[ENH]: Add functions to mrtrix3 interface

.zenodo.json

@@ -891,16 +891,6 @@
       "name": "Mihai, Paul Glad",
       "orcid": "0000-0001-5715-6442"
     },
-    {
-      "affiliation": "Department of Psychology, Stanford University",
-      "name": "Gorgolewski, Krzysztof J.",
-      "orcid": "0000-0003-3321-7583"
-    },
-    {
-      "affiliation": "MIT, HMS",
-      "name": "Ghosh, Satrajit",
-      "orcid": "0000-0002-5312-6729"
-    },
     {
       "affiliation": "University of Tübingen and MPI for Biological Cybernertics",
       "name": "Bannert, Michael M.",
@@ -909,13 +899,27 @@
     {
       "affiliation": "Research Centre Juelich",
       "name": "Wu, Jianxiao",
-      "orcid": "0000-0002-4866-272X",
+      "orcid": "0000-0002-4866-272X"
+    },
+    {
+      "affiliation": "Department of Neurology, BG-University Hospital Bergmannsheil Bochum, Germany",
+      "name": "Butry, Lionel"
     },
     {
       "affiliation": "Lund University",
       "name": "Anijärv, Toomas Erik",
-      "orcid": "0000-0002-3650-4230",
+      "orcid": "0000-0002-3650-4230"
+    },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Gorgolewski, Krzysztof J.",
+      "orcid": "0000-0003-3321-7583"
     },
+    {
+      "affiliation": "MIT, HMS",
+      "name": "Ghosh, Satrajit",
+      "orcid": "0000-0002-5312-6729"
+    }
   ],
   "keywords": [
     "neuroimaging",

nipype/interfaces/mrtrix3/__init__.py

@@ -30,4 +30,7 @@
     SHConv,
     TensorMetrics,
     TransformFSLConvert,
+    MaskFilter,
+    MTNormalise,
+    Generate5tt2gmwmi,
 )

nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py

@@ -37,7 +37,6 @@ def test_Generate5tt_inputs():
         ),
         in_file=dict(
             argstr="%s",
-            extensions=None,
             mandatory=True,
             position=-2,
         ),

nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt2gmwmi.py

@@ -0,0 +1,79 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..utils import Generate5tt2gmwmi
+
+
+def test_Generate5tt2gmwmi_inputs():
+    input_map = dict(
+        args=dict(
+            argstr="%s",
+        ),
+        bval_scale=dict(
+            argstr="-bvalue_scaling %s",
+        ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        grad_file=dict(
+            argstr="-grad %s",
+            extensions=None,
+            xor=["grad_fsl"],
+        ),
+        grad_fsl=dict(
+            argstr="-fslgrad %s %s",
+            xor=["grad_file"],
+        ),
+        in_bval=dict(
+            extensions=None,
+        ),
+        in_bvec=dict(
+            argstr="-fslgrad %s %s",
+            extensions=None,
+        ),
+        in_file=dict(
+            argstr="%s",
+            extensions=None,
+            mandatory=True,
+            position=-2,
+        ),
+        mask_in=dict(
+            argstr="-mask_in %s",
+            extensions=None,
+            position=-3,
+        ),
+        mask_out=dict(
+            argstr="%s",
+            extensions=None,
+            mandatory=True,
+            position=-1,
+        ),
+        nthreads=dict(
+            argstr="-nthreads %d",
+            nohash=True,
+        ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
+    )
+    inputs = Generate5tt2gmwmi.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_Generate5tt2gmwmi_outputs():
+    output_map = dict(
+        mask_out=dict(
+            extensions=None,
+        ),
+    )
+    outputs = Generate5tt2gmwmi.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/mrtrix3/tests/test_auto_MTNormalise.py

@@ -0,0 +1,103 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..utils import MTNormalise
+
+
+def test_MTNormalise_inputs():
+    input_map = dict(
+        args=dict(
+            argstr="%s",
+        ),
+        bval_scale=dict(
+            argstr="-bvalue_scaling %s",
+        ),
+        csf_fod=dict(
+            argstr="%s",
+            extensions=None,
+            position=5,
+        ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        gm_fod=dict(
+            argstr="%s",
+            extensions=None,
+            position=3,
+        ),
+        grad_file=dict(
+            argstr="-grad %s",
+            extensions=None,
+            xor=["grad_fsl"],
+        ),
+        grad_fsl=dict(
+            argstr="-fslgrad %s %s",
+            xor=["grad_file"],
+        ),
+        in_bval=dict(
+            extensions=None,
+        ),
+        in_bvec=dict(
+            argstr="-fslgrad %s %s",
+            extensions=None,
+        ),
+        mask=dict(
+            argstr="-mask %s",
+            extensions=None,
+            position=-1,
+        ),
+        nthreads=dict(
+            argstr="-nthreads %d",
+            nohash=True,
+        ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
+        out_file_csf=dict(
+            argstr="%s",
+            extensions=None,
+            position=6,
+        ),
+        out_file_gm=dict(
+            argstr="%s",
+            extensions=None,
+            position=4,
+        ),
+        out_file_wm=dict(
+            argstr="%s",
+            extensions=None,
+            position=2,
+        ),
+        wm_fod=dict(
+            argstr="%s",
+            extensions=None,
+            position=1,
+        ),
+    )
+    inputs = MTNormalise.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_MTNormalise_outputs():
+    output_map = dict(
+        out_file_csf=dict(
+            extensions=None,
+        ),
+        out_file_gm=dict(
+            extensions=None,
+        ),
+        out_file_wm=dict(
+            extensions=None,
+        ),
+    )
+    outputs = MTNormalise.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/mrtrix3/tests/test_auto_MaskFilter.py

@@ -0,0 +1,54 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..utils import MaskFilter
+
+
+def test_MaskFilter_inputs():
+    input_map = dict(
+        args=dict(
+            argstr="%s",
+        ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        filter=dict(
+            argstr="%s",
+            mandatory=True,
+            position=-2,
+        ),
+        in_file=dict(
+            argstr="%s",
+            extensions=None,
+            mandatory=True,
+            position=-3,
+        ),
+        npass=dict(
+            argstr="-npass %d",
+            position=1,
+        ),
+        out_file=dict(
+            argstr="%s",
+            extensions=None,
+            mandatory=True,
+            name_source=["input_image"],
+            position=-1,
+        ),
+    )
+    inputs = MaskFilter.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_MaskFilter_outputs():
+    output_map = dict(
+        out_file=dict(
+            extensions=None,
+        ),
+    )
+    outputs = MaskFilter.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value