ENH/DEP: Change flag for surface processing

- Add new flag `--surface-recon-method` to support various surface processing pipelines:
  - FreeSurfer's `recon-all` and `infant_recon_all`, as well as a new `mcribs` option.
- Deprecate redundant `--force-reconall` flag.

Author: mgxd

nibabies/cli/parser.py

@@ -664,6 +664,12 @@ def _slice_time_ref(value, parser):
         action="store_true",
         help="Force traditional FreeSurfer surface reconstruction.",
     )
+    g_baby.add_argument(
+        "--surface-recon-method",
+        choices=("infantfs", "freesurfer", "mcribs"),
+        default="infantfs",
+        help="Method to use for surface reconstruction",
+    )
     return parser
 
 
@@ -674,6 +680,14 @@ def parse_args(args=None, namespace=None):
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
 
+    # Deprecations
+    if opts.force_reconall:
+        config.loggers.cli.warning(
+            "--force-reconall is deprecated and will be removed in a future release."
+            "To run traditional `recon-all`, use `--surface-recon-method freesurfer` instead."
+        )
+        opts.surface_recon_method = "freesurfer"
+
     if opts.config_file:
         skip = {} if opts.reports_only else {"execution": ("run_uuid",)}
         config.load(opts.config_file, skip=skip)

nibabies/config.py

@@ -543,8 +543,6 @@ class workflow(_Config):
     """Remove the mean from fieldmaps."""
     force_syn = None
     """Run *fieldmap-less* susceptibility-derived distortions estimation."""
-    force_reconall = False
-    """Force traditional FreeSurfer surface reconstruction instead of infant version."""
     hires = None
     """Run FreeSurfer ``recon-all`` with the ``-hires`` flag."""
     ignore = None
@@ -578,6 +576,8 @@ class workflow(_Config):
     spaces = None
     """Keeps the :py:class:`~niworkflows.utils.spaces.SpatialReferences`
     instance keeping standard and nonstandard spaces."""
+    surface_recon_method = "infantfs"
+    """Method to use for surface reconstruction."""
     topup_max_vols = 5
     """Maximum number of volumes to use with TOPUP, per-series (EPI or BOLD)."""
     use_aroma = None