specified positions, requires for gradient exports

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",
  )
@@ -261,68 +261,86 @@ 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",
  )
 
 
 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