@@ -788,6 +788,11 @@
 {
 "name": "Tambini, Arielle"
 },
+{
+"affiliation": "Weill Cornell Medicine",
+"name": "Xie, Xihe",
+"orcid": "0000-0001-6595-2473"
+},
 {
 "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.",
 "name": "Mihai, Paul Glad",

@@ -18,6 +18,7 @@
 ResponseSD,
 ACTPrepareFSL,
 ReplaceFSwithFIRST,
+DWIPreproc,
 DWIDenoise,
 MRDeGibbs,
 DWIBiasCorrect,

@@ -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 +242,139 @@ 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=0, mandatory=True, desc="input DWI image"
+)
+out_file = File(
+"preproc.mif",
+argstr="%s",
+mandatory=True,
+position=1,
+usedefault=True,
+desc="output file after preprocessing",
+)
+rpe_options = traits.Enum(
+"none",
+"pair",
+"all",
+"header",
+argstr="-rpe_%s",
+position=2,
+mandatory=True,
+desc='Specify acquisition phase-encoding design. "none" for no reversed phase-encoding image, "all" for all DWIs have opposing phase-encoding acquisition, "pair" for using a pair of b0 volumes for inhomogeneity field estimation only, and "header" for phase-encoding information can be found in the image header(s)',
+)
+pe_dir = traits.Str(
+argstr="-pe_dir %s",
+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",
+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="Manually provide additional command-line options to the eddy command",
+)
+topup_options = traits.Str(
+argstr='-topup_options "%s"',
+desc="Manually provide additional command-line options to the topup command",
+)
+export_grad_mrtrix = traits.Bool(
+argstr="-export_grad_mrtrix", desc="export new gradient files in mrtrix format"
+)
+export_grad_fsl = traits.Bool(
+argstr="-export_grad_fsl", desc="export gradient files in FSL format"
+)
+out_grad_mrtrix = File(
+"grad.b",
+argstr="%s",
+usedefault=True,
+requires=["export_grad_mrtrix"],
+desc="name of new gradient file",
+)
+out_grad_fsl = traits.Tuple(
+File("grad.bvecs", usedefault=True, desc="bvecs"),
+File("grad.bvals", usedefault=True, desc="bvals"),
+argstr="%s, %s",
+requires=["export_grad_fsl"],
+desc="Output (bvecs, bvals) gradients FSL format",
+)
+
+
+class DWIPreprocOutputSpec(TraitedSpec):
+out_file = File(argstr="%s", desc="output preprocessed image series")
+out_grad_mrtrix = File(
+"grad.b",
+argstr="%s",
+usedefault=True,
+desc="preprocessed gradient file in mrtrix3 format",
+)
+out_fsl_bvec = File(
+"grad.bvecs",
+argstr="%s",
+usedefault=True,
+desc="exported fsl gradient bvec file",
+)
+out_fsl_bval = File(
+"grad.bvals",
+argstr="%s",
+usedefault=True,
+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 = 'none'
+>>> preproc.inputs.out_file = "preproc.mif"
+>>> preproc.inputs.eddy_options = '--slm=linear --repol' # linear second level model and replace outliers
+>>> preproc.inputs.export_grad_mrtrix = True # export final gradient table in MRtrix format
+>>> 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 -rpe_none -eddy_options "--slm=linear --repol" -export_grad_mrtrix grad.b -pe_dir j -readout_time 0.165240'
+>>> preproc.run() # doctest: +SKIP
+"""
+
+_cmd = "dwifslpreproc"
+input_spec = DWIPreprocInputSpec
+output_spec = DWIPreprocOutputSpec
+
+def _list_outputs(self):
+outputs = self.output_spec().get()
+outputs["out_file"] = op.abspath(self.inputs.out_file)
+if self.inputs.export_grad_mrtrix:
+outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix)
+if self.inputs.export_grad_fsl:
+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",

@@ -0,0 +1,54 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..preprocess import DWIPreproc
+
+
+def test_DWIPreproc_inputs():
+input_map = dict(
+align_seepi=dict(argstr="-align_seepi"),
+args=dict(argstr="%s"),
+bval_scale=dict(argstr="-bvalue_scaling %s"),
+eddy_options=dict(argstr='-eddy_options "%s"'),
+environ=dict(nohash=True, usedefault=True),
+export_grad_fsl=dict(argstr="-export_grad_fsl"),
+export_grad_mrtrix=dict(argstr="-export_grad_mrtrix"),
+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_epi=dict(argstr="-se_epi %s", extensions=None),
+in_file=dict(argstr="%s", extensions=None, mandatory=True, position=0),
+nthreads=dict(argstr="-nthreads %d", nohash=True),
+out_file=dict(
+argstr="%s", extensions=None, mandatory=True, position=1, usedefault=True
+),
+out_grad_fsl=dict(argstr="%s, %s", requires=["export_grad_fsl"]),
+out_grad_mrtrix=dict(
+argstr="%s",
+extensions=None,
+requires=["export_grad_mrtrix"],
+usedefault=True,
+),
+pe_dir=dict(argstr="-pe_dir %s", mandatory=True),
+ro_time=dict(argstr="-readout_time %f"),
+rpe_options=dict(argstr="-rpe_%s", mandatory=True, position=2),
+topup_options=dict(argstr='-topup_options "%s"'),
+)
+inputs = DWIPreproc.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_DWIPreproc_outputs():
+output_map = dict(
+out_file=dict(argstr="%s", extensions=None),
+out_fsl_bval=dict(argstr="%s", extensions=None, usedefault=True),
+out_fsl_bvec=dict(argstr="%s", extensions=None, usedefault=True),
+out_grad_mrtrix=dict(argstr="%s", extensions=None, usedefault=True),
+)
+outputs = DWIPreproc.output_spec()
+
+for key, metadata in list(output_map.items()):
+for metakey, value in list(metadata.items()):
+assert getattr(outputs.traits()[key], metakey) == value