Merge pull request #3445 from effigies/mrtrix3-squash

ENH: Add MRTrix3 interfaces (pared-down gh-3426)

Author: effigies

nipype/interfaces/mrtrix3/__init__.py

@@ -2,29 +2,32 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 # -*- coding: utf-8 -*-
 """MRTrix3 provides software tools to perform various types of diffusion MRI analyses."""
+from .connectivity import BuildConnectome, LabelConfig, LabelConvert
+from .preprocess import (
+    ACTPrepareFSL,
+    DWIBiasCorrect,
+    DWIDenoise,
+    DWIPreproc,
+    MRDeGibbs,
+    ReplaceFSwithFIRST,
+    ResponseSD,
+)
+from .reconst import ConstrainedSphericalDeconvolution, EstimateFOD, FitTensor
+from .tracking import Tractography
 from .utils import (
-    Mesh2PVE,
-    Generate5tt,
+    TCK2VTK,
     BrainMask,
-    TensorMetrics,
     ComputeTDI,
-    TCK2VTK,
-    MRMath,
+    DWIExtract,
+    Generate5tt,
+    Mesh2PVE,
+    MRCat,
     MRConvert,
+    MRMath,
     MRResize,
-    DWIExtract,
-    SHConv,
+    MRTransform,
     SH2Amp,
+    SHConv,
+    TensorMetrics,
+    TransformFSLConvert,
 )
-from .preprocess import (
-    ResponseSD,
-    ACTPrepareFSL,
-    ReplaceFSwithFIRST,
-    DWIPreproc,
-    DWIDenoise,
-    MRDeGibbs,
-    DWIBiasCorrect,
-)
-from .tracking import Tractography
-from .reconst import FitTensor, EstimateFOD, ConstrainedSphericalDeconvolution
-from .connectivity import LabelConfig, LabelConvert, BuildConnectome

nipype/interfaces/mrtrix3/base.py

@@ -79,6 +79,15 @@ class MRTrix3BaseInputSpec(CommandLineInputSpec):
         exists=True, argstr="-fslgrad %s %s", desc="bvecs file in FSL format"
     )
     in_bval = File(exists=True, desc="bvals file in FSL format")
+    out_bvec = File(
+        exists=False,
+        argstr="-export_grad_fsl %s %s",
+        desc="export bvec file in FSL format",
+    )
+    out_bval = File(
+        exists=False,
+        desc="export bval file in FSL format",
+    )
 
 
 class MRTrix3Base(CommandLine):
@@ -96,6 +105,8 @@ def _format_arg(self, name, trait_spec, value):
 
         if name == "in_bvec":
             return trait_spec.argstr % (value, self.inputs.in_bval)
+        if name == "out_bvec":
+            return trait_spec.argstr % (value, self.inputs.out_bval)
 
         return super(MRTrix3Base, self)._format_arg(name, trait_spec, value)
 

nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py

@@ -40,6 +40,13 @@ def test_BrainMask_inputs():
             argstr="-nthreads %d",
             nohash=True,
         ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
         out_file=dict(
             argstr="%s",
             extensions=None,

nipype/interfaces/mrtrix3/tests/test_auto_ConstrainedSphericalDeconvolution.py

@@ -77,6 +77,13 @@ def test_ConstrainedSphericalDeconvolution_inputs():
             argstr="-nthreads %d",
             nohash=True,
         ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
         predicted_signal=dict(
             argstr="-predicted_signal %s",
             extensions=None,

nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py

@@ -48,6 +48,13 @@ def test_DWIBiasCorrect_inputs():
             argstr="-nthreads %d",
             nohash=True,
         ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
         out_file=dict(
             argstr="%s",
             extensions=None,

nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py

@@ -55,6 +55,13 @@ def test_DWIDenoise_inputs():
             argstr="-nthreads %d",
             nohash=True,
         ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
         out_file=dict(
             argstr="%s",
             extensions=None,

nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py

@@ -46,6 +46,13 @@ def test_DWIExtract_inputs():
             argstr="-nthreads %d",
             nohash=True,
         ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
         out_file=dict(
             argstr="%s",
             extensions=None,

nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py

@@ -56,6 +56,13 @@ def test_DWIPreproc_inputs():
             argstr="-nthreads %d",
             nohash=True,
         ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
         out_file=dict(
             argstr="%s",
             extensions=None,

nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py

@@ -80,6 +80,13 @@ def test_EstimateFOD_inputs():
             argstr="-nthreads %d",
             nohash=True,
         ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
         predicted_signal=dict(
             argstr="-predicted_signal %s",
             extensions=None,

nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py

@@ -47,6 +47,13 @@ def test_FitTensor_inputs():
             argstr="-nthreads %d",
             nohash=True,
         ),
+        out_bval=dict(
+            extensions=None,
+        ),
+        out_bvec=dict(
+            argstr="-export_grad_fsl %s %s",
+            extensions=None,
+        ),
         out_file=dict(
             argstr="%s",
             extensions=None,