Merge pull request #2909 from gpiantoni/master

FIX: parsing of filename in AlignEpiAnatPy when filename does not have +

Author: satra

nipype/interfaces/afni/preprocess.py

@@ -168,15 +168,17 @@ class AlignEpiAnatPy(AFNIPythonCommand):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        anat_prefix = ''.join(
-            self._gen_fname(self.inputs.anat).split('+')[:-1])
-        epi_prefix = ''.join(
-            self._gen_fname(self.inputs.in_file).split('+')[:-1])
+        anat_prefix = self._gen_fname(self.inputs.anat)
+        epi_prefix = self._gen_fname(self.inputs.in_file)
+        if '+' in anat_prefix:
+            anat_prefix = ''.join(anat_prefix.split('+')[:-1])
+        if '+' in epi_prefix:
+            epi_prefix = ''.join(epi_prefix.split('+')[:-1])
         outputtype = self.inputs.outputtype
         if outputtype == 'AFNI':
             ext = '.HEAD'
         else:
-            Info.output_type_to_ext(outputtype)
+            ext = Info.output_type_to_ext(outputtype)
         matext = '.1D'
         suffix = self.inputs.suffix
         if self.inputs.anat2epi:

nipype/interfaces/afni/utils.py

@@ -143,7 +143,7 @@ class AFNItoNIFTI(AFNICommand):
     input_spec = AFNItoNIFTIInputSpec
     output_spec = AFNICommandOutputSpec
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         path, base, ext = split_filename(value)
         if ext.lower() not in ['.nii', '.nii.gz', '.1d', '.1D']:
             ext += '.nii'