initial attempt at adding mrtrix commands

Author: josephmje

nipype/interfaces/fsl/epi.py

@@ -1383,7 +1383,7 @@ def _list_outputs(self):
         # If the output directory isn't defined, the interface seems to use
         # the default but not set its value in `self.inputs.output_dir`
         if not isdefined(self.inputs.output_dir):
-            out_dir = os.path.abspath(os.path.basename(self.inputs.base_name) + '.qc.nii.gz')
+            out_dir = os.path.abspath(os.path.basename(self.inputs.base_name) + '.qc')
         else:
             out_dir = os.path.abspath(self.inputs.output_dir)
 
@@ -1421,4 +1421,3 @@ def _list_outputs(self):
             outputs['clean_volumes'] = clean_volumes
 
         return outputs
-

nipype/interfaces/mrtrix3/__init__.py

@@ -6,7 +6,7 @@
 from .utils import (Mesh2PVE, Generate5tt, BrainMask, TensorMetrics,
                     ComputeTDI, TCK2VTK, MRMath, MRConvert, DWIExtract)
 from .preprocess import (ResponseSD, ACTPrepareFSL, ReplaceFSwithFIRST,
-                         DWIDenoise)
+                         DWIDenoise, MRDeGibbs, DWIBiasCorrect)
 from .tracking import Tractography
 from .reconst import FitTensor, EstimateFOD
 from .connectivity import LabelConfig, LabelConvert, BuildConnectome

nipype/interfaces/mrtrix3/preprocess.py

@@ -21,7 +21,7 @@ class DWIDenoiseInputSpec(MRTrix3BaseInputSpec):
     mask = File(
         exists=True,
         argstr='-mask %s',
-        position=1,
+        #osition=1,
         desc='mask image')
     extent = traits.Tuple((traits.Int, traits.Int, traits.Int),
         argstr='-extent %d,%d,%d',
@@ -75,6 +75,149 @@ class DWIDenoise(MRTrix3Base):
     output_spec = DWIDenoiseOutputSpec
 
 
+class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
+    in_file = File(
+        exists=True,
+        argstr='%s',
+        position=-2,
+        mandatory=True,
+        desc='input DWI image')
+    axes = InputMultiObject(
+        traits.Int,
+        value=[0],
+        usedefault=True,
+        argstr='-axes %d',
+        desc='select the slice axes (default = 0)')
+    nshifts = InputMultiObject(
+        traits.Int,
+        value=[20],
+        usedefault=True,
+        argstr='-nshifts %d',
+        desc='discretizaiton of subpixel spacing (default = 20)')
+    minW = InputMultiObject(
+        traits.Int,
+        value=[1],
+        usedefault=True,
+        argstr='-minW %d',
+        desc='left border of window used for TV computation (default = 1)')
+    maxW = InputMultiObject(
+        traits.Int,
+        value=[3],
+        usedefault=True,
+        argstr='-maxW %d',
+        desc='right border of window used for TV computation (default = 3)')
+    out_file = File(name_template='%s_unring',
+        name_source='in_file',
+        keep_extension=True,
+        argstr="%s",
+        position=-1,
+        desc="the output unringed DWI image")
+
+class MRDeGibbsOutputSpec(TraitedSpec):
+    out_file = File(desc="the output unringed DWI image", exists=True)
+
+class MRDeGibbs(MRTrix3Base):
+    """
+    Remove Gibbs ringing artifacts.
+
+    This application attempts to remove Gibbs ringing artefacts from MRI images
+    using the method of local subvoxel-shifts proposed by Kellner et al.
+
+    This command is designed to run on data directly after it has been
+    reconstructed by the scanner, before any interpolation of any kind has
+    taken place. You should not run this command after any form of motion
+    correction (e.g. not after dwipreproc). Similarly, if you intend running
+    dwidenoise, you should run this command afterwards, since it has the
+    potential to alter the noise structure, which would impact on dwidenoise’s
+    performance.
+
+    Note that this method is designed to work on images acquired with full
+    k-space coverage. Running this method on partial Fourier (‘half-scan’) data
+    may lead to suboptimal and/or biased results, as noted in the original
+    reference below. There is currently no means of dealing with this; users
+    should exercise caution when using this method on partial Fourier data, and
+    inspect its output for any obvious artefacts.
+
+    For more information, see
+    <https://mrtrix.readthedocs.io/en/latest/reference/commands/mrdegibbs.html>
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> unring = mrt.MRDeGibbs()
+    >>> unring.inputs.in_file = 'dwi.mif'
+    >>> unring.cmdline
+    'mrdegibbs dwi.mif dwi_unring.mif'
+    >>> unring.run()
+    """
+
+    _cmd = 'mrdegibbs'
+    input_spec = MRDeGibbsInputSpec
+    output_spec = MRDeGibbsOutputSpec
+
+
+class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
+    in_file = File(
+        exists=True,
+        argstr='%s',
+        position=-2,
+        mandatory=True,
+        desc='input DWI image')
+    mask = File(
+        argstr='-mask %s',
+        desc='mask image')
+    bias = File(
+        argstr='-bias %s',
+        desc='bias field')
+    ants = traits.Bool(
+        True,
+        argstr='-ants',
+        desc='use ANTS N4')
+    fsl = traits.Bool(
+        False,
+        argstr='-fsl',
+        desc='use FSL FAST',
+        min_ver='5.0.10')
+    grad = File(
+        argstr='-grad %s',
+        desc='diffusion gradient table in MRtrix format')
+    fslgrad = File(
+        argstr='-fslgrad %s %s',
+        desc='diffusion gradient table in FSL bvecs/bvals format')
+    out_file = File(name_template='%s_unbias',
+        name_source='in_file',
+        keep_extension=True,
+        argstr="%s",
+        position=-1,
+        desc="the output bias corrected DWI image")
+
+class DWIBiasCorrectOutputSpec(TraitedSpec):
+    out_file = File(desc="the output bias corrected DWI image", exists=True)
+
+class DWIBiasCorrect(MRTrix3Base):
+    """
+    Perform B1 field inhomogeneity correction for a DWI volume series.
+
+    For more information, see
+    <https://mrtrix.readthedocs.io/en/latest/reference/scripts/dwibiascorrect.html>
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> bias_correct = mrt.DWIBiasCorrect()
+    >>> bias_correct.inputs.in_file = 'dwi.mif'
+    >>> bias_correct.cmdline
+    'dwibiascorrect dwi.mif dwi_unbias.mif'
+    >>> bias_correct.run()
+    """
+
+    _cmd = 'dwibiascorrect'
+    input_spec = DWIBiasCorrectInputSpec
+    output_spec = DWIBiasCorrectOutputSpec
+
+
 class ResponseSDInputSpec(MRTrix3BaseInputSpec):
     algorithm = traits.Enum(
         'msmt_5tt',