ENH: Allow for mcribs surface processing

Author: mgxd

nibabies/workflows/anatomical/base.py

@@ -401,19 +401,23 @@ def init_infant_anat_wf(
     if not freesurfer:
         return wf
 
-    if config.workflow.force_reconall:
+    if config.workflow.surface_recon_method == 'freesurfer':
         from smriprep.workflows.surfaces import init_surface_recon_wf
 
         surface_recon_wf = init_surface_recon_wf(omp_nthreads=omp_nthreads, hires=hires)
-    else:
-        from .surfaces import init_infant_surface_recon_wf
+    elif config.workflow.surface_recon_method == 'infantfs':
+        from .surfaces import init_infantfs_surface_recon_wf
 
         # if running with precomputed aseg, or JLF, pass the aseg along to FreeSurfer
         use_aseg = bool(precomp_aseg or segmentation_atlases)
-        surface_recon_wf = init_infant_surface_recon_wf(
+        surface_recon_wf = init_infantfs_surface_recon_wf(
             age_months=age_months,
             use_aseg=use_aseg,
         )
+    elif config.workflow.surface_recon_method == 'mcribs':
+        from .surfaces import init_mcribs_surface_recon_wf
+
+        surface_recon_wf = init_mcribs_surface_recon_wf(use_aseg=bool(precomp_aseg))
 
     # fmt:off
     wf.connect([

nibabies/workflows/anatomical/surfaces.py

@@ -30,7 +30,13 @@
 ]
 
 
-def init_mcribs_surface_recon_wf(*, mcribs_dir=None, name="mcribs_surface_recon_wf"):
+def init_mcribs_surface_recon_wf(*, use_aseg, mcribs_dir=None, name="mcribs_surface_recon_wf"):
+    """
+    Reconstruct cortical surfaces using the M-CRIB-S pipeline.
+
+    This workflow injects a precomputed segmentation into the M-CRIB-S pipeline, bypassing the
+    DrawEM segmentation step that is normally performed.
+    """
     from niworkflows.interfaces.nibabel import MapLabels, ReorientImage
 
     from ...interfaces.mcribs import MCRIBReconAll
@@ -136,6 +142,7 @@ def init_mcribs_surface_recon_wf(*, mcribs_dir=None, name="mcribs_surface_recon_
     # fmt:on
     return wf
 
+
 from nipype.interfaces import fsl
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
@@ -144,7 +151,9 @@ def init_mcribs_surface_recon_wf(*, mcribs_dir=None, name="mcribs_surface_recon_
 from ...interfaces.workbench import CreateSignedDistanceVolume
 
 
-def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_surface_recon_wf"):
+def init_infantfs_surface_recon_wf(
+    *, age_months, use_aseg=False, name="infantfs_surface_recon_wf"
+):
     from nibabies.interfaces.freesurfer import InfantReconAll
 
     # Synchronized inputs to smriprep.workflows.surfaces.init_surface_recon_wf