fix: pass in cortex mask to apply workflow

Author: mgxd

nibabies/workflows/anatomical/apply.py

@@ -62,6 +62,7 @@ def init_infant_anat_apply_wf(
                 'white',
                 'pial',
                 'midthickness',
+                'cortex_mask',
                 reg_sphere,
                 # template workflow inputs
                 'std_t1w',
@@ -235,6 +236,7 @@ def init_infant_anat_apply_wf(
                     (reg_sphere, 'inputnode.sphere_reg_fsLR'),
                 ]),
                 (inputnode, morph_grayords_wf, [
+                    ('cortex_mask', 'inputnode.roi'),
                     ('midthickness', 'inputnode.midthickness'),
                     (reg_sphere, 'inputnode.sphere_reg_fsLR'),
                 ]),

nibabies/workflows/base.py

@@ -534,6 +534,7 @@ def init_single_subject_wf(
                 ('outputnode.white', 'inputnode.white'),
                 ('outputnode.pial', 'inputnode.pial'),
                 ('outputnode.midthickness', 'inputnode.midthickness'),
+                ('outputnode.cortex_mask', 'inputnode.cortex_mask'),
                 (f'outputnode.{reg_sphere}', f'inputnode.{reg_sphere}'),
                 ('outputnode.sulc', 'inputnode.sulc'),
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),