FIX: DTITK nonlinear workflow origin reslicing

nipype/interfaces/dcm2nii.py

@@ -264,7 +264,7 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
         position=-1,
         copyfile=False,
         mandatory=True,
-        desc=('A set of filenames to be converted. Note that the current ' 
+        desc=('A set of filenames to be converted. Note that the current '
               'version (1.0.20180328) of dcm2niix converts any files in the '
               'directory. To only convert specific files they should be in an '
               'isolated directory'),

nipype/tests/test_nipype.py

@@ -12,7 +12,7 @@ def test_nipype_info():
     assert exception_not_raised
 
 
-@pytest.mark.skipif(not get_nipype_gitversion(), 
+@pytest.mark.skipif(not get_nipype_gitversion(),
                     reason="not able to get version from get_nipype_gitversion")
 def test_git_hash():
     # removing the first "g" from gitversion

nipype/workflows/dmri/dtitk/tensor_registration.py

@@ -52,10 +52,11 @@ def diffeomorphic_tensor_pipeline(name='DiffeoTen',
                                   params={'array_size': (128, 128, 64)}):
     """
     Workflow that performs a diffeomorphic registration
-    (Rigid and Affine follwed by Diffeomorphic)
+    (Rigid and Affine followed by Diffeomorphic)
     Note: the requirements for a diffeomorphic registration specify that
     the dimension 0 is a power of 2 so images are resliced prior to
-    registration
+    registration. Remember to move origin and reslice prior to applying xfm to
+    another file!
 
     Example
     -------
@@ -75,7 +76,9 @@ def diffeomorphic_tensor_pipeline(name='DiffeoTen',
                          fields=['out_file', 'out_file_xfm',
                                  'fixed_resliced', 'moving_resliced']),
                          name='outputnode')
-
+    origin_node_fixed = pe.Node(dtitk.TVAdjustVoxSp(origin=(0, 0, 0)),
+                                name='origin_node_fixed')
+    origin_node_moving = origin_node_fixed.clone(name='origin_node_moving')
     reslice_node_pow2 = pe.Node(dtitk.TVResample(
                                 origin=(0, 0, 0),
                                 array_size=params['array_size']),
@@ -92,14 +95,23 @@ def diffeomorphic_tensor_pipeline(name='DiffeoTen',
     compose_xfm_node = pe.Node(dtitk.ComposeXfm(), name='compose_xfm_node')
     apply_xfm_node = pe.Node(dtitk.DiffeoSymTensor3DVol(),
                              name='apply_xfm_node')
+    adjust_vs_node_to_input = pe.Node(dtitk.TVAdjustVoxSp(),
+                                      name='adjust_vs_node_to_input')
+    reslice_node_to_input = pe.Node(dtitk.TVResample(),
+                                    name='reslice_node_to_input')
+    input_fa = pe.Node(dtitk.TVtool(in_flag='fa'), name='input_fa')
 
     wf = pe.Workflow(name=name)
 
+    # calculate input FA image for origin reference
+    wf.connect(inputnode, 'fixed_file', input_fa, 'in_file')
     # Reslice input images
-    wf.connect(inputnode, 'fixed_file', reslice_node_pow2, 'in_file')
+    wf.connect(inputnode, 'fixed_file', origin_node_fixed, 'in_file')
+    wf.connect(origin_node_fixed, 'out_file', reslice_node_pow2, 'in_file')
     wf.connect(reslice_node_pow2, 'out_file',
                reslice_node_moving, 'target_file')
-    wf.connect(inputnode, 'moving_file', reslice_node_moving, 'in_file')
+    wf.connect(inputnode, 'moving_file', origin_node_moving, 'in_file')
+    wf.connect(origin_node_moving, 'out_file', reslice_node_moving, 'in_file')
     # Rigid registration
     wf.connect(reslice_node_pow2, 'out_file', rigid_node, 'fixed_file')
     wf.connect(reslice_node_moving, 'out_file', rigid_node, 'moving_file')
@@ -118,8 +130,13 @@ def diffeomorphic_tensor_pipeline(name='DiffeoTen',
     # Apply transform
     wf.connect(reslice_node_moving, 'out_file', apply_xfm_node, 'in_file')
     wf.connect(compose_xfm_node, 'out_file', apply_xfm_node, 'transform')
+    # Move origin and reslice to match original fixed input image
+    wf.connect(apply_xfm_node, 'out_file', adjust_vs_node_to_input, 'in_file')
+    wf.connect(input_fa, 'out_file', adjust_vs_node_to_input, 'target_file')
+    wf.connect(adjust_vs_node_to_input, 'out_file', reslice_node_to_input, 'in_file')
+    wf.connect(input_fa, 'out_file', reslice_node_to_input, 'target_file')
     # Send to output
-    wf.connect(apply_xfm_node, 'out_file', outputnode, 'out_file')
+    wf.connect(reslice_node_to_input, 'out_file', outputnode, 'out_file')
     wf.connect(compose_xfm_node, 'out_file', outputnode, 'out_file_xfm')
     wf.connect(reslice_node_pow2, 'out_file', outputnode, 'fixed_resliced')
     wf.connect(reslice_node_moving, 'out_file', outputnode, 'moving_resliced')

tools/checkspecs.py

@@ -287,7 +287,7 @@ def test_specs(self, uri):
                         and "requires" not in trait.__dict__\
                         and "xor" not in trait.__dict__:
                     if trait.trait_type.__class__.__name__ is "Range"\
-                            and trait.default == trait.trait_type._low: 
+                            and trait.default == trait.trait_type._low:
                         continue
                     bad_specs.append(
                         [uri, c, 'Inputs', traitname, 'default value is set, no value for usedefault'])