Merge pull request #141 from nipreps/add_fs_seed

Add FreeSurfer seed to segmentation workflows

Author: mnoergaard

petprep/config.py

@@ -671,6 +671,8 @@ class seeds(_Config):
     """Seed used for antsRegistration, antsAI, antsMotionCorr"""
     numpy = None
     """Seed used by NumPy"""
+    freesurfer = None
+    """Seed used by FreeSurfer utilities"""
 
     @classmethod
     def init(cls):
@@ -682,6 +684,7 @@ def init(cls):
         # functions to set program specific seeds
         cls.ants = _set_ants_seed()
         cls.numpy = _set_numpy_seed()
+        cls.freesurfer = _set_freesurfer_seed()
 
 
 def _set_ants_seed():
@@ -700,6 +703,13 @@ def _set_numpy_seed():
     return val
 
 
+def _set_freesurfer_seed():
+    """Fix random seed for FreeSurfer utilities"""
+    val = random.randint(1, 65536)
+    os.environ['FREESURFER_RANDOM_SEED'] = str(val)
+    return val
+
+
 def from_dict(settings, init=True, ignore=None):
     """Read settings from a flat dictionary.
 

petprep/interfaces/segmentation.py

@@ -27,6 +27,13 @@
 from nipype.interfaces.freesurfer.petsurfer import GTMSeg
 from nipype.utils.filemanip import fname_presuffix
 
+from .. import config
+
+
+def _set_freesurfer_seed(runtime):
+    runtime.environ['FREESURFER_RANDOM_SEED'] = str(config.seeds.freesurfer)
+    return runtime
+
 
 class SegmentBSInputSpec(BaseInterfaceInputSpec):
     subjects_dir = Directory(exists=True, mandatory=True, desc='FreeSurfer subjects directory')
@@ -143,6 +150,7 @@ class MRISclimbicSeg(CommandLine):
     output_spec = MRISclimbicSegOutputSpec
 
     def _run_interface(self, runtime):
+        _set_freesurfer_seed(runtime)
         outputs = self._list_outputs()
         expected = [outputs['out_file'], outputs['out_stats']]
 
@@ -186,6 +194,7 @@ class SegmentHA_T1(FSCommand):
     output_spec = SegmentHA_T1OutputSpec
 
     def _run_interface(self, runtime):
+        _set_freesurfer_seed(runtime)
         fs_path = os.path.join(self.inputs.subjects_dir, self.inputs.subject_id, 'mri')
         expected = [
             'lh.hippoAmygLabels-T1.v22.FSvoxelSpace.mgz',
@@ -324,6 +333,7 @@ class SegmentGTM(GTMSeg):
     """Run ``gtmseg`` unless outputs already exist."""
 
     def _run_interface(self, runtime):
+        _set_freesurfer_seed(runtime)
         subj_dir = Path(self.inputs.subjects_dir) / self.inputs.subject_id
         seg_file = subj_dir / 'mri' / self.inputs.out_file
         stats_file = subj_dir / 'stats' / Path(self.inputs.out_file).with_suffix('.stats').name
@@ -563,6 +573,10 @@ def _list_outputs(self):
                     outputs[name] = os.path.abspath(value)
         return outputs
 
+    def _run_interface(self, runtime):
+        _set_freesurfer_seed(runtime)
+        return super()._run_interface(runtime)
+
     def _format_arg(self, name, spec, value):
         if name in ('summary_file', 'ctab_out_file', 'avgwf_txt_file'):
             if not isinstance(value, bool):

petprep/interfaces/tests/test_segmentation_interface.py

@@ -1,6 +1,8 @@
 from pathlib import Path
+from types import SimpleNamespace
 
-from ..segmentation import SegmentBS, SegmentGTM, SegmentWM
+from ... import config
+from ..segmentation import MRISclimbicSeg, SegmentBS, SegmentGTM, SegmentWM, _set_freesurfer_seed
 
 
 def test_segmentgtm_skip(tmp_path):
@@ -15,6 +17,24 @@ def test_segmentgtm_skip(tmp_path):
 
     assert res.runtime.returncode == 0
     assert Path(res.outputs.out_file) == subj_dir / 'mri' / 'gtmseg.mgz'
+    assert res.runtime.environ['FREESURFER_RANDOM_SEED'] == str(config.seeds.freesurfer)
+
+
+def test_mrisclimbicseg_seed(tmp_path):
+    subjects_dir = tmp_path / 'subjects'
+    subject_dir = subjects_dir / 'sub-01'
+    subject_dir.mkdir(parents=True)
+
+    out_file = subject_dir / 'sub-01_sclimbic.nii.gz'
+    out_stats = subject_dir / 'sub-01_sclimbic.stats'
+    out_file.write_text('')
+    out_stats.write_text('')
+
+    seg = MRISclimbicSeg(out_file=str(out_file), sd=str(subjects_dir), subjects=['sub-01'])
+    res = seg.run()
+
+    assert res.runtime.returncode == 0
+    assert res.runtime.environ['FREESURFER_RANDOM_SEED'] == str(config.seeds.freesurfer)
 
 
 def _fake_bs_run(self, cmd):
@@ -47,3 +67,11 @@ def test_segmentwm_stdout_stderr(monkeypatch, tmp_path):
     res = seg.run()
     assert res.outputs.stdout == 'wm out'
     assert res.outputs.stderr == 'wm err'
+
+
+def test_set_freesurfer_seed_runtime():
+    runtime = SimpleNamespace(environ={})
+
+    runtime = _set_freesurfer_seed(runtime)
+
+    assert runtime.environ['FREESURFER_RANDOM_SEED'] == str(config.seeds.freesurfer)

petprep/tests/test_config.py

@@ -104,18 +104,21 @@ def test_config_spaces():
 
 
 @pytest.mark.parametrize(
-    ('master_seed', 'ants_seed', 'numpy_seed'), [(1, 17612, 8272), (100, 19094, 60232)]
+    ('master_seed', 'ants_seed', 'numpy_seed', 'freesurfer_seed'),
+    [(1, 17612, 8272, 33433), (100, 19094, 60232, 59629)],
 )
-def test_prng_seed(master_seed, ants_seed, numpy_seed):
+def test_prng_seed(master_seed, ants_seed, numpy_seed, freesurfer_seed):
     """Ensure seeds are properly tracked"""
     seeds = config.seeds
     with patch.dict(os.environ, {}):
         seeds.load({'_random_seed': master_seed}, init=True)
         assert seeds.master == master_seed
         assert seeds.ants == ants_seed
         assert seeds.numpy == numpy_seed
+        assert seeds.freesurfer == freesurfer_seed
         assert os.getenv('ANTS_RANDOM_SEED') == str(ants_seed)
+        assert os.getenv('FREESURFER_RANDOM_SEED') == str(freesurfer_seed)
 
     _reset_config()
-    for seed in ('_random_seed', 'master', 'ants', 'numpy'):
+    for seed in ('_random_seed', 'master', 'ants', 'numpy', 'freesurfer'):
         assert getattr(config.seeds, seed) is None