From 69a7493f54f6877bd64a4ca19b11bcf0e4c0df16 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Wed, 25 Nov 2020 19:20:29 -0500
Subject: [PATCH 01/14] added mrtrix3 dwifslpreproc as interface

---
 nipype/interfaces/mrtrix3/preprocess.py | 115 ++++++++++++++++++++++++
 1 file changed, 115 insertions(+)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index aa3347c7f9..b29c54242a 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/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",

From 7544744b2ec32a38fad58e0300f5fd647e10f2a6 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Wed, 25 Nov 2020 21:49:40 -0500
Subject: [PATCH 02/14] use defaults added for outputs

---
 nipype/interfaces/mrtrix3/preprocess.py | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index b29c54242a..feef9af418 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -299,10 +299,12 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
     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_mrtrix = File(
+        "dwi.b", argstr="%s", usedefault=True, desc="name of new gradient file"
+    )
     out_grad_fsl = traits.Tuple(
-        File("dwi.bvecs", desc="bvecs"),
-        File("dwi.bvals", desc="bvals"),
+        File("dwi.bvecs", usedefault=True, desc="bvecs"),
+        File("dwi.bvals", usedefault=True, desc="bvals"),
         argstr="%s, %s",
         desc="Output (bvecs, bvals) gradients FSL format",
     )
@@ -313,8 +315,18 @@ class DWIPreprocOutputtSpec(TraitedSpec):
     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")
+    out_fsl_bvec = File(
+        "dwi.bvecs",
+        argstr="%s",
+        usedefault=True,
+        desc="exported fsl gradient bvec file",
+    )
+    out_fsl_bval = File(
+        "dwi.bvals",
+        argstr="%s",
+        usedefault=True,
+        desc="exported fsl gradient bval file",
+    )
 
 
 class DWIPreproc(MRTrix3Base):

From 33df5fc751f7458ade5308446eb4f11f3d50ce92 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Sat, 28 Nov 2020 10:56:49 -0500
Subject: [PATCH 03/14] Added dwifslpreproc interface to __init__

---
 nipype/interfaces/mrtrix3/__init__.py   | 1 +
 nipype/interfaces/mrtrix3/preprocess.py | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/__init__.py b/nipype/interfaces/mrtrix3/__init__.py
index f60e837310..53af56ef65 100644
--- a/nipype/interfaces/mrtrix3/__init__.py
+++ b/nipype/interfaces/mrtrix3/__init__.py
@@ -18,6 +18,7 @@
     ResponseSD,
     ACTPrepareFSL,
     ReplaceFSwithFIRST,
+    DWIPreproc,
     DWIDenoise,
     MRDeGibbs,
     DWIBiasCorrect,
diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index feef9af418..de2fdf610e 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -310,7 +310,7 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
     )
 
 
-class DWIPreprocOutputtSpec(TraitedSpec):
+class DWIPreprocOutputSpec(TraitedSpec):
     out_file = File(argstr="%s", desc="output preprocessed image series")
     out_grad_mrtrix = File(
         argstr="%s", desc="preprocessed gradient file in mrtrix3 format"
@@ -354,7 +354,7 @@ class DWIPreproc(MRTrix3Base):
 
     _cmd = "dwifslpreproc"
     input_spec = DWIPreprocInputSpec
-    output_spec = DWIPreprocOutputtSpec
+    output_spec = DWIPreprocOutputSpec
 
     def _list_outputs(self):
         outputs = self.output_spec().get()

From 30ab4ebb3cbbe9002fcccd06611b6d227889064a Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Sat, 28 Nov 2020 11:15:27 -0500
Subject: [PATCH 04/14] edited doc string to correct order

---
 nipype/interfaces/mrtrix3/preprocess.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index de2fdf610e..fe743b6ee5 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -343,13 +343,12 @@ class DWIPreproc(MRTrix3Base):
     >>> 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`
+    `dwifslpreproc dwi.mif preproc.mif -rpe_none -pe_dir j -readout_time 0.165240 -grad dwi.b`
     """
 
     _cmd = "dwifslpreproc"

From 8fcf5ec63fc9398bdc66769f628784b2fa964239 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Mon, 30 Nov 2020 11:50:16 -0500
Subject: [PATCH 05/14] added doctest skip

---
 nipype/interfaces/mrtrix3/preprocess.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index fe743b6ee5..38b99cbcd6 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -349,6 +349,7 @@ class DWIPreproc(MRTrix3Base):
     >>> preproc.inputs.pe_dir = 'j'     # 'PhaseEncodingDirection' in BIDS JSON metadata files
     >>> preproc.cmdline
     `dwifslpreproc dwi.mif preproc.mif -rpe_none -pe_dir j -readout_time 0.165240 -grad dwi.b`
+    >>> preproc.run()                             # doctest: +SKIP
     """
 
     _cmd = "dwifslpreproc"

From 2be461c726c586cfc28759a75d5daac5ffbff26d Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Mon, 30 Nov 2020 12:10:49 -0500
Subject: [PATCH 06/14] added MRtrix3 gradient empty test data

---
 nipype/testing/data/grad.b | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 nipype/testing/data/grad.b

diff --git a/nipype/testing/data/grad.b b/nipype/testing/data/grad.b
new file mode 100644
index 0000000000..e69de29bb2

From fb3f6194bac36bebf1440c373622f2c60bb41af7 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Mon, 30 Nov 2020 12:11:51 -0500
Subject: [PATCH 07/14] specified positions, requires for gradient exports

---
 nipype/interfaces/mrtrix3/preprocess.py | 47 +++++++++++++++++--------
 1 file changed, 33 insertions(+), 14 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index 38b99cbcd6..cb4fcadf26 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -245,13 +245,13 @@ def _format_arg(self, name, trait_spec, value):
 
 class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
-        exists=True, argstr="%s", position=-5, mandatory=True, desc="input DWI image"
+        exists=True, argstr="%s", position=-6, mandatory=True, desc="input DWI image"
     )
     out_file = File(
         "preproc.mif",
         argstr="%s",
         mandatory=True,
-        position=-4,
+        position=-5,
         usedefault=True,
         desc="output file after preprocessing",
     )
@@ -261,51 +261,66 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         "-rpe_all",
         "-rpe_header",
         argstr="%s",
-        position=-3,
+        position=-4,
         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,
+        position=-3,
         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,
+        position=-2,
         desc="Total readout time of input series (in seconds)",
     )
     in_epi = File(
         exists=True,
         argstr="-se_epi %s",
+        position=-1,
         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",
+        position=0,
         desc="Achieve alignment between the SE-EPI images used for inhomogeneity field estimation, and the DWIs",
     )
     eddy_options = traits.Str(
         argstr="-eddy_options %s",
+        position=1,
         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",
+        position=1,
         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"
+        argstr="-export_grad_mrtrix",
+        position=2,
+        desc="export new gradientt files in mrtrix format",
     )
     export_grad_fsl = traits.Bool(
-        argstr="-export_grad_fsl", desc="export gradient files in FSL format"
+        argstr="-export_grad_fsl",
+        position=2,
+        desc="export gradient files in FSL format",
     )
     out_grad_mrtrix = File(
-        "dwi.b", argstr="%s", usedefault=True, desc="name of new gradient file"
+        "grad.b",
+        argstr="%s",
+        usedefault=True,
+        position=3,
+        requires=["export_grad_mrtrix"],
+        desc="name of new gradient file",
     )
     out_grad_fsl = traits.Tuple(
-        File("dwi.bvecs", usedefault=True, desc="bvecs"),
-        File("dwi.bvals", usedefault=True, desc="bvals"),
+        File("grad.bvecs", usedefault=True, desc="bvecs"),
+        File("grad.bvals", usedefault=True, desc="bvals"),
         argstr="%s, %s",
+        position=3,
+        requires=["export_grad_fsl"],
         desc="Output (bvecs, bvals) gradients FSL format",
     )
 
@@ -313,16 +328,19 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
 class DWIPreprocOutputSpec(TraitedSpec):
     out_file = File(argstr="%s", desc="output preprocessed image series")
     out_grad_mrtrix = File(
-        argstr="%s", desc="preprocessed gradient file in mrtrix3 format"
+        "grad.b",
+        argstr="%s",
+        usedefault=True,
+        desc="preprocessed gradient file in mrtrix3 format",
     )
     out_fsl_bvec = File(
-        "dwi.bvecs",
+        "grad.bvecs",
         argstr="%s",
         usedefault=True,
         desc="exported fsl gradient bvec file",
     )
     out_fsl_bval = File(
-        "dwi.bvals",
+        "grad.bvals",
         argstr="%s",
         usedefault=True,
         desc="exported fsl gradient bval file",
@@ -344,7 +362,8 @@ class DWIPreproc(MRTrix3Base):
     >>> preproc.inputs.in_file = 'dwi.mif'
     >>> preproc.inputs.rpe_options = '-rpe_none'
     >>> preproc.inputs.out_file = "preproc.mif"
-    >>> preproc.inputs.grad_file = "dwi.b"
+    >>> preproc.inputs.eddy_options = '"--slm=linear --repol"'
+    >>> 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

From 4f4f9e50abcbee7c0751da1b62766ff0e338d057 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Mon, 30 Nov 2020 12:49:54 -0500
Subject: [PATCH 08/14] finalized docstring example and pytest

---
 nipype/interfaces/mrtrix3/preprocess.py       | 30 +++++-----
 .../mrtrix3/tests/test_auto_DWIPreproc.py     | 55 +++++++++++++++++++
 2 files changed, 70 insertions(+), 15 deletions(-)
 create mode 100644 nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index cb4fcadf26..f1ef381a2a 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -245,13 +245,13 @@ def _format_arg(self, name, trait_spec, value):
 
 class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
-        exists=True, argstr="%s", position=-6, mandatory=True, desc="input DWI image"
+        exists=True, argstr="%s", position=-10, mandatory=True, desc="input DWI image"
     )
     out_file = File(
         "preproc.mif",
         argstr="%s",
         mandatory=True,
-        position=-5,
+        position=-9,
         usedefault=True,
         desc="output file after preprocessing",
     )
@@ -261,57 +261,57 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         "-rpe_all",
         "-rpe_header",
         argstr="%s",
-        position=-4,
+        position=-8,
         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=-3,
+        position=-7,
         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=-2,
+        position=-6,
         desc="Total readout time of input series (in seconds)",
     )
     in_epi = File(
         exists=True,
         argstr="-se_epi %s",
-        position=-1,
+        position=-5,
         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",
-        position=0,
+        position=-4,
         desc="Achieve alignment between the SE-EPI images used for inhomogeneity field estimation, and the DWIs",
     )
     eddy_options = traits.Str(
         argstr="-eddy_options %s",
-        position=1,
+        position=-3,
         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",
-        position=1,
+        position=-3,
         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",
-        position=2,
+        position=-2,
         desc="export new gradientt files in mrtrix format",
     )
     export_grad_fsl = traits.Bool(
         argstr="-export_grad_fsl",
-        position=2,
+        position=-2,
         desc="export gradient files in FSL format",
     )
     out_grad_mrtrix = File(
         "grad.b",
         argstr="%s",
         usedefault=True,
-        position=3,
+        position=-1,
         requires=["export_grad_mrtrix"],
         desc="name of new gradient file",
     )
@@ -319,7 +319,7 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         File("grad.bvecs", usedefault=True, desc="bvecs"),
         File("grad.bvals", usedefault=True, desc="bvals"),
         argstr="%s, %s",
-        position=3,
+        position=-1,
         requires=["export_grad_fsl"],
         desc="Output (bvecs, bvals) gradients FSL format",
     )
@@ -362,12 +362,12 @@ class DWIPreproc(MRTrix3Base):
     >>> preproc.inputs.in_file = 'dwi.mif'
     >>> preproc.inputs.rpe_options = '-rpe_none'
     >>> preproc.inputs.out_file = "preproc.mif"
-    >>> preproc.inputs.eddy_options = '"--slm=linear --repol"'
+    >>> 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 -pe_dir j -readout_time 0.165240 -grad dwi.b`
+    'dwifslpreproc dwi.mif preproc.mif -rpe_none -pe_dir j -readout_time 0.165240 -eddy_options "--slm=linear --repol " -export_grad_mrtrix grad.b'
     >>> preproc.run()                             # doctest: +SKIP
     """
 
diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py
new file mode 100644
index 0000000000..55793a873b
--- /dev/null
+++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py
@@ -0,0 +1,55 @@
+# 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", position=-4),
+        args=dict(argstr="%s"),
+        bval_scale=dict(argstr="-bvalue_scaling %s"),
+        eddy_options=dict(argstr="-eddy_options %s", position=-3),
+        environ=dict(nohash=True, usedefault=True),
+        export_grad_fsl=dict(argstr="-export_grad_fsl", position=-2),
+        export_grad_mrtrix=dict(argstr="-export_grad_mrtrix", position=-2),
+        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, position=-5),
+        in_file=dict(argstr="%s", extensions=None, mandatory=True, position=-10),
+        nthreads=dict(argstr="-nthreads %d", nohash=True),
+        out_file=dict(
+            argstr="%s", extensions=None, mandatory=True, position=-9, usedefault=True
+        ),
+        out_grad_fsl=dict(argstr="%s, %s", position=-1, requires=["export_grad_fsl"]),
+        out_grad_mrtrix=dict(
+            argstr="%s",
+            extensions=None,
+            position=-1,
+            requires=["export_grad_mrtrix"],
+            usedefault=True,
+        ),
+        pe_dir=dict(argstr="-pe_dir %s", mandatory=True, position=-7),
+        ro_time=dict(argstr="-readout_time %f", position=-6),
+        rpe_options=dict(argstr="%s", mandatory=True, position=-8),
+        topup_options=dict(argstr="-topup_options %s", position=-3),
+    )
+    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

From 983840c5657f34c203c02fbfdce5b723bf41a6d1 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Mon, 30 Nov 2020 13:05:46 -0500
Subject: [PATCH 09/14] added entry to contribution list

---
 .zenodo.json | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.zenodo.json b/.zenodo.json
index 0baed9eaa9..eb0bafe320 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -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",

From 7926025ad466dbab44508b508e53e98a538d1d39 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Thu, 3 Dec 2020 14:55:30 -0500
Subject: [PATCH 10/14] simplify phase-encoding design input

Moved `-rpe_` to `argstr` for simpler input.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/mrtrix3/preprocess.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index f1ef381a2a..0a38f1a492 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -256,11 +256,11 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         desc="output file after preprocessing",
     )
     rpe_options = traits.Enum(
-        "-rpe_none",
-        "-rpe_pair",
-        "-rpe_all",
-        "-rpe_header",
-        argstr="%s",
+        "none",
+        "pair",
+        "all",
+        "header",
+        argstr="-rpe_%s",
         position=-8,
         mandatory=True,
         desc="Specify acquisition phase-encoding design, one of the -rpe_* options must be provided",

From e8bddbc9a72482c775429ee015428a1400d23718 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Thu, 3 Dec 2020 15:12:47 -0500
Subject: [PATCH 11/14] Apply suggestions from code review

Fixed typos and improved `-eddy` and `-topup` optional inputs.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/mrtrix3/preprocess.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index 0a38f1a492..e24de6c702 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -288,19 +288,19 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         desc="Achieve alignment between the SE-EPI images used for inhomogeneity field estimation, and the DWIs",
     )
     eddy_options = traits.Str(
-        argstr="-eddy_options %s",
+        argstr="-eddy_options \"%s\"",
         position=-3,
-        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)",
+        desc="Manually provide additional command-line options to the eddy command",
     )
     topup_options = traits.Str(
-        argstr="-topup_options %s",
+        argstr="-topup_options \"%s\"",
         position=-3,
-        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)",
+        desc="Manually provide additional command-line options to the topup command",
     )
     export_grad_mrtrix = traits.Bool(
         argstr="-export_grad_mrtrix",
         position=-2,
-        desc="export new gradientt files in mrtrix format",
+        desc="export new gradient files in mrtrix format",
     )
     export_grad_fsl = traits.Bool(
         argstr="-export_grad_fsl",
@@ -360,14 +360,14 @@ class DWIPreproc(MRTrix3Base):
     >>> import nipype.interfaces.mrtrix3 as mrt
     >>> preproc = mrt.DWIPreproc()
     >>> preproc.inputs.in_file = 'dwi.mif'
-    >>> preproc.inputs.rpe_options = '-rpe_none'
+    >>> 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.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 -pe_dir j -readout_time 0.165240 -eddy_options "--slm=linear --repol " -export_grad_mrtrix grad.b'
+    'dwifslpreproc dwi.mif preproc.mif -rpe_none -pe_dir j -readout_time 0.165240 -eddy_options "--slm=linear --repol" -export_grad_mrtrix grad.b'
     >>> preproc.run()                             # doctest: +SKIP
     """
 
@@ -378,9 +378,9 @@ class DWIPreproc(MRTrix3Base):
     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:
+        if self.inputs.export_grad_mrtrix:
             outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix)
-        if self.inputs.export_grad_fsl == True:
+        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])
 

From 4ac4e622f66753f559687fee9695d4e407fb5ebb Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sun, 6 Dec 2020 16:08:39 -0500
Subject: [PATCH 12/14] Update nipype/interfaces/mrtrix3/preprocess.py

Co-authored-by: Xihe Xie <axiezai@gmail.com>
---
 nipype/interfaces/mrtrix3/preprocess.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index e24de6c702..7f13d14a30 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -263,7 +263,7 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         argstr="-rpe_%s",
         position=-8,
         mandatory=True,
-        desc="Specify acquisition phase-encoding design, one of the -rpe_* options must be provided",
+        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",

From d33e9b4520ab1559ed1d7cfd9d850228cb218429 Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Mon, 7 Dec 2020 22:47:59 -0500
Subject: [PATCH 13/14] fixed input positions according to review

---
 nipype/interfaces/mrtrix3/preprocess.py       | 28 ++++++-------------
 .../mrtrix3/tests/test_auto_DWIPreproc.py     | 25 ++++++++---------
 2 files changed, 20 insertions(+), 33 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index 7f13d14a30..dd215a4802 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -245,13 +245,13 @@ def _format_arg(self, name, trait_spec, value):
 
 class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
-        exists=True, argstr="%s", position=-10, mandatory=True, desc="input DWI image"
+        exists=True, argstr="%s", position=0, mandatory=True, desc="input DWI image"
     )
     out_file = File(
         "preproc.mif",
         argstr="%s",
         mandatory=True,
-        position=-9,
+        position=1,
         usedefault=True,
         desc="output file after preprocessing",
     )
@@ -261,57 +261,46 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         "all",
         "header",
         argstr="-rpe_%s",
-        position=-8,
+        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)",
+        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",
-        position=-7,
         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=-6,
         desc="Total readout time of input series (in seconds)",
     )
     in_epi = File(
         exists=True,
         argstr="-se_epi %s",
-        position=-5,
         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",
-        position=-4,
         desc="Achieve alignment between the SE-EPI images used for inhomogeneity field estimation, and the DWIs",
     )
     eddy_options = traits.Str(
-        argstr="-eddy_options \"%s\"",
-        position=-3,
+        argstr='-eddy_options "%s"',
         desc="Manually provide additional command-line options to the eddy command",
     )
     topup_options = traits.Str(
-        argstr="-topup_options \"%s\"",
-        position=-3,
+        argstr='-topup_options "%s"',
         desc="Manually provide additional command-line options to the topup command",
     )
     export_grad_mrtrix = traits.Bool(
-        argstr="-export_grad_mrtrix",
-        position=-2,
-        desc="export new gradient files in mrtrix format",
+        argstr="-export_grad_mrtrix", desc="export new gradient files in mrtrix format"
     )
     export_grad_fsl = traits.Bool(
-        argstr="-export_grad_fsl",
-        position=-2,
-        desc="export gradient files in FSL format",
+        argstr="-export_grad_fsl", desc="export gradient files in FSL format"
     )
     out_grad_mrtrix = File(
         "grad.b",
         argstr="%s",
         usedefault=True,
-        position=-1,
         requires=["export_grad_mrtrix"],
         desc="name of new gradient file",
     )
@@ -319,7 +308,6 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
         File("grad.bvecs", usedefault=True, desc="bvecs"),
         File("grad.bvals", usedefault=True, desc="bvals"),
         argstr="%s, %s",
-        position=-1,
         requires=["export_grad_fsl"],
         desc="Output (bvecs, bvals) gradients FSL format",
     )
diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py
index 55793a873b..76fae6548f 100644
--- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py
+++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIPreproc.py
@@ -4,35 +4,34 @@
 
 def test_DWIPreproc_inputs():
     input_map = dict(
-        align_seepi=dict(argstr="-align_seepi", position=-4),
+        align_seepi=dict(argstr="-align_seepi"),
         args=dict(argstr="%s"),
         bval_scale=dict(argstr="-bvalue_scaling %s"),
-        eddy_options=dict(argstr="-eddy_options %s", position=-3),
+        eddy_options=dict(argstr='-eddy_options "%s"'),
         environ=dict(nohash=True, usedefault=True),
-        export_grad_fsl=dict(argstr="-export_grad_fsl", position=-2),
-        export_grad_mrtrix=dict(argstr="-export_grad_mrtrix", position=-2),
+        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, position=-5),
-        in_file=dict(argstr="%s", extensions=None, mandatory=True, position=-10),
+        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=-9, usedefault=True
+            argstr="%s", extensions=None, mandatory=True, position=1, usedefault=True
         ),
-        out_grad_fsl=dict(argstr="%s, %s", position=-1, requires=["export_grad_fsl"]),
+        out_grad_fsl=dict(argstr="%s, %s", requires=["export_grad_fsl"]),
         out_grad_mrtrix=dict(
             argstr="%s",
             extensions=None,
-            position=-1,
             requires=["export_grad_mrtrix"],
             usedefault=True,
         ),
-        pe_dir=dict(argstr="-pe_dir %s", mandatory=True, position=-7),
-        ro_time=dict(argstr="-readout_time %f", position=-6),
-        rpe_options=dict(argstr="%s", mandatory=True, position=-8),
-        topup_options=dict(argstr="-topup_options %s", position=-3),
+        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()
 

From a1c43ad68e28a5063e3f04a87d48efe968ebda3a Mon Sep 17 00:00:00 2001
From: Xihe Xie <axiezai@gmail.com>
Date: Mon, 7 Dec 2020 22:53:59 -0500
Subject: [PATCH 14/14] fixed doc string for new positions

---
 nipype/interfaces/mrtrix3/preprocess.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index dd215a4802..ef67365f0b 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -355,7 +355,7 @@ class DWIPreproc(MRTrix3Base):
     >>> 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 -pe_dir j -readout_time 0.165240 -eddy_options "--slm=linear --repol" -export_grad_mrtrix grad.b'
+    '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
     """