ENH: Add segmentation output to FSL's epi_reg (#2661)

* Add segmentation output to FSL's epi_reg
* Update .zenodo.json

Author: weningerleon

.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/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(),