ENH: Add segmentation output to FSL's epi_reg

.zenodo.json

@@ -574,6 +574,10 @@
     {
       "name": "McDermottroe, Conor"
     },
+    {
+      "affiliation": "Institute of Imaging & Computer Vision, RWTH Aachen University, Germany",
+      "name": "Weninger, Leon"
+    },
     {
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
@@ -587,4 +591,4 @@
   ],
   "license": "Apache-2.0",
   "upload_type": "software"
-}
+}

nipype/interfaces/ants/registration.py

@@ -125,7 +125,7 @@ class ANTSOutputSpec(TraitedSpec):
 
 
 class ANTS(ANTSCommand):
-    """ANTS wrapper for registration of images 
+    """ANTS wrapper for registration of images
     (old, use Registration instead)
 
     Examples

nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py

@@ -52,8 +52,8 @@ def test_AntsJointFusion_inputs():
             hash_files=False,
         ),
         out_label_post_prob_name_format=dict(
-            requires=['out_label_fusion', 'out_intensity_fusion_name_format'],
-        ),
+            requires=['out_label_fusion',
+                      'out_intensity_fusion_name_format'], ),
         patch_metric=dict(argstr='-m %s', ),
         patch_radius=dict(
             argstr='-p %s',

nipype/interfaces/fsl/epi.py

@@ -947,6 +947,8 @@ class EpiRegOutputSpec(TraitedSpec):
                     structural space')
     wmseg = File(
         exists=True, desc='white matter segmentation used in flirt bbr')
+    seg = File(
+        exists=True, desc='white matter, gray matter, csf segmentation')
     wmedge = File(exists=True, desc='white matter edges for visualization')
 
 
@@ -1013,6 +1015,8 @@ def _list_outputs(self):
             os.getcwd(), self.inputs.out_base + '_fast_wmedge.nii.gz')
         outputs['wmseg'] = os.path.join(
             os.getcwd(), self.inputs.out_base + '_fast_wmseg.nii.gz')
+        outputs['seg'] = os.path.join(
+            os.getcwd(), self.inputs.out_base + '_fast_seg.nii.gz')
 
         return outputs
 

nipype/interfaces/fsl/tests/test_auto_EpiReg.py

@@ -61,6 +61,7 @@ def test_EpiReg_outputs():
         fullwarp=dict(),
         out_1vol=dict(),
         out_file=dict(),
+        seg=dict(),
         shiftmap=dict(),
         wmedge=dict(),
         wmseg=dict(),

nipype/interfaces/io.py

@@ -124,7 +124,7 @@ def add_traits(base, names, trait_type=None):
 
 
 def _get_head_bucket(s3_resource, bucket_name):
-    """ Try to get the header info of a bucket, in order to 
+    """ Try to get the header info of a bucket, in order to
     check if it exists and its permissions
     """
 

nipype/testing/data/reg_average_cmd

@@ -0,0 +1 @@
+reg_average /filesrv/weninger/code/nipype/nipype/testing/data/avg_out.nii.gz -avg im1.nii im2.nii im3.nii -omp 1

nipype/utils/filemanip.py

@@ -662,7 +662,7 @@ def loadpkl(infile, versioning=False):
 
         return unpkl
 
-    # Unpickling problems    
+    # Unpickling problems
     except Exception as e:
         if not versioning:
             raise e

nipype/utils/tests/test_filemanip.py

@@ -547,7 +547,7 @@ class PickledBreaker:
     def __setstate__(self, d):
         raise Exception()
 
-        
+
 def test_versioned_pklization(tmpdir):
     tmpdir.chdir()
 
@@ -560,7 +560,7 @@ def test_versioned_pklization(tmpdir):
 
             loadpkl('./pickled.pkz', versioning=True)
 
-        
+
 def test_unversioned_pklization(tmpdir):
     tmpdir.chdir()