ENH: Minimize clipping prior to surface reconstruction with MCRIBS

nibabies/workflows/anatomical/fit.py

@@ -1030,7 +1030,6 @@ def init_infant_anat_fit_wf(
         surface_recon_wf = init_mcribs_surface_recon_wf(
             omp_nthreads=omp_nthreads,
             use_aseg=bool(anat_aseg),
-            use_mask=True,
             precomputed=precomputed,
             mcribs_dir=str(config.execution.mcribs_dir),
         )
@@ -1040,10 +1039,8 @@ def init_infant_anat_fit_wf(
                 ('subject_id', 'inputnode.subject_id'),
                 ('subjects_dir', 'inputnode.subjects_dir'),
             ]),
-            (t2w_buffer, surface_recon_wf, [
-                ('t2w_preproc', 'inputnode.t2w'),
-                ('t2w_mask', 'inputnode.in_mask'),
-            ]),
+            (t2w_validate, surface_recon_wf, [('out_file', 'inputnode.t2w')]),
+            (t2w_buffer, surface_recon_wf, [('t2w_mask', 'inputnode.in_mask'),]),
             (aseg_buffer, surface_recon_wf, [
                 ('anat_aseg', 'inputnode.in_aseg'),
             ]),
@@ -1950,7 +1947,6 @@ def init_infant_single_anat_fit_wf(
         surface_recon_wf = init_mcribs_surface_recon_wf(
             omp_nthreads=omp_nthreads,
             use_aseg=bool(anat_aseg),
-            use_mask=True,
             precomputed=precomputed,
             mcribs_dir=str(config.execution.mcribs_dir),
         )
@@ -1960,10 +1956,8 @@ def init_infant_single_anat_fit_wf(
                 ('subject_id', 'inputnode.subject_id'),
                 ('subjects_dir', 'inputnode.subjects_dir'),
             ]),
-            (anat_buffer, surface_recon_wf, [
-                ('anat_preproc', 'inputnode.t2w'),
-                ('anat_mask', 'inputnode.in_mask'),
-            ]),
+            (anat_validate, surface_recon_wf, [('out_file', 'inputnode.t2w')]),
+            (anat_buffer, surface_recon_wf, [('anat_mask', 'inputnode.in_mask')]),
             (aseg_buffer, surface_recon_wf, [
                 ('anat_aseg', 'inputnode.in_aseg'),
             ]),

nibabies/workflows/anatomical/surfaces.py

@@ -6,6 +6,7 @@
 from nipype.interfaces import freesurfer as fs
 from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
+from nipype.interfaces.ants import N4BiasFieldCorrection
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow
 from niworkflows.interfaces.freesurfer import (
@@ -14,6 +15,7 @@
 from niworkflows.interfaces.freesurfer import (
     PatchedRobustRegister as RobustRegister,
 )
+from niworkflows.interfaces.morphology import BinaryDilation
 from niworkflows.interfaces.patches import FreeSurferSource
 from smriprep.interfaces.freesurfer import MakeMidthickness
 from smriprep.interfaces.workbench import SurfaceResample
@@ -42,7 +44,6 @@ def init_mcribs_surface_recon_wf(
     *,
     omp_nthreads: int,
     use_aseg: bool,
-    use_mask: bool,
     precomputed: dict,
     mcribs_dir: str | None = None,
     name: str = 'mcribs_surface_recon_wf',
@@ -119,7 +120,7 @@ def init_mcribs_surface_recon_wf(
     fs_to_mcribs = pe.Node(MapLabels(mappings=fs2mcribs), name='fs_to_mcribs')
 
     t2w_las = pe.Node(ReorientImage(target_orientation='LAS'), name='t2w_las')
-    seg_las = t2w_las.clone(name='seg_las')
+    seg_las = pe.Node(ReorientImage(target_orientation='LAS'), name='seg_las')
 
     mcribs_recon = pe.Node(
         MCRIBReconAll(
@@ -136,17 +137,25 @@ def init_mcribs_surface_recon_wf(
         mcribs_recon.inputs.outdir = mcribs_dir
         mcribs_recon.config = {'execution': {'remove_unnecessary_outputs': False}}
 
-    if use_mask:
-        # If available, dilated mask and use in recon-neonatal-cortex
-        from niworkflows.interfaces.morphology import BinaryDilation
-
-        mask_dil = pe.Node(BinaryDilation(radius=3), name='mask_dil')
-        mask_las = t2w_las.clone(name='mask_las')
-        workflow.connect([
-            (inputnode, mask_dil, [('in_mask', 'in_mask')]),
-            (mask_dil, mask_las, [('out_mask', 'in_file')]),
-            (mask_las, mcribs_recon, [('out_file', 'mask_file')]),
-        ])  # fmt:skip
+    # dilated mask and use in recon-neonatal-cortex
+    mask_dil = pe.Node(BinaryDilation(radius=3), name='mask_dil')
+    mask_las = pe.Node(ReorientImage(target_orientation='LAS'), name='mask_las')
+
+    # N4BiasCorrection occurs in MCRIBTissueSegMCRIBS (which is skipped)
+    # Run it (with mask to rescale intensities) prior injection
+    n4_mcribs = pe.Node(
+        N4BiasFieldCorrection(
+            dimension=3,
+            bspline_fitting_distance=200,
+            save_bias=True,
+            copy_header=True,
+            n_iterations=[50] * 5,
+            convergence_threshold=1e-7,
+            rescale_intensities=True,
+            shrink_factor=4,
+        ),
+        name='n4_mcribs',
+    )
 
     mcribs_postrecon = pe.Node(
         MCRIBReconAll(autorecon_after_surf=True, nthreads=omp_nthreads),
@@ -160,11 +169,16 @@ def init_mcribs_surface_recon_wf(
     workflow.connect([
         (inputnode, t2w_las, [('t2w', 'in_file')]),
         (inputnode, fs_to_mcribs, [('in_aseg', 'in_file')]),
+        (inputnode, mask_dil, [('in_mask', 'in_mask')]),
+        (mask_dil, mask_las, [('out_mask', 'in_file')]),
+        (mask_las, mcribs_recon, [('out_file', 'mask_file')]),
         (fs_to_mcribs, seg_las, [('out_file', 'in_file')]),
         (inputnode, mcribs_recon, [
             ('subjects_dir', 'subjects_dir'),
             ('subject_id', 'subject_id')]),
-        (t2w_las, mcribs_recon, [('out_file', 't2w_file')]),
+        (t2w_las, n4_mcribs, [('out_file', 'input_image')]),
+        (mask_las, n4_mcribs, [('out_file', 'mask_image')]),
+        (n4_mcribs, mcribs_recon, [('output_image', 't2w_file')]),
         (seg_las, mcribs_recon, [('out_file', 'segmentation_file')]),
         (inputnode, mcribs_postrecon, [
             ('subjects_dir', 'subjects_dir'),