Merge pull request #916 from juhuntenburg/fix/DcmStack

Fix/dcm stack

Author: satra

nipype/interfaces/dcmstack.py

@@ -22,6 +22,7 @@
                                    )
 import nibabel as nb
 from nipype.interfaces.traits_extension import isdefined, Undefined
+import imghdr
 
 have_dcmstack = True
 try:
@@ -83,6 +84,9 @@ class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
                                   "any default exclude filters")
     include_regexes = traits.List(desc="Meta data to include, overriding any "
                                   "exclude filters")
+    force_read = traits.Bool(True, usedefault=True, 
+                             desc=('Force reading files without DICM marker'))
+
 
 class DcmStackOutputSpec(TraitedSpec):
     out_file = File(exists=True)
@@ -125,8 +129,9 @@ def _run_interface(self, runtime):
                                                      include_regexes)
         stack = dcmstack.DicomStack(meta_filter=meta_filter)
         for src_path in src_paths:
-            src_dcm = dicom.read_file(src_path, force=True)
-            stack.add_dcm(src_dcm)
+            if not imghdr.what(src_path)=="gif":
+                src_dcm = dicom.read_file(src_path, force=self.inputs.force_read)
+                stack.add_dcm(src_dcm)
         nii = stack.to_nifti(embed_meta=True)
         nw = NiftiWrapper(nii)
         self.out_path = \

nipype/interfaces/tests/test_auto_DcmStack.py

@@ -7,6 +7,8 @@ def test_DcmStack_inputs():
     ),
     embed_meta=dict(),
     exclude_regexes=dict(),
+    force_read=dict(usedefault=True,
+    ),
     include_regexes=dict(),
     out_ext=dict(usedefault=True,
     ),

nipype/interfaces/tests/test_auto_GroupAndStack.py

@@ -7,6 +7,8 @@ def test_GroupAndStack_inputs():
     ),
     embed_meta=dict(),
     exclude_regexes=dict(),
+    force_read=dict(usedefault=True,
+    ),
     include_regexes=dict(),
     out_ext=dict(usedefault=True,
     ),