@@ -892,11 +892,7 @@
 "orcid": "0000-0002-5312-6729"
 }
 ],
-"keywords": [
-"neuroimaging",
-"workflow",
-"pipeline"
-],
+"keywords": ["neuroimaging", "workflow", "pipeline"],
 "license": "Apache-2.0",
 "upload_type": "software"
 }

@@ -5,21 +5,26 @@
 import os.path as op
 
 from ..base import (
-CommandLineInputSpec,
 CommandLine,
-traits,
-TraitedSpec,
+CommandLineInputSpec,
+Directory,
 File,
-isdefined,
-Undefined,
 InputMultiObject,
+TraitedSpec,
+Undefined,
+isdefined,
+traits,
 )
-from .base import MRTrix3BaseInputSpec, MRTrix3Base
+from .base import MRTrix3Base, MRTrix3BaseInputSpec
 
 
 class DWIDenoiseInputSpec(MRTrix3BaseInputSpec):
 in_file = File(
-exists=True, argstr="%s", position=-2, mandatory=True, desc="input DWI image"
+exists=True,
+argstr="%s",
+position=-2,
+mandatory=True,
+desc="input DWI image",
 )
 mask = File(exists=True, argstr="-mask %s", position=1, desc="mask image")
 extent = traits.Tuple(
@@ -88,7 +93,11 @@ class DWIDenoise(MRTrix3Base):
 
 class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
 in_file = File(
-exists=True, argstr="%s", position=-2, mandatory=True, desc="input DWI image"
+exists=True,
+argstr="%s",
+position=-2,
+mandatory=True,
+desc="input DWI image",
 )
 axes = traits.ListInt(
 default_value=[0, 1],
@@ -177,7 +186,11 @@ class MRDeGibbs(MRTrix3Base):
 
 class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
 in_file = File(
-exists=True, argstr="%s", position=-2, mandatory=True, desc="input DWI image"
+exists=True,
+argstr="%s",
+position=-2,
+mandatory=True,
+desc="input DWI image",
 )
 in_mask = File(argstr="-mask %s", desc="input mask image for bias field estimation")
 use_ants = traits.Bool(
@@ -252,7 +265,11 @@ def _list_outputs(self):
 
 class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
 in_file = File(
-exists=True, argstr="%s", position=0, mandatory=True, desc="input DWI image"
+exists=True,
+argstr="%s",
+position=0,
+mandatory=True,
+desc="input DWI image",
 )
 out_file = File(
 "preproc.mif",
@@ -274,7 +291,6 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
 )
 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(
@@ -290,33 +306,49 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
 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",
+json_import = File(
+exists=True,
+argstr="-json_import %s",
+desc="Import image header information from an associated JSON file (may be necessary to determine phase encoding information)",
 )
 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"
+eddy_options = traits.Str(
+argstr='-eddy_options "%s"',
+desc="Manually provide additional command-line options to the eddy command",
+)
+eddy_mask = File(
+exists=True,
+argstr="-eddy_mask %s",
+desc="Provide a processing mask to use for eddy, instead of having dwifslpreproc generate one internally using dwi2mask",
+)
+eddy_slspec = File(
+exists=True,
+argstr="-eddy_slspec %s",
+desc="Provide a file containing slice groupings for eddy's slice-to-volume registration",
+)
+eddyqc_text = Directory(
+exists=False,
+argstr="-eddyqc_text %s",
+desc="Copy the various text-based statistical outputs generated by eddy, and the output of eddy_qc (if installed), into an output directory",
 )
-export_grad_fsl = traits.Bool(
-argstr="-export_grad_fsl", desc="export gradient files in FSL format"
+eddyqc_all = Directory(
+exists=False,
+argstr="-eddyqc_all %s",
+desc="Copy ALL outputs generated by eddy (including images), and the output of eddy_qc (if installed), into an output directory",
 )
 out_grad_mrtrix = File(
 "grad.b",
-argstr="%s",
-usedefault=True,
-requires=["export_grad_mrtrix"],
-desc="name of new gradient file",
+argstr="-export_grad_mrtrix %s",
+desc="export new gradient files in mrtrix format",
 )
 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",
+File("grad.bvecs", desc="bvecs"),
+File("grad.bvals", desc="bvals"),
+argstr="-export_grad_fsl %s, %s",
+desc="export gradient files in FSL format",
 )
 
 
@@ -358,7 +390,7 @@ class DWIPreproc(MRTrix3Base):
 >>> 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.out_grad_mrtrix = "grad.b" # 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
@@ -394,7 +426,11 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec):
 desc="response estimation algorithm (multi-tissue)",
 )
 in_file = File(
-exists=True, argstr="%s", position=-5, mandatory=True, desc="input DWI image"
+exists=True,
+argstr="%s",
+position=-5,
+mandatory=True,
+desc="input DWI image",
 )
 mtt_file = File(argstr="%s", position=-4, desc="input 5tt image")
 wm_file = File(
@@ -518,10 +554,17 @@ class ReplaceFSwithFIRSTInputSpec(CommandLineInputSpec):
 desc="input anatomical image",
 )
 in_t1w = File(
-exists=True, argstr="%s", mandatory=True, position=-3, desc="input T1 image"
+exists=True,
+argstr="%s",
+mandatory=True,
+position=-3,
+desc="input T1 image",
 )
 in_config = File(
-exists=True, argstr="%s", position=-2, desc="connectome configuration file"
+exists=True,
+argstr="%s",
+position=-2,
+desc="connectome configuration file",
 )
 
 out_file = File(

@@ -13,19 +13,27 @@ def test_DWIPreproc_inputs():
 bval_scale=dict(
 argstr="-bvalue_scaling %s",
 ),
+eddy_mask=dict(
+argstr="-eddy_mask %s",
+extensions=None,
+),
 eddy_options=dict(
 argstr='-eddy_options "%s"',
 ),
+eddy_slspec=dict(
+argstr="-eddy_slspec %s",
+extensions=None,
+),
+eddyqc_all=dict(
+argstr="-eddyqc_all %s",
+),
+eddyqc_text=dict(
+argstr="-eddyqc_text %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,
@@ -52,6 +60,10 @@ def test_DWIPreproc_inputs():
 mandatory=True,
 position=0,
 ),
+json_import=dict(
+argstr="-json_import %s",
+extensions=None,
+),
 nthreads=dict(
 argstr="-nthreads %d",
 nohash=True,
@@ -71,18 +83,14 @@ def test_DWIPreproc_inputs():
 usedefault=True,
 ),
 out_grad_fsl=dict(
-argstr="%s, %s",
-requires=["export_grad_fsl"],
+argstr="-export_grad_fsl %s, %s",
 ),
 out_grad_mrtrix=dict(
-argstr="%s",
+argstr="-export_grad_mrtrix %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",