ENH: Persist M-CRIB-S output directory when used

Author: mgxd

nibabies/cli/parser.py

@@ -767,6 +767,11 @@ def parse_args(args=None, namespace=None):
             config.execution.nibabies_dir = output_dir
         elif output_layout == "legacy":
             config.execution.nibabies_dir = output_dir / "nibabies"
+    if config.workflow.surface_recon_method == "mcribs":
+        if output_layout == "bids":
+            config.execution.mcribs_dir = output_dir / "sourcedata" / "mcribs"
+        elif output_layout == "legacy":
+            config.execution.mcribs_dir = output_dir / "mcribs"
 
     # Wipe out existing work_dir
     if opts.clean_workdir and work_dir.exists():

nibabies/config.py

@@ -394,6 +394,8 @@ class execution(_Config):
     """Output verbosity."""
     low_mem = None
     """Utilize uncompressed NIfTIs and other tricks to minimize memory allocation."""
+    mcribs_dir = None
+    """M-CRIB-S processing and output directory."""
     md_only_boilerplate = False
     """Do not convert boilerplate from MarkDown to LaTex and HTML."""
     nibabies_dir = None
@@ -439,6 +441,7 @@ class execution(_Config):
         "fs_subjects_dir",
         "layout",
         "log_dir",
+        "mcribs_dir",
         "nibabies_dir",
         "output_dir",
         "segmentation_atlases_dir",

nibabies/workflows/anatomical/base.py

@@ -417,7 +417,10 @@ def init_infant_anat_wf(
     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))
+        surface_recon_wf = init_mcribs_surface_recon_wf(
+            use_aseg=bool(precomp_aseg),
+            mcribs_dir=config.execution.mcribs_dir,  # Needed to preserve runs
+        )
 
     # fmt:off
     wf.connect([