TEST: Smoke-test FSInjectBrainExtracted interface

niworkflows/interfaces/tests/test_freesurfer.py

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+from pathlib import Path
+import numpy as np
+import nibabel as nb
+from ..freesurfer import FSInjectBrainExtracted
+
+
+def test_inject_skullstrip(tmp_path):
+    t1_mgz = tmp_path / 'sub-01' / 'mri' / 'T1.mgz'
+    t1_mgz.parent.mkdir(parents=True)
+    # T1.mgz images are uint8
+    nb.MGHImage(np.ones((5,5,5), dtype=np.uint8), np.eye(4)).to_filename(str(t1_mgz))
+
+    mask_nii = tmp_path / 'mask.nii.gz'
+    # Masks may be in a different space (and need resampling), but should be boolean,
+    # or uint8 in NIfTI
+    nb.Nifti1Image(np.ones((6,6,6), dtype=np.uint8),
+                   np.eye(4)).to_filename(str(mask_nii))
+
+    res = FSInjectBrainExtracted(subjects_dir=str(tmp_path),
+                                 subject_id='sub-01',
+                                 in_brain=str(mask_nii)).run()
+
+    assert Path.exists(tmp_path / 'sub-01' / 'mri' / 'brainmask.auto.mgz')
+    assert Path.exists(tmp_path / 'sub-01' / 'mri' / 'brainmask.mgz')
+
+    # Run a second time to hit "already exists" condition
+    res = FSInjectBrainExtracted(subjects_dir=str(tmp_path),
+                                 subject_id='sub-01',
+                                 in_brain=str(mask_nii)).run()
+