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 Fixed typos and improved `-eddy` and `-topup` optional inputs. Co-authored-by: Chris Markiewicz <effigies@gmail.com>

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])