Merge pull request #3248 from GalBenZvi/patch-1

FIX: Handle changes in CLI structure of mrtrix3.DWIBiasCorrect

Author: effigies

.zenodo.json

@@ -697,6 +697,10 @@
       "affiliation": "Sagol School of Neuroscience, Tel Aviv University",
       "name": "Baratz, Zvi"
     },
+    {
+      "affiliation": "Sagol School of Neuroscience, Tel Aviv University",
+      "name": "Ben-Zvi, Gal"
+    },
     {
       "name": "Matsubara, K"
     },

nipype/interfaces/mrtrix3/preprocess.py

@@ -181,15 +181,17 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
     )
     in_mask = File(argstr="-mask %s", desc="input mask image for bias field estimation")
     use_ants = traits.Bool(
-        argstr="-ants",
+        argstr="ants",
         mandatory=True,
         desc="use ANTS N4 to estimate the inhomogeneity field",
+        position=0,
         xor=["use_fsl"],
     )
     use_fsl = traits.Bool(
-        argstr="-fsl",
+        argstr="fsl",
         mandatory=True,
         desc="use FSL FAST to estimate the inhomogeneity field",
+        position=0,
         xor=["use_ants"],
     )
     bias = File(argstr="-bias %s", desc="bias field")
@@ -224,14 +226,20 @@ class DWIBiasCorrect(MRTrix3Base):
     >>> bias_correct.inputs.in_file = 'dwi.mif'
     >>> bias_correct.inputs.use_ants = True
     >>> bias_correct.cmdline
-    'dwibiascorrect -ants dwi.mif dwi_biascorr.mif'
+    'dwibiascorrect ants dwi.mif dwi_biascorr.mif'
     >>> bias_correct.run()                             # doctest: +SKIP
     """
 
     _cmd = "dwibiascorrect"
     input_spec = DWIBiasCorrectInputSpec
     output_spec = DWIBiasCorrectOutputSpec
-
+    def _format_arg(self, name, trait_spec, value):
+        if name in ("use_ants", "use_fsl"):
+            ver = self.version
+            # Changed in version 3.0, after release candidates
+            if ver is not None and (ver[0] < "3" or ver.startswith("3.0_RC")):
+                return f"-{trait_spec.argstr}"
+        return super()._format_arg(name, trait_spec, value)
 
 class ResponseSDInputSpec(MRTrix3BaseInputSpec):
     algorithm = traits.Enum(

nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py

@@ -58,13 +58,15 @@ def test_DWIBiasCorrect_inputs():
             position=-1,
         ),
         use_ants=dict(
-            argstr="-ants",
+            argstr="ants",
             mandatory=True,
+            position=0,
             xor=["use_fsl"],
         ),
         use_fsl=dict(
-            argstr="-fsl",
+            argstr="fsl",
             mandatory=True,
+            position=0,
             xor=["use_ants"],
         ),
     )