DTI related fixes.

Author: chrisgorgo

nipype/workflows/dmri/fsl/epi.py

@@ -241,7 +241,7 @@ def create_eddy_correct_pipeline(name='eddy_correct'):
     split = pe.Node(fsl.Split(dimension='t'), name='split')
     pick_ref = pe.Node(niu.Select(), name='pick_ref')
     coregistration = pe.MapNode(fsl.FLIRT(no_search=True, padding_size=1,
-                                dof=12, interp='spline'), name='coregistration', iterfield=['in_file'])
+                                interp='trilinear'), name='coregistration', iterfield=['in_file'])
     merge = pe.Node(fsl.Merge(dimension='t'), name='merge')
     outputnode = pe.Node(
         niu.IdentityInterface(fields=['eddy_corrected']),

nipype/workflows/dmri/fsl/tests/test_dti.py

@@ -42,11 +42,11 @@ def test_create_bedpostx_pipeline():
     original_bedpostx.inputs.bvecs = bvecs_file
     original_bedpostx.inputs.bvals = bvals_file
     original_bedpostx.inputs.environ['FSLPARALLEL'] = ""
-    original_bedpostx.inputs.fibres = 2
-    original_bedpostx.inputs.weight = 1
-    original_bedpostx.inputs.burn_period = 1000
-    original_bedpostx.inputs.jumps = 1250
-    original_bedpostx.inputs.sampling = 25
+    original_bedpostx.inputs.n_fibres = 2
+    original_bedpostx.inputs.fudge = 1
+    original_bedpostx.inputs.burn_in = 1000
+    original_bedpostx.inputs.n_jumps = 1250
+    original_bedpostx.inputs.sample_every = 25
 
     test_f1 = pe.Node(util.AssertEqual(), name="mean_f1_test")
     test_f2 = pe.Node(util.AssertEqual(), name="mean_f2_test")

nipype/workflows/dmri/fsl/tests/test_tbss.py

@@ -116,7 +116,7 @@ def _tbss_test_helper(estimate_skeleton):
     pipeline.connect(tbss, 'tbss4.outputnode.skeleton_mask', tbss4_test_mean_FA_skeleton_mask, 'volume1')
     pipeline.connect(tbss4_original_datasource, 'mean_FA_skeleton_mask', tbss4_test_mean_FA_skeleton_mask, 'volume2')
 
-    pipeline.run(plugin='Linear')
+    pipeline.run(plugin='MultiProc')
     os.chdir(old_dir)
     shutil.rmtree(test_dir)