Merge branch 'master' of https://github.com/nipy/nipype into fix/ersh

Author: mgxd

nipype/interfaces/ants/segmentation.py

@@ -1129,12 +1129,30 @@ def _format_arg(self, opt, spec, val):
             retval = ''
             if not isdefined(self.inputs.out_label_fusion):
                 retval = '-o {0}'.format(self.inputs.out_intensity_fusion_name_format)
+        elif opt == 'atlas_image':
+            atlas_image_cmd = " ".join(
+                ['-g [{0}]'.format(", ".join("'%s'" % fn for fn in ai))
+                                   for ai in self.inputs.atlas_image]
+            )
+            retval = atlas_image_cmd
+        elif opt == 'target_image':
+            target_image_cmd = " ".join(
+                ['-t [{0}]'.format(", ".join("'%s'" % fn for fn in ai))
+                                   for ai in self.inputs.target_image]
+            )
+            retval = target_image_cmd
+        elif opt == 'atlas_segmentation_image':
+            assert len(val) == len(self.inputs.atlas_image), "Number of specified " \
+                "segmentations should be identical to the number of atlas image " \
+                "sets {0}!={1}".format(len(val), len(self.inputs.atlas_image))
+
+            atlas_segmentation_image_cmd = " ".join(
+                ['-l {0}'.format(fn) for fn in self.inputs.atlas_segmentation_image]
+            )
+            retval = atlas_segmentation_image_cmd
         else:
-            if opt == 'atlas_segmentation_image':
-                assert len(val) == len(self.inputs.atlas_image), "Number of specified " \
-                    "segmentations should be identical to the number of atlas image " \
-                    "sets {0}!={1}".format(len(val), len(self.inputs.atlas_image))
-            return super(ANTSCommand, self)._format_arg(opt, spec, val)
+
+            return super(AntsJointFusion, self)._format_arg(opt, spec, val)
         return retval
 
     def _list_outputs(self):

nipype/utils/filemanip.py

@@ -31,6 +31,7 @@
 
 related_filetype_sets = [
     ('.hdr', '.img', '.mat'),
+    ('.nii', '.mat'),
     ('.BRIK', '.HEAD'),
 ]
 

nipype/utils/tests/test_filemanip.py

@@ -324,7 +324,7 @@ def test_json():
         ('/path/test.hdr',  3, ['/path/test.hdr', '/path/test.img', '/path/test.mat']),
         ('/path/test.BRIK', 2, ['/path/test.BRIK', '/path/test.HEAD']),
         ('/path/test.HEAD', 2, ['/path/test.BRIK', '/path/test.HEAD']),
-        ('/path/foo.nii',   1, [])
+        ('/path/foo.nii',   2, ['/path/foo.nii', '/path/foo.mat'])
         ])
 def test_related_files(file, length, expected_files):
     related_files = get_related_files(file)