added mrtrix3 dwifslpreproc as interface

nipype/interfaces/mrtrix3/preprocess.py

@@ -233,6 +233,7 @@ class DWIBiasCorrect(MRTrix3Base):
     _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
@@ -241,6 +242,120 @@ def _format_arg(self, name, trait_spec, value):
                 return f"-{trait_spec.argstr}"
         return super()._format_arg(name, trait_spec, value)
 
+
+class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
+    in_file = File(
+        exists=True, argstr="%s", position=-5, mandatory=True, desc="input DWI image"
+    )
+    out_file = File(
+        "preproc.mif",
+        argstr="%s",
+        mandatory=True,
+        position=-4,
+        usedefault=True,
+        desc="output file after preprocessing",
+    )
+    rpe_options = traits.Enum(
+        "-rpe_none",
+        "-rpe_pair",
+        "-rpe_all",
+        "-rpe_header",
+        argstr="%s",
+        position=-3,
+        mandatory=True,
+        desc="Specify acquisition phase-encoding design, one of the -rpe_* options must be provided",
+    )
+    pe_dir = traits.Str(
+        argstr="-pe_dir %s",
+        position=-2,
+        mandatory=True,
+        desc="Specify the phase encoding direction of the input series, can be a signed axis number (e.g. -0, 1, +2), an axis designator (e.g. RL, PA, IS), or NIfTI axis codes (e.g. i-, j, k)",
+    )
+    ro_time = traits.Float(
+        argstr="-readout_time %f",
+        position=-1,
+        desc="Total readout time of input series (in seconds)",
+    )
+    in_epi = File(
+        exists=True,
+        argstr="-se_epi %s",
+        desc="Provide an additional image series consisting of spin-echo EPI images, which is to be used exclusively by topup for estimating the inhomogeneity field (i.e. it will not form part of the output image series)",
+    )
+    align_seepi = traits.Bool(
+        argstr="-align_seepi",
+        desc="Achieve alignment between the SE-EPI images used for inhomogeneity field estimation, and the DWIs",
+    )
+    eddy_options = traits.Str(
+        argstr="-eddy_options %s",
+        desc="-eddy_options ” EddyOptions” Manually provide additional command-line options to the eddy command (provide a string within quotation marks that contains at least one space, even if only passing a single command-line option to eddy)",
+    )
+    topup_options = traits.Str(
+        argstr="-topup_options %s",
+        desc="-topup_options ” TopupOptions” Manually provide additional command-line options to the topup command (provide a string within quotation marks that contains at least one space, even if only passing a single command-line option to topup)",
+    )
+    export_grad_mrtrix = traits.Bool(
+        argstr="-export_grad_mrtrix", desc="export new gradientt files in mrtrix format"
+    )
+    export_grad_fsl = traits.Bool(
+        argstr="-export_grad_fsl", desc="export gradient files in FSL format"
+    )
+    out_grad_mrtrix = File("dwi.b", argstrt="%s", desc="name of new gradient file")
+    out_grad_fsl = traits.Tuple(
+        File("dwi.bvecs", desc="bvecs"),
+        File("dwi.bvals", desc="bvals"),
+        argstr="%s, %s",
+        desc="Output (bvecs, bvals) gradients FSL format",
+    )
+
+
+class DWIPreprocOutputtSpec(TraitedSpec):
+    out_file = File(argstr="%s", desc="output preprocessed image series")
+    out_grad_mrtrix = File(
+        argstr="%s", desc="preprocessed gradient file in mrtrix3 format"
+    )
+    out_fsl_bvec = File("dwi.bvecs", desc="exported fsl gradient bvec file")
+    out_fsl_bval = File("dwi.bvals", desc="exported fsl gradient bval file")
+
+
+class DWIPreproc(MRTrix3Base):
+    """
+    Perform diffusion image pre-processing using FSL's eddy tool; including inhomogeneity distortion correction using FSL's topup tool if possible
+
+    For more information, see
+    <https://mrtrix.readthedocs.io/en/latest/reference/commands/dwifslpreproc.html>
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> preproc = mrt.DWIPreproc()
+    >>> preproc.inputs.in_file = 'dwi.mif'
+    >>> preproc.inputs.rpe_options = '-rpe_none'
+    >>> preproc.inputs.eddy_options = '"--slm=linear --repol"'
+    >>> preproc.inputs.out_file = "preproc.mif"
+    >>> preproc.inputs.grad_file = "dwi.b"
+    >>> preproc.inputs.ro_time = 0.165240   # 'TotalReadoutTime' in BIDS JSON metadata files
+    >>> preproc.inputs.pe_dir = 'j'     # 'PhaseEncodingDirection' in BIDS JSON metadata files
+    >>> preproc.cmdline
+    `dwifslpreproc dwi.mif preproc.mif -eddy_options "--slm=linear " -rpe_none -pe_dir j -grad dwi.b -readout_time 0.165240`
+    """
+
+    _cmd = "dwifslpreproc"
+    input_spec = DWIPreprocInputSpec
+    output_spec = DWIPreprocOutputtSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs["out_file"] = op.abspath(self.inputs.out_file)
+        if self.inputs.export_grad_mrtrix == True:
+            outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix)
+        if self.inputs.export_grad_fsl == True:
+            outputs["out_fsl_bvec"] = op.abspath(self.inputs.out_grad_fsl[0])
+            outputs["out_fsl_bval"] = op.abspath(self.inputs.out_grad_fsl[1])
+
+        return outputs
+
+
 class ResponseSDInputSpec(MRTrix3BaseInputSpec):
     algorithm = traits.Enum(
         "msmt_5tt",