Merge pull request #329 from mgxd/enh/recon-desc

FIX: Clean up MCRIBS outputs

nibabies/cli/parser.py

@@ -761,6 +761,12 @@ def parse_args(args=None, namespace=None):
         # Ensure the directory is created
         config.execution.mcribs_dir.mkdir(exist_ok=True, parents=True)
 
+        # While waiting to confirm licensing for TemplateFlow distribution,
+        # include templates used to bring data to fsLR space
+        from nibabies.utils.misc import save_fsLR_mcribs
+
+        save_fsLR_mcribs(config.execution.mcribs_dir)
+
     # Wipe out existing work_dir
     if opts.clean_workdir and work_dir.exists():
         from niworkflows.utils.misc import clean_directory

nibabies/utils/misc.py

@@ -1,11 +1,14 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Miscellaneous utilities."""
+from __future__ import annotations
 
+import shutil
 from pathlib import Path
 from typing import Union
 
-from .. import __version__
+from nibabies import __version__
+from nibabies.data import load_resource
 
 
 def fix_multi_source_name(in_files):
@@ -135,3 +138,17 @@ def get_file(pkg: str, src_path: Union[str, Path]) -> str:
     ref = files(pkg) / str(src_path)
     fl = file_manager.enter_context(as_file(ref))
     return str(fl)
+
+
+def save_fsLR_mcribs(mcribs_dir: str | Path) -> None:
+    template_dir = Path(mcribs_dir) / 'templates_fsLR'
+    template_dir.mkdir(exist_ok=True)
+
+    for src in load_resource('atlases').glob('*sphere.surf.gii'):
+        if not (dst := (template_dir / src.name)).exists():
+            try:
+                shutil.copyfile(src, dst)
+            except Exception:
+                import warnings
+
+                warnings.warn(f"Could not save {src.name} to MCRIBS outputs")

nibabies/workflows/anatomical/base.py

@@ -196,12 +196,12 @@ def init_infant_anat_wf(
 
     # Define output workflows
     anat_reports_wf = init_anat_reports_wf(
-        surface_recon=freesurfer, output_dir=output_dir, sloppy=sloppy
+        surface_recon=recon_method, output_dir=output_dir, sloppy=sloppy
     )
 
     anat_derivatives_wf = init_anat_derivatives_wf(
         bids_root=bids_root,
-        surface_recon=freesurfer,
+        surface_recon=recon_method,
         num_t1w=num_t1w,
         num_t2w=num_t2w,
         output_dir=output_dir,
@@ -427,7 +427,7 @@ def init_infant_anat_wf(
             ])
             # fmt:on
 
-    if not freesurfer:
+    if not recon_method:
         return wf
 
     if recon_method == 'freesurfer':

nibabies/workflows/anatomical/outputs.py

@@ -367,9 +367,9 @@ def init_anat_derivatives_wf(
                 "anat_tpms",
                 "anat2std_xfm",
                 "std2anat_xfm",
+                # FS
                 "anat2fsnative_xfm",
                 "fsnative2anat_xfm",
-                # FS
                 "anat_fs_aseg",
                 "anat_fs_aparc",
                 "anat_ribbon",
@@ -766,7 +766,7 @@ def init_anat_derivatives_wf(
     ds_reg_fsLR = pe.MapNode(
         DerivativesDataSink(
             base_directory=output_dir,
-            space="fsLR",
+            space="dHCP" if surface_recon == "mcribs" else "fsLR",
             desc="reg",
             suffix="sphere",
             extension=".surf.gii",

nibabies/workflows/anatomical/resampling.py

@@ -62,8 +62,8 @@ def init_anat_fsLR_resampling_wf(
         atlases = load_resource('atlases')
         # use dHCP 32k fsLR instead
         select_surfaces.inputs.template_spheres = [
-            str(atlases / 'dHCP' / 'dHCP.week42.L.sphere.surf.gii'),
-            str(atlases / 'dHCP' / 'dHCP.week42.R.sphere.surf.gii'),
+            str(atlases / 'tpl-dHCP_space-fsLR_hemi-L_den-32k_desc-week42_sphere.surf.gii'),
+            str(atlases / 'tpl-dHCP_space-fsLR_hemi-R_den-32k_desc-week42_sphere.surf.gii'),
         ]
     else:
         select_surfaces.inputs.template_spheres = [
@@ -242,8 +242,8 @@ def init_mcribs_morph_grayords_wf(
 
     atlases = load_resource('atlases')
     resample.inputs.new_sphere = [  # 32k
-        str(atlases / 'dHCP' / 'dHCP.week42.L.sphere.surf.gii'),
-        str(atlases / 'dHCP' / 'dHCP.week42.R.sphere.surf.gii'),
+        str(atlases / 'tpl-dHCP_space-fsLR_hemi-L_den-32k_desc-week42_sphere.surf.gii'),
+        str(atlases / 'tpl-dHCP_space-fsLR_hemi-R_den-32k_desc-week42_sphere.surf.gii'),
     ] * 3
     resample.inputs.out_file = [
         f"space-fsLR_hemi-{h}_den-{grayord_density}_{morph}.shape.gii"

nibabies/workflows/anatomical/surfaces.py

@@ -252,12 +252,12 @@ def init_mcribs_sphere_reg_wf(*, name="mcribs_sphere_reg_wf"):
         name="project_unproject",
     )
     project_unproject.inputs.sphere_project_to = [
-        atlases / 'mcribs' / 'lh.sphere.reg2.surf.gii',
-        atlases / 'mcribs' / 'rh.sphere.reg2.surf.gii',
+        atlases / 'tpl-fsaverage_hemi-L_den-41k_desc-reg_sphere.surf.gii',
+        atlases / 'tpl-fsaverage_hemi-R_den-41k_desc-reg_sphere.surf.gii',
     ]
     project_unproject.inputs.sphere_unproject_from = [
-        atlases / 'mcribs' / 'lh.sphere.reg.dHCP42.surf.gii',
-        atlases / 'mcribs' / 'rh.sphere.reg.dHCP42.surf.gii',
+        atlases / 'tpl-dHCP_space-fsaverage_hemi-L_den-41k_desc-reg_sphere.surf.gii',
+        atlases / 'tpl-dHCP_space-fsaverage_hemi-R_den-41k_desc-reg_sphere.surf.gii',
     ]
 
     # fmt:off

nibabies/workflows/bold/resampling.py

@@ -592,8 +592,8 @@ def init_bold_fsLR_resampling_wf(
         atlases = load_resource('atlases')
         # use dHCP 32k fsLR instead
         select_surfaces.inputs.template_spheres = [
-            str(atlases / 'dHCP' / 'dHCP.week42.L.sphere.surf.gii'),
-            str(atlases / 'dHCP' / 'dHCP.week42.R.sphere.surf.gii'),
+            str(atlases / 'tpl-dHCP_space-fsLR_hemi-L_den-32k_desc-week42_sphere.surf.gii'),
+            str(atlases / 'tpl-dHCP_space-fsLR_hemi-R_den-32k_desc-week42_sphere.surf.gii'),
         ]
     else:
         select_surfaces.inputs.template_spheres = [