rf: dcm2niix

Author: mgxd

nipype/interfaces/dcm2nii.py

@@ -412,28 +412,35 @@ def _run_interface(self, runtime):
         # may use return code 1 despite conversion
         runtime = super(Dcm2niix, self)._run_interface(
             runtime, correct_return_codes=(0, 1, ))
-        (self.output_files, self.bvecs,
-         self.bvals, self.bids) = self._parse_stdout(runtime.stdout)
+        self._parse_files(self._parse_stdout(runtime.stdout))
         return runtime
 
     def _parse_stdout(self, stdout):
-        outfiles, bvals, bvecs, bids = [], [], [], []
+        filenames = []
         for line in stdout.split("\n"):
             if line.startswith("Convert "):  # output
                 fname = str(re.search('\S+/\S+', line).group(0))
-                fname = os.path.abspath(fname)
-                outtypes = (".nii", ".nii.gz", ".bval", ".bvec", ".json")
-                # search for relevant files, and sort accordingly
-                for fl in search_files(fname, outtypes):
-                    if fl.endswith(".nii") or fl.endswith(".gz"):
-                        outfiles.append(fl)
-                    elif fl.endswith(".bval"):
-                        bvals.append(fl)
-                    elif fl.endswith(".bvec"):
-                        bvecs.append(fl)
-                    elif fl.endswith(".json"):
-                        bids.append(fl)
-        return outfiles, bvecs, bvals, bids
+                filenames.append(os.path.abspath(fname))
+        return filenames
+
+    def _parse_files(self, filenames):
+        outfiles, bvals, bvecs, bids = [], [], [], []
+        outtypes = (".nii", ".nii.gz", ".bval", ".bvec", ".json")
+        for filename in filenames:
+            # search for relevant files, and sort accordingly
+            for fl in search_files(filename, outtypes):
+                if fl.endswith(".nii") or fl.endswith(".gz"):
+                    outfiles.append(fl)
+                elif fl.endswith(".bval"):
+                    bvals.append(fl)
+                elif fl.endswith(".bvec"):
+                    bvecs.append(fl)
+                elif fl.endswith(".json"):
+                    bids.append(fl)
+        self.output_files = outfiles
+        self.bvecs = bvecs
+        self.bvals = bvals
+        self.bids = bids
 
     def _list_outputs(self):
         outputs = self.output_spec().get()