Merge pull request #1730 from nipy/chrisfilo-patch-2

Conform with BIDS Derivatives label names

Author: chrisgorgo

nipype/algorithms/confounds.py

@@ -182,7 +182,7 @@ def _run_interface(self, runtime):
         if self.inputs.save_all:
             out_file = self._gen_fname('dvars', ext='tsv')
             np.savetxt(out_file, np.vstack(dvars).T, fmt=b'%0.8f', delimiter=b'\t',
-                       header='std DVARS\tnon-std DVARS\tvx-wise std DVARS')
+                       header='std DVARS\tnon-std DVARS\tvx-wise std DVARS', comments='')
             self._results['out_all'] = out_file
 
         return runtime
@@ -255,7 +255,7 @@ def _run_interface(self, runtime):
             'out_file': op.abspath(self.inputs.out_file),
             'fd_average': float(fd_res.mean())
         }
-        np.savetxt(self.inputs.out_file, fd_res, header='framewise_displacement')
+        np.savetxt(self.inputs.out_file, fd_res, header='FramewiseDisplacement', comments='')
 
         if self.inputs.save_plot:
             tr = None
@@ -364,7 +364,7 @@ def _run_interface(self, runtime):
 
         self._set_header()
         np.savetxt(components_file, components, fmt=b"%.10f", delimiter='\t',
-                   header=self._make_headers(components.shape[1]))
+                   header=self._make_headers(components.shape[1]), comments='')
         return runtime
 
     def _list_outputs(self):

nipype/algorithms/tests/test_confounds.py

@@ -28,10 +28,10 @@ def test_fd():
 
     with open(res.outputs.out_file) as all_lines:
         for line in all_lines:
-            yield assert_in, 'framewise_displacement', line
+            yield assert_in, 'FramewiseDisplacement', line
             break
 
-    yield assert_true, np.allclose(ground_truth, np.loadtxt(res.outputs.out_file), atol=.16)
+    yield assert_true, np.allclose(ground_truth, np.loadtxt(res.outputs.out_file, skiprows=1), atol=.16)
     yield assert_true, np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-2
 
     rmtree(tempdir)

nipype/interfaces/nilearn.py

@@ -48,7 +48,7 @@ class SignalExtractionInputSpec(BaseInterfaceInputSpec):
                                        'with 4D probability maps.')
     include_global = traits.Bool(False, usedefault=True,
                                  desc='If True, include an extra column '
-                                 'labeled "global", with values calculated from the entire brain '
+                                 'labeled "GlobalSignal", with values calculated from the entire brain '
                                  '(instead of just regions).')
     detrend = traits.Bool(False, usedefault=True, desc='If True, perform detrending using nilearn.')
 
@@ -66,7 +66,7 @@ class SignalExtraction(BaseInterface):
     >>> seinterface.inputs.in_file = 'functional.nii'
     >>> seinterface.inputs.label_files = 'segmentation0.nii.gz'
     >>> seinterface.inputs.out_file = 'means.tsv'
-    >>> segments = ['CSF', 'gray', 'white']
+    >>> segments = ['CSF', 'GrayMatter', 'WhiteMatter']
     >>> seinterface.inputs.class_labels = segments
     >>> seinterface.inputs.detrend = True
     >>> seinterface.inputs.include_global = True
@@ -129,7 +129,7 @@ def _process_inputs(self):
             global_label_data = self._4d(global_label_data, label_data.affine)
             global_masker = nl.NiftiLabelsMasker(global_label_data, detrend=self.inputs.detrend)
             maskers.insert(0, global_masker)
-            self.inputs.class_labels.insert(0, 'global')
+            self.inputs.class_labels.insert(0, 'GlobalSignal')
 
         for masker in maskers:
             masker.set_params(detrend=self.inputs.detrend)

nipype/interfaces/tests/test_nilearn.py

@@ -27,8 +27,8 @@ class TestSignalExtraction(unittest.TestCase):
         '4d_label_file': '4dlabels.nii',
         'out_file': 'signals.tsv'
     }
-    labels = ['csf', 'gray', 'white']
-    global_labels = ['global'] + labels
+    labels = ['CSF', 'GrayMatter', 'WhiteMatter']
+    global_labels = ['GlobalSignal'] + labels
 
     def setUp(self):
         self.orig_dir = os.getcwd()