # Make sure we always go through these two checks
     if not anat_only and not subject_data["bold"]: