fixed some bugs in the interface to dwifslpreproc

Author: GalKepler

nipype/interfaces/mrtrix3/preprocess.py

@@ -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],
@@ -177,9 +186,15 @@ 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"
     )
-    in_mask = File(argstr="-mask %s", desc="input mask image for bias field estimation")
     use_ants = traits.Bool(
         argstr="ants",
         mandatory=True,
@@ -245,7 +260,11 @@ def _format_arg(self, name, trait_spec, value):
 
 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",
@@ -267,7 +286,7 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
     )
     pe_dir = traits.Str(
         argstr="-pe_dir %s",
-        mandatory=True,
+        mandatory=False,
         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(
@@ -283,16 +302,42 @@ 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",
     )
+    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",
+    )
+    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",
+    )
     export_grad_mrtrix = traits.Bool(
-        argstr="-export_grad_mrtrix", 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", desc="export gradient files in FSL format"
@@ -367,7 +412,9 @@ 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)
+            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])
@@ -387,7 +434,11 @@ 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(
@@ -397,9 +448,15 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec):
         usedefault=True,
         desc="output WM response text file",
     )
-    gm_file = File(argstr="%s", position=-2, desc="output GM response text file")
-    csf_file = File(argstr="%s", position=-1, desc="output CSF response text file")
-    in_mask = File(exists=True, argstr="-mask %s", desc="provide initial mask image")
+    gm_file = File(
+        argstr="%s", position=-2, desc="output GM response text file"
+    )
+    csf_file = File(
+        argstr="%s", position=-1, desc="output CSF response text file"
+    )
+    in_mask = File(
+        exists=True, argstr="-mask %s", desc="provide initial mask image"
+    )
     max_sh = InputMultiObject(
         traits.Int,
         argstr="-lmax %s",
@@ -511,10 +568,17 @@ 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(